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- B(3) - The Perl Compiler Backend
- b(1) - build system driver
- B2C2(4) - webcamd driver for B2C2 FlexcopII(b)/III
- B2G(1) - Traditional to Simplified Chinese converter
- B2I_PVK_BIO_EX(3ossl) - Decode and encode functions for reading and writing MSBLOB format private keys
- B2SUM(1) - generate checksums using the BLAKE2 hash function
- b3270(1) - IBM host access tool back end
- B43-FWCUTTER(1) - Utility for extracting Broadcom 43xx firmware
- BASE64(3) - base-64 encoder and decoder
- B::Asmdata(3) - Autogenerated data about Perl ops, used to generate bytecode
- B::Assembler(3) - Assemble Perl bytecode
- B::Bblock(3) - Walk basic blocks
- B::Bytecode(3) - Perl compiler's bytecode backend
- B::Bytecode56(3) - Perl 5.6 compiler's bytecode backend
- B::C(3) - Perl compiler's C backend
- B::CC(3) - Perl compiler's optimized C translation backend
- B::Compiling(3) - Expose PL_compiling to perl
- B::Concise(3) - Walk Perl syntax tree, printing concise info about ops
- B::COW(3) - B::COW additional B helpers to check COW status
- B::Deobfuscate(3) - Deobfuscate source code
- B::Deobfuscate::Dict::Flowers(3) - B::Deobfuscate::Dict::Flowers
- B::Deobfuscate::Dict::PGPHashWords(3) - B::Deobfuscate::Dict::PGPHashWords
- B::Deparse(3) - Perl compiler backend to produce perl code
- B::Disassembler(3) - Disassemble Perl bytecode
- Flags(3) - Friendlier flags for B
- B::Generate(3) - Create your own op trees.
- B::Hooks::AtRuntime(3) - Lower blocks from compile time to runtime
- B::Hooks::EndOfScope(3) - Execute code after a scope finished compilation
- B::Hooks::EndOfScope::PP(3) - Execute code after a scope finished compilation - PP implementation
- B::Hooks::EndOfScope::XS(3) - Execute code after a scope finished compilation - XS implementation
- B::Hooks::OP::Annotation(3) - annotate and delegate hooked OPs
- B::Hooks::OP::Check(3) - Wrap OP check callbacks
- B::Hooks::OP::Check::EntersubForCV(3) - Invoke callbacks on construction of entersub OPs for certain CVs
- B::Hooks::OP::PPAddr(3) - Hook into opcode execution
- B::Hooks::Parser(3) - Interface to perl's parser variables
- B::Keywords(3) - Lists of reserved barewords and symbol names
- B::Module::Info(3) - information about Perl modules
- B::Op_private(3) - OP op_private flag definitions
- B::OPCheck(3) - PL_check hacks using Perl callbacks
- perlcompile(3) - Introduction to the Perl Compiler-Translator
- perloptree(3) - The Perl op tree
- B::Showlex(3) - Show lexical variables used in functions or files
- B::Size2(3) - Measure size of Perl OPs and SVs
- B::Size2::Terse(3) - Printing info about ops and their (estimated) size
- B::Stackobj(3) - Stack and type annotation helper module for the CC backend
- Stash(3) - show what stashes are loaded
- B::Terse(3) - Walk Perl syntax tree, printing terse info about ops
- B::Utils(3) - Helper functions for op tree manipulation
- B::Utils::OP(3) - op related utility functions for perl
- B::Xref(3) - Generates cross reference reports for Perl programs
- BABELD(8) - ad-hoc network routing daemon
- BABELTRACE(1) - Babeltrace Trace Viewer and Converter
- BABELTRACE-LOG(1) - Babeltrace Log Converter
- backend(7) - cups backend transmission interfaces
- BACKEND-SPEC(7) - interface between jw and its backends
- BACKGAMMON(6) - the game of backgammon
- BACKLIGHT(8) - configure backlight hardware
- BACKLIGHT(9) - BACKLIGHT methods
- BACKTRACE(3) - fill in the backtrace of the currently executing thread
- BACKUPD(8) - Cyrus IMAP documentation
- BackupPC(1)
- BackupPC::XS(3) - Perl extension for BackupPC libraries
- backupuser(1) - User backup utility
- Bacula(8) - The Network Backup Solution
- BACULA-DIR(8) - Bacula Director
- BACULA-SD(8) - Bacula's Storage Daemon
- BACULA-TRAY-MONITOR(1) - Bacula's 'System Tray' monitor
- BADBLOCKS(8) - search a device for bad blocks
- Badger(3) - Perl Application Programming Toolkit
- Badger::App(3) - base class application module
- Badger::Apps(3) - factory module for application modules
- Badger::Base(3) - base class module
- Badger::Class(3) - class metaprogramming module
- Badger::Class::Config(3) - class mixin for configuration
- Badger::Class::Methods(3) - metaprogramming module for adding methods to a class
- Badger::Class::Vars(3) - class module for defining package variables
- Badger::Codec(3) - base class for encoding/decoding data
- Badger::Codec::Base64(3) - encode/decode data using MIME::Base64
- Badger::Codec::Chain(3) - encode/decode data using multiple codecs
- Badger::Codec::Encode(3) - codec wrapper around Encode
- Badger::Codec::Encoding(3) - base class codec for different encodings
- Badger::Codec::HTML(3) - encode and decode reserved characters in HTML
- Badger::Codec::JSON(3) - encode/decode data using JSON
- Badger::Codec::Storable(3) - encode/decode data using Storable
- Badger::Codec::Timestamp(3) - encode/decode a timestamp via Badger::Timestamp
- Badger::Codec::TT(3) - encode/decode data using TT data syntax
- Badger::Codec::Unicode(3) - encode/decode Unicode
- Badger::Codec::URI(3) - URI encode/decode
- Badger::Codec::URL(3) - URL encode/decode
- Badger::Codec::YAML(3) - encode/decode data using YAML
- Badger::Codecs(3) - modules for encoding and decoding data
- Badger::Comparable(3) - base class for comparable objects
- Badger::Config(3) - configuration module
- Badger::Config::Filesystem(3) - reads configuration files in a directory
- Badger::Constants(3) - defines constants for other Badger modules
- Badger::Data(3) - base class for data object
- Badger::Data::Facet(3) - base class validation facet for simple data types
- Badger::Data::Facet::Class(3) - metaprogramming module for data facet classes
- Badger::Data::Facet::List(3) - base class for list validation facets
- Badger::Data::Facet::List::MaxSize(3) - validation facet for the size of a list
- Badger::Data::Facet::List::MinSize(3) - validation facet for the size of a list
- Badger::Data::Facet::List::Size(3) - validation facet for the size of a list
- Badger::Data::Facet::Number(3) - base class for numerical validation facets
- Badger::Data::Facet::Number::Max(3) - validation facet for a minimum numerical value
- Badger::Data::Facet::Number::Min(3) - validation facet for a minimum numerical value
- Badger::Data::Facet::Text(3) - base class for text validation facets
- Badger::Data::Facet::Text::Length(3) - validation facet for text length
- Badger::Data::Facet::Text::MaxLength(3) - validation facet for text length
- Badger::Data::Facet::Text::MinLength(3) - validation facet for text length
- Badger::Data::Facet::Text::Pattern(3) - validation facet for text pattern match
- Badger::Data::Facet::Text::Whitespace(3) - validation facet for whitespace
- Badger::Data::Facets(3) - factory module for data validation facets.
- Badger::Data::Type(3) - base class for data types
- Badger::Data::Type::Class(3) - metaprogramming module for data type classes
- Badger::Data::Type::Number(3) - base class data type for numbers
- Badger::Data::Type::Simple(3) - base class for simple data types
- Badger::Data::Type::Text(3) - base class data type for text
- Badger::Data::Types(3) - factory module for Badger::Data::Type objects
- Badger::Date(3) - simple object representation of a date
- Badger::Debug(3) - base class mixin module implement debugging methods
- Badger::Duration(3) - simple class for representing durations
- Badger::Exception(3) - structured exception for error handling
- Badger::Exporter(3) - symbol exporter
- Badger::Factory(3) - base class factory module
- Badger::Factory::Class(3) - class module for Badger::Factory sub-classes
- Badger::Filesystem(3) - filesystem functionality
- Badger::Filesystem::Base(3) - common functionality for Badger::Filesystem modules
- Badger::Filesystem::Directory(3) - directory object
- Badger::Filesystem::File(3) - file object
- Badger::Filesystem::Path(3) - generic filesystem path object
- Badger::Filesystem::Virtual(3) - virtual filesystem
- Badger::Filesystem::Visitor(3) - visitor for traversing filesystems
- Badger::Filter(3) - object for simple filtering
- Badger::Hub(3) - central repository of shared resources
- Badger::Hub::Badger(3) - central hub for accessing Badger components
- Badger::Log(3) - log for errors, warnings and other messages
- Badger::Log::File(3) - writes log messages to a log file
- Badger::Logic(3) - parse and evaluate simple logical expressions
- Badger::Mixin(3) - base class mixin object
- Badger::Modules(3) - a module for loading modules
- Badger::Period(3) - base class for Badger::Date and Badger::Time
- Badger::Prototype(3) - base class for creating prototype classes
- Badger::Rainbow(3) - colour functionality
- Badger::Test(3) - test module
- Badger::Test::Manager(3) - test manager module
- Badger::Timestamp(3) - object representation of a timestamp
- Badger::URL(3) - representation of a Uniform Resource Locator (URL)
- Badger::Utils(3) - various utility functions
- Badger::Workplace(3) - a place to do work
- Badger::Workspace(3) - an object representing a project workspace
- BADWOLF(1) - minimalist and privacy-oriented web browser based on WebKitGTK
- baka-mplayer(1) - A free and open source, cross-platform, libmpv based multimedia player.
- BALANCE(1) - A simple TCP proxy with load balancing and failover mechanisms.
- BALLERBURG(6) - A castle combat game
- BalloonContents(1) - BalloonContents - Afterstep BalloonContents
- BALLS(1) - preprocessor for space-filling models in Raster3D molecular graphics package
- Balsa(1) - the GNOME e-mail client.
- BambooTracker(1) - YM2608 (OPNA) tracker
- Banner(1.0) - the Banner for Afterstep
- BANNER(6) - print large banner on printer
- BAOBAB(1) - A graphical disk usage analyzer for the GNOME desktop
- BAR(1) - show information about a data transfer
- barchart(n) - Bar chart for plotting X-Y coordinate data.
- BARCODE(1) - a stand alone program to run the barcode library
- BARCODE(3) - a library to create and print bar codes
- barcode(6) - draws a random sequence of barcodes for the products you enjoy
- ZBar(3) - Perl interface to the ZBar Barcode Reader
- ZBar::Image(3) - image object to scan for bar codes
- ZBar::ImageScanner(3) - scan images for bar codes
- ZBar::Processor(3) - self-contained bar code reader
- ZBar::Symbol(3) - bar code scan result object
- BAREOS(8) - Backup Archiving REcovery Open Sourced
- BAREOS-DBCHECK(8) - Bareos's Catalog Database Check/Clean program
- BAREOS-DIR(8) - Bareos Director
- BAREOS-FD(8) - Bareos's File Daemon
- BAREOS-SD(8) - Bareos's Storage Daemon
- bareword::filehandles(3) - disables bareword filehandles
- BARGRAPH(1) - compile bar graphs into pic input
- BARMAN(1) - Barman Commands
- BARMAN(5) - Barman Configurations
- BARMAN-ARCHIVE-WAL(1) - Barman Sub-Commands
- BARMAN-BACKUP(1) - Barman Sub-Commands
- BARMAN-CHECK(1) - Barman Sub-Commands
- BARMAN-CHECK-BACKUP(1) - Barman Sub-Commands
- BARMAN-CLOUD-BACKUP(1) - Barman-cloud Commands
- BARMAN-CLOUD-BACKUP-DELETE(1) - Barman-cloud Commands
- BARMAN-CLOUD-BACKUP-KEEP(1) - Barman-cloud Commands
- BARMAN-CLOUD-BACKUP-LIST(1) - Barman-cloud Commands
- BARMAN-CLOUD-BACKUP-SHOW(1) - Barman-cloud Commands
- BARMAN-CLOUD-CHECK-WAL-ARCHIVE(1) - Barman-cloud Commands
- BARMAN-CLOUD-RESTORE(1) - Barman-cloud Commands
- BARMAN-CLOUD-WAL-ARCHIVE(1) - Barman-cloud Commands
- BARMAN-CLOUD-WAL-RESTORE(1) - Barman-cloud Commands
- BARMAN-CONFIG-SWITCH(1) - Barman Sub-Commands
- BARMAN-CONFIG-UPDATE(1) - Barman Sub-Commands
- BARMAN-CRON(1) - Barman Sub-Commands
- BARMAN-DELETE(1) - Barman Sub-Commands
- BARMAN-DIAGNOSE(1) - Barman Sub-Commands
- BARMAN-GENERATE-MANIFEST(1) - Barman Sub-Commands
- BARMAN-GET-WAL(1) - Barman Sub-Commands
- BARMAN-KEEP(1) - Barman Sub-Commands
- BARMAN-LIST-FILES(1) - Barman Sub-Commands
- BARMAN-LIST-PROCESSES(1) - Barman Sub-Commands
- BARMAN-LIST-SERVERS(1) - Barman Sub-Commands
- BARMAN-LIST_BACKUPS(1) - Barman Sub-Commands
- BARMAN-LOCK-DIRECTORY-CLEANUP(1) - Barman Sub-Commands
- BARMAN-PUT-WAL(1) - Barman Sub-Commands
- BARMAN-REBUILD-XLOGDB(1) - Barman Sub-Commands
- BARMAN-RECEIVE-WAL(1) - Barman Sub-Commands
- BARMAN-REPLICATION-STATUS(1) - Barman Sub-Commands
- BARMAN-RESTORE(1) - Barman Sub-Commands
- BARMAN-SHOW-BACKUP(1) - Barman Sub-Commands
- BARMAN-SHOW-SERVERS(1) - Barman Sub-Commands
- BARMAN-STATUS(1) - Barman Sub-Commands
- BARMAN-SWITCH-WAL(1) - Barman Sub-Commands
- BARMAN-SWITCH-XLOG(1) - Barman Sub-Commands
- BARMAN-SYNC-BACKUP(1) - Barman Sub-Commands
- BARMAN-SYNC-INFO(1) - Barman Sub-Commands
- BARMAN-SYNC-WALS(1) - Barman Sub-Commands
- BARMAN-TERMINATE-PROCESS(1) - Barman Sub-Commands
- BARMAN-VERIFY(1) - Barman Sub-Commands
- BARMAN-VERIFY-BACKUP(1) - Barman Sub-Commands
- BARMAN-WAL-ARCHIVE(1) - Barman-cli Commands
- BARMAN-WAL-RESTORE(1) - Barman-cli Commands
- BARRIER(1) - syncronize a process on a number of machines.
- BARRIERC(1) - Barrier Keyboard/Mouse Client
- BARRIERD(1) - syncronize a process on a number of machines.
- BARRIERS(1) - Barrier Keyboard/Mouse Server
- Base(1) - Base - essential AfterStep configuration options
- Base(3) - This is the base class of searching and indexing
- base(3) - Establish an ISA relationship with base classes at compile time
- base64(3) - Provides base64 encode and decode, see RFC 2045.
- base64(n) - Encoding "base64"
- BASE64URL(1) - Base64Url encode or decode FILE, or standard input, to standard output.
- BASE91(1) - basE91 encode/decode data
- Baseball::Sabermetrics(3) - A Baseball Statistics Module
- BASENAME(1) - return filename or directory portion of pathname
- BASENAME(3) - extract the base portion of a pathname
- BASH(1) - GNU Bourne-Again SHell
- BASH-COMPLETE(1) - bash-completion magic script
- Bash::Completion(3) - Extensible system to provide bash completion
- Bash::Completion::Plugin(3) - base class for Bash::Completion plugins
- Bash::Completion::Plugins::BashComplete(3) - Plugin for bash-complete
- Bash::Completion::Plugins::Perldoc(3) - complete perldoc command
- Bash::Completion::Request(3) - Abstract a completion request
- Bash::Completion::Utils(3) - Set of utility functions that help writting plugins
- BASHBUG(1) - report a bug in bash
- bashdb(1) - bash debugger script
- basic-stats(1) - Command-line statistics made trivial
- BASIC_DB_AUTH(8) - Database auth helper for Squid
- basic_getpwnam_auth(8) - Local Users auth helper for Squid
- basic_ncsa_auth(8) - NCSA httpd-style password file authentication helper for Squid
- basic_pam_auth(8) - PAM Basic authentication helper for Squid
- BASIC_POP3_AUTH(8) - POP3 authenticator for Squid
- basic_radius_auth(8) - Squid RADIUS authentication helper
- BASKETLOSSES(1) - Example of Modeling Losses Across Correlated Assets
- BASTET(6) - Tetris(r) clone with "bastard" block-choosing AI
- bastille(8) - open-source jail automation and management tool
- bastille-bootstrap(8) - Bootstrap a release or template(s).
- bastille-clone(8) - Clone an existing jail.
- bastille-cmd(8) - Execute command(s) inside jail(s).
- bastille-config(8) - Get, set, add or remove properties from jail(s).
- bastille-console(8) - Console into a jail.
- bastille-convert(8) - Convert a jail from thin to thick; convert a jail to a custom release.
- bastille-cp(8) - Copy file(s)/directorie(s) from host to jail(s).
- bastille-create(8) - Create a jail.
- bastille-destroy(8) - Destroy jail(s) or release(s).
- bastille-edit(8) - Edit jail configuration files (advanced).
- bastille-etcupdate(8) - Update /etc for jail(s).
- bastille-export(8) - Export a jail.
- bastille-htop(8) - Interactive process viewer (requires htop).
- bastille-import(8) - Import a jail.
- bastille-jcp(8) - Copy file(s)/directorie(s) from jail to jail(s).
- bastille-limits(8) - Apply resource limits to jail(s). See rctl(8) and cpuset(1).
- bastille-list(8) - List jails, releases, templates and more...
- bastille-migrate(8) - Migrate jail(s) to a remote system.
- bastille-monitor(8) - Monitor and attempt to restart jail service(s).
- bastille-mount(8) - Mount file(s)/directorie(s) inside jail(s).
- bastille-network(8) - Add or remove interface(s) from jail(s).
- bastille-pkg(8) - Manage packages inside jail(s). See pkg(8).
- bastille-rcp(8) - Copy file(s)/directorie(s) from jail to host.
- bastille-rdr(8) - Redirect host port to jail port.
- bastille-rename(8) - Rename a jail.
- bastille-restart(8) - Restart a jail.
- bastille-service(8) - Manage services within jail(s).
- bastille-setup(8) - Auto-configure network, firewall, storage and more...
- bastille-start(8) - Start stopped jail(s).
- bastille-stop(8) - Stop running jail(s).
- bastille-sysrc(8) - Edit rc files inside jail(s).
- bastille-tags(8) - Add or remove tags to jail(s).
- bastille-template(8) - Apply templates to jail(s).
- bastille-top(8) - Process viewer. See top(1).
- bastille-umount(8) - Unmount file(s)/directorie(s) from jail(s).
- bastille-update(8) - Update a jail or release.
- bastille-upgrade(8) - Upgrade a jail to new release.
- bastille-verify(8) - Compare release against a 'known good' index.
- bastille-zfs(8) - Manage ZFS options/attributes for jail(s).
- bastille.conf(5) - Configuration file for Bastille
- BAT(1) - a cat(1) clone with syntax highlighting and Git integration.
- BATCHER(8) - Article batching for InterNetNews
- BATS(1) - Bash Automated Testing System
- BATS(7) - Bats test file format
- batteredplanet(6) - screen saver.
- BATTLESHIP() - battleship, nbbattleship
- BATTLESTAR(6) - a tropical adventure game
- BATTMOND(1) - monitor battery level on ACPI-enabled (laptop) computers
- batv-filter(8) - BATV (Bounce Address Tag Validation) filter for sendmail
- BAYESOL(1) - a Bayes solution calculator for use with dbacl.
- BBC(1) - check on BBoards
- bbcsd(3) - bbcsd: ??
- BBE(1) - binary block editor
- BBFTP(1) - transfer files using compression and parallel streams
- BBFTPD(1) - BBFTP protocol server
- BBKEYS(1) - a general XWindow keygrabber
- BBKEYSRC(5) - bbkeys configuration file
- bbmail(1) - mailbox flag for X
- BBOX(1) - prints out the bounding box of a rawppm or rawpbm image
- BBS::Client(3) - A Client Module For BBS Systems
- UserInfo(3) - Base class of BBS::UserInfo::XXX
- Maple3(3) - Get user information of Maple3-style BBS
- Maple3itoc(3) - Get user information of Maple3itoc-style BBS
- Ptt(3) - Get user information of PTT-style BBS
- SOB(3) - Get user information of SOB-style BBS
- Wretch(3) - Get user information of Wretch-style BBS
- BBSBOARD(1) - Internet to BBS email-post handler
- BBSCOMD(1) - OurNet BBS Remote Access Daemon
- BBSMAIL(1) - Internet to BBS email-gateway handler
- BC(1) - arbitrary-precision decimal arithmetic language and calculator
- BCAL(1) - Storage expression calculator.
- BCC(1) - Bruce's C compiler
- BCC-CC1(1) - C compiler backend
- BCD(6) - reformat input as punch cards
- BCE(4) - QLogic NetXtreme II (BCM5706/5708/5709/5716) PCI/PCIe Gigabit Ethernet adapter driver
- BCFTOOLS(1) - utilities for variant calling and manipulating VCFs and BCFs.
- BCHUNK(1) - CD image format conversion from bin/cue to iso/cdr
- BCLOCK(1) - round X clock with bezier curve hands
- BCM283X_PWM(4) - bcm283x_pwm - driver for Raspberry Pi 2/3 PWM
- BCM5974(4) - Wellspring touchpad driver
- BCMA(4) - Broadcom AMBA Backplane driver
- BCMFW(8) - load firmware for Broadcom BCM2033 Bluetooth USB devices
- BCMP(3) - compare byte string
- BCMXCP(8) - Driver for UPSes supporting the serial BCM/XCP protocol
- BCMXCP_USB(8) - Experimental driver for UPSes supporting the BCM/XCP protocol over USB
- BCOMPS(1) - biconnected components filter for graphs
- BCONSOLE(1) - Bareos's management Console
- BCONSOLE(8) - Bacula's management Console
- BCOPY(3) - copy byte string
- BCOPY(8) - Bareos's 'Copy from volume'
- BCRELAY(8) - a broadcast relay daemon
- BcVersions(3) - ByteLoader bytecode versions
- BCWIPE(1) - securely erase data from magnetic and solid-state memory
- BDB(3) - Asynchronous Berkeley DB access
- BDD101(1) - Mutli Reduced Ordered Binary Decision Diagrams
- BDDTOABLCCT(3) - converts a BDD into an ABL within a circuit
- bdep(1) - project dependency manager
- bdep-argument-grouping(1) - argument grouping facility
- bdep-ci(1) - submit project test request to CI server
- bdep-clean(1) - clean project in build configurations
- bdep-common-options(1) - details on common options
- bdep-config(1) - manage project build configurations
- bdep-default-options-files(1) - specifying default options
- bdep-deinit(1) - deinitialize project in build configurations
- bdep-fetch(1) - fetch list of available project dependencies
- bdep-help(1) - show help for a command or help topic
- bdep-init(1) - initialize project in build configurations
- bdep-new(1) - create and initialize new project
- bdep-projects-configs(1) - specifying projects and configurations
- bdep-publish(1) - publish project to archive repository
- bdep-release(1) - manage project's version during release
- bdep-status(1) - print status of project and/or its dependencies
- bdep-sync(1) - synchronize project and build configurations
- bdep-test(1) - test project in build configurations
- bdep-update(1) - update project in build configurations
- BDES(1) - encrypt/decrypt using the Data Encryption Standard (DES)
- BDF2GDFONT(1) - Convert X11 "BDF" fonts into a loadable font format for GD.
- BDF2SFD(1) - BDF to SFD converter
- BDFRESIZE(1) - Resize BDF Format Font
- BDFTOPCF(1) - convert X font from Bitmap Distribution Format to Portable Compiled Format
- bdftruncate(1) - generate truncated BDF font from ISO 10646-1-encoded BDF font
- bdiff(1) - big diff
- bdsdc(3) - bdsdc: bidiagonal SVD, divide and conquer
- bdsqr(3) - bdsqr: bidiagonal SVD, QR iteration (dqds)
- bdsvd_driver(3) - --- bidiagonal ---
- bdsvdx(3) - bdsvdx: bidiagonal SVD, bisection
- bdy(1gv) - bdy - boundary curve finder
- bdy(3gv) - bdy - boundary curve finder
- BEADM(8) - manage boot environments with ZFS
- beam_lib(3) - An interface to the BEAM file format.
- DADBY(1) - high-available distributed key-value storage system
- Beanstalk::Client(3) - Client class to talk to beanstalkd server
- Beanstalk::Job(3) - Class to represent a job from a beanstalkd server
- Beanstalk::Pool(3) - Use a pool of beanstalkd servers
- Beanstalk::Stats(3) - Class to represent stats results from the beanstalk server
- BEANSTALKD(1) - simple, fast work queue
- BEAR(1) - a tool to generate compilation database for Clang tooling.
- BEAROFFDUMP(6) - dump a position from the GNU Backgammon bearoff database
- BEASTIE.4TH(8) - FreeBSD ASCII art boot module
- beats(6) - create offset beating figures
- BEAV(1) - binary file editor and viewer
- BECTL(8) - manage ZFS boot environments
- BED(6) - maze editor for block
- bedup(8) - deduplication program with additional knowledge of burp
- BEEP(1) - play a beep sound
- beep(n) - ring the bell
- BEET(1) - music tagger and library organizer
- BEETSCONFIG(5) - beets configuration file
- beforelight(1) - screen saver
- BEGIN(7) - start a transaction block
- BEGIN(1) - start a new block of code
- BEH(3) - Generic behavioural data structures
- BEH_DEBUG(3) - BEH structures displayer-debugger
- BEH_DEPEND(3) - compute forward dependencies in a description
- BEH_ERROR(3) - beh_error() prints an error message on the standard error output depending on an error code. The code parameter determines the message to be printed.
- BEH_MAKBDD(3) - create a BDD for each expression in a description
- BEH_MAKGEX(3) - create a GEX for each expression in a description
- BEH_MESSAGE(3) - beh_message() prints an error message on the standard output depending on a message code. The code parameter determines the message to be printed.
- BEINSTALL.SH(8) - install a boot environment using the current FreeBSD source tree
- BELKIN(8) - Driver for Belkin serial UPS equipment
- BELKINUNV(8) - Driver for Belkin "Universal UPS" and compatible
- bell(n) - Ring a display's bell
- bemenu(1) - dynamic menu inspired by dmenu(1)
- bench(8) - http benchmark
- bench2graph(1) - draws Postscript graphs from Autobench output (using gnuplot)
- Benchmark(3) - Benchmark running times of Perl code
- delta(3) - calculate Benchmark::Timer object call overhead
- Benchmark::Dumb(3) - Benchmark.pm compatibility layer for Dumbbench
- Forking(3) - Run benchmarks in separate processes
- Benchmark::Stopwatch(3) - simple timing of stages of your code.
- Benchmark::Timer(3) - Benchmarking with statistical confidence
- benchmark_data(3) - Retrieve gathered benchmarking values.
- benchmark_enable(3) - Toggle the gathering of benchmark data on / off.
- benchmark_timestamp(3) - Sample a timekeeping source.
- benchmark_tracedata(3) - Add a datapoint to the ongoing tracebuffer
- Bencode(3) - BitTorrent serialisation format
- BENQ(4) - webcamd driver for Benq DC E300 USB camera
- LBER_ENCODE(3) - OpenLDAP LBER simplified Basic Encoding Rules library routines for encoding
- LBER_TYPES(3) - OpenLDAP LBER types and allocation functions
- LBER_DECODE(3) - OpenLDAP LBER simplified Basic Encoding Rules library routines for decoding
- BerkeleyDB(3) - Perl extension for Berkeley DB version 2, 3, 4, 5 or 6
- BERMUDANSWAPTION(1) - Example of using QuantLib
- BERRY(1) - floating window manager
- BERRYC(1) - client for berry window manager
- BESSIDE-NG(8) - crack a WEP or WPA key without user intervention and collaborate with WPA cracking statistics
- BESSIDE-NG-CRAWLER(1) - filter EAPOL frames from a directory of capture files.
- Best(3) - Load modules with fallback
- BESTFCOM(8) - Driver for Best Power Fortress/Ferrups
- bestfit(1) - Optimally choose files to be put on a CD (or other media)
- bestfit_color(3) - Finds a palette color fitting the requested RGB values. Allegro game programming library.
- BESTFORTRESS(8) - Driver for old Best Fortress UPS equipment
- bestill(6) - screen saver.
- BESTUFERRUPS(8) - Driver for Best Power Micro-Ferrups
- BESTUPS(8) - Driver for Best Power / SOLA (Phoenixtec protocol) UPS equipment
- Bevel(1) - Bevel - Afterstep Bevel
- BEXTRACT(8) - Bareos's 'Extract from volume'
- BEZ2MESH(1gv) - dices a BEZ file to a list of MESHes
- BF_COMPACT(1) - shell script to compact a bogofilter directory
- BF_COPY(1) - shell script to copy a bogofilter working directory
- BF_ENCRYPT(3ossl) - Blowfish encryption
- BF_TAR(1) - shell script to write a tar file of a bogofilter directory to stdout
- BFD(3) - Impromptu dumping of data structures for debugging purposes
- BFE(4) - Broadcom BCM4401 Ethernet Device Driver
- bfort(1) - program to extract short definitions for a Fortran to C interface
- BFS(1) - breadth-first search for your files
- BFST(1) - bFst is a Bayesian approach to Fst. Importantly bFst accounts for genotype uncertainty in the model using genotype likelihoods. For a more detailed description see: `A Bayesian approach to inferring...
- BFTPD(8) - B FTP Daemon
- bg-installer(1) - Standardized installer program.
- BG5CONV(1) - convert a TeX document in Big 5 encoding into `preprocessed' form.
- bg_test(6) - test the background mode of svgalib
- BGE(4) - Broadcom BCM57xx/BCM590x Gigabit/Fast Ethernet driver
- bgerror(n) - Command invoked to process background errors
- bgexec(n) - Run programs in the background while handling Tk events. kill - Terminate program or send signal.
- bggen(1) - generates colored backgrounds on X11 displays
- BGPCTL(8) - control the BGP routing daemon
- BGPD(8) - Border Gateway Protocol (BGP) routing daemon
- BGPD.CONF(5) - BGP routing daemon configuration file
- BGPLGD(8) - a bgpctl FastCGI server
- BGPQ3(8) - bgp filtering automation tool
- BGPQ4(8) - bgp filtering automation tool
- BGPUMA(1) - A program to search BGP Update files for CIDR blocks or Autonomous Systems
- BGROT(1) - a program to alleviate background boredom
- BGS(1) - background setter
- bgzip(1) - Block compression/decompression utility
- bhm(8) - program to send SMTP mail to /dev/null
- BHND(4) - Broadcom Home Networking Division interconnect bus
- BHND(9) - BHND driver programming interface
- BHND_CHIPC(4) - Broadcom Home Networking Division ChipCommon Driver
- BHND_EROM(9) - BHND device enumeration table parsing
- BHND_PMU(4) - Broadcom Home Networking Division PMU Driver
- BHNDB(4) - Broadcom Home Networking Division interconnect bridge driver
- BHNDB_PCI(4) - Broadcom Home Networking Division PCI host bridge driver
- BHYVE(4) - virtual machine monitor
- BHYVE(8) - run a guest operating system inside a virtual machine
- BHYVE_CONFIG(5) - bhyve configuration variables
- BHYVECTL(8) - control utility for bhyve instances
- BHYVELOAD(8) - load a FreeBSD
- BIB-1 ATTRIBUTE SET(7) - Bib-1 Attribute Set
- BIB2RIS(1) - converts bibtex bibliographic data to the RIS format
- BIBCLEAN(1) - prettyprint and syntax check BibTeX and Scribe bibliography data base files
- BIBCURSED(1) - manipulate BibTeX files
- Biber(3) - main module for biber, a bibtex replacement for users of biblatex
- BIBER(1) - A bibtex replacement for users of biblatex
- Biber::Annotation(3) - Biber::Annotation objects
- Biber::Config(3) - Configuration items which need to be saved across the lifetime of a Biber object
- Biber::Constants(3) - global constants for biber
- Biber::DataList(3) - Biber::DataList objects
- Biber::DataLists(3) - Biber::DataLists objects
- Biber::DataModel(3) - Biber::DataModel objects
- Biber::Date::Format(3) - Biber::Date::Format objects
- Biber::Entries(3) - Biber::Entries objects
- Biber::Entry(3) - Biber::Entry objects
- Biber::Entry::Name(3) - Biber::Entry::Name objects
- Biber::Entry::Names(3) - Biber::Entry::Names objects
- Biber::Input::file::biblatexml(3) - look in a BibLaTeXML file for an entry and create it if found
- Biber::Input::file::bibtex(3) - look in a BibTeX file for an entry and create it if found
- Biber::Internals(3) - Internal methods for processing the bibliographic data
- Biber::LangTag(3) - Biber::LangTag objects
- Biber::LangTags(3) - Biber::LangTags objects
- Biber::LaTeX::Recode(3) - Encode/Decode chars to/from UTF-8/lacros in LaTeX
- Biber::Output::base(3) - base class for Biber output modules.
- Biber::Output::bbl(3) - class for Biber output of .bbl
- Biber::Output::bblxml(3) - class for Biber output of .bbl in XML format
- Biber::Output::biblatexml(3) - class for biblatexml output
- Biber::Output::bibtex(3) - class for bibtex output
- Biber::Output::dot(3) - class for Biber output of GraphViz .dot files
- Biber::Section(3) - Biber::Section objects
- Biber::Sections(3) - Biber::Sections objects
- Biber::UCollate(3) - Biber::UCollate objects
- Biber::Utils(3) - Various utility subs used in Biber
- BIBLE(1) - Lookup words and verses in the Bible (King James version)
- BIBLESYNC(7) - multicast navigation synchronization in Bible programs
- BIBTEX(1) - make a bibliography for (La)TeX
- BIBTEX2HTML(BIB2BIB) - A translator of bibliography databases into HTML
- BibTeX::Parser(3) - A pure perl BibTeX parser
- BibTeX::Parser::Author(3) - Contains a single author for a BibTeX document.
- BibTeX::Parser::Entry(3) - Contains a single entry of a BibTeX document.
- bibtexconv(1) - BibTeX Converter
- bibtexconv-odt(1) - ODT Helper Script for BibTeX Converter
- BIBVIEW(1) - an X based graphical user interface for manipulating BibTeX databases
- BICKER_SER(8) - Driver for Bicker DC UPS via serial port connections
- BICON(1) - a bidirectional console
- iconv(1) - charset conversion utility
- iconv(3) - charset conversion function
- iconv_close(3) - charset converter deallocation function
- iconv_open(3) - charset converter allocation function
- biew(1) - console hex viewer/editor and disassembler.
- BIFF(1) - be notified if mail arrives and who it is from
- BIG5(5) - “Big Five” encoding for Traditional Chinese text
- Bigarray(3) - Large, multi-dimensional, numerical arrays.
- Bigarray.Array0(3) - Zero-dimensional arrays.
- Bigarray.Array1(3) - One-dimensional arrays.
- Bigarray.Array2(3) - Two-dimensional arrays.
- Bigarray.Array3(3) - Three-dimensional arrays.
- Bigarray.Genarray(3) - no description
- BIGFILE(1) - kill (or signal) a process when a file grows too big
- bigfloat(3) - transparent big floating point number support for Perl
- bigint(3) - transparent big integer support for Perl
- BigIP::iControl(3) - A Perl interface to the F5 iControl API
- BigIP::ParseConfig(3) - F5/BigIP configuration parser
- bignum(3) - transparent big number support for Perl
- bigrat(3) - transparent big rational number support for Perl
- Bigtop(3) - A web application data language processor
- BIGTOP(1) - the parser/generater for the bigtop langauge
- Bigtop::Backend::CGI(3) - defines the legal keywords for cgi backends
- Bigtop::Backend::CGI::Gantry(3) - A generated server for the [% app_name %] app
- Bigtop::Backend::Conf(3) - defines the legal keywords for conf backends
- Bigtop::Backend::Conf::Gantry(3) - makes Config::Gantry conf files
- Bigtop::Backend::Conf::General(3) - makes Config::General conf files
- Bigtop::Backend::Control(3) - defines legal keywords in control blocks
- Bigtop::Backend::Control::Gantry(3) - controller generator for the Gantry framework
- Bigtop::Backend::Diagram::GraphvizSql(3) - generates dot language file for data model
- Bigtop::Backend::HttpdConf(3) - defines the legal keywords for httpd conf backends
- Bigtop::Backend::HttpdConf::Gantry(3) - httpd.conf generator for the Gantry framework
- Bigtop::Backend::Init::Std(3) - Bigtop backend which works sort of like h2xs
- Bigtop::Backend::Model(3) - defines legal keywords in table and field blocks
- Bigtop::Backend::Model::GantryCDBI(3) - model for [% table_name %] table (stub part)
- Bigtop::Backend::Model::GantryDBIxClass(3) - schema class for [% app_name +%]
- Bigtop::Backend::SiteLook::GantryDefault(3) - Bigtop to generate site appearance files
- Bigtop::Backend::SQL(3) - defines legal keywords in table and field blocks
- Bigtop::Backend::SQL::DB2(3) - backend to generate sql for DB2 database creation
- Bigtop::Backend::SQL::MySQL(3) - backend to generate sql for MySQL database creation
- Bigtop::Backend::SQL::Postgres(3) - backend to generate sql for Postgres database creation
- Bigtop::Backend::SQL::SQLite(3) - backend to generate sql for SQLite database creation
- Bigtop::Deparser(3) - given an AST, makes a corresponding bigtop source file
- Bigtop::Docs::About(3) - A document explaining Bigtop's features and history
- Bigtop::Docs::AutoBackends(3) - lists all backends and their config statements
- Bigtop::Docs::Cookbook(3) - Bigtop syntax by example
- Bigtop::Docs::FullKeywords(3) - Descriptions of all Bigtop keywords
- Bigtop::Docs::Modules(3) - An annotated list of modules in the Bigtop distribution
- Bigtop::Docs::QuickKeywords(3) - Short descriptions of all Bigtop keywords
- Bigtop::Docs::QuickStart(3) - The fastest ways to Gantry apps with Bigtop
- Bigtop::Docs::Syntax(3) - An introduction to Bigtop syntax description
- Bigtop::Docs::TentRef(3) - tentmaker reference (best viewed in html)
- Bigtop::Docs::TentTut(3) - tentmaker tutorial (best viewed in html)
- Bigtop::Docs::TOC(3) - Table of Contents for Bigtop::Docs::* documentation modules
- Bigtop::Docs::Tutorial(3) - a simple case study of building a web app with bigtop
- Bigtop::Docs::Vim(3) - How to get vim syntax things for Bigtop files
- Bigtop::Grammar(3) - generated by Parse::RecDescent from bigtop.grammar
- Bigtop::grammar(3) - generated by Parse::RecDescent from bigtop.grammar
- Bigtop::Keywords(3) - A central place to describe all bigtop keywords
- Bigtop::Parser(3) - the Parse::RecDescent grammar driven parser for bigtop files
- Bigtop::ScriptHelp(3) - A helper modules for command line utilities
- Bigtop::ScriptHelp::Style(3) - Factory for scripts' command line and standard in handlers
- Bigtop::ScriptHelp::Style::Kickstart(3) - handles kickstart syntax for scripts
- Bigtop::ScriptHelp::Style::Pg8Live(3) - gets its descriptions from Postgresql
- Bigtop::TentMaker(3) - A Gantry App to Help You Code Bigtop Files
- Bigtop::TentMakerPath(3) - keeps track of where the tentmaker templates live
- BIGVIA(3) - draws a non minimal via as a bunch of vias
- bigyear(1) - print a calendar, one month per page
- BIL(special file) - Builder Interface Language for the CDE Application Builder
- BIN(3) - grouped memory allocation
- bin(n) - Encoding "bin"
- bin2c(1) - embed data files into C as variables
- BIN2ECM(1) - encoder and decoder for the error code modeler format
- hexdump(1) - reversible hexdump
- bin2obj(1) - The Free Pascal binary to pascal include file converter.
- BIN2REC(1) - converts biosignal data produced with rec2bin, into a gdf file. rec2bin and bin2rec are complementary functions, which can be useful to dump data, edit date and revert it back into the original...
- BIN_DEC_HEX(1) - How to use binary, decimal, and hexadecimal notation.
- binary(3) - Library for handling binary data.
- binary(n) - Insert and extract fields from binary strings
- binary2ascii(1) - Convert binary numbers to textual representation
- binaryhorizon(6) - A system of path tracing particles evolves continuously.
- binaryring(6) - A system of path tracing particles evolves continuously from an initial creation.
- BINBLOOM(15 Sep 2021) - Find firmware loading address and UDS database (if any)
- bincimap-up(1) - Authentication stub for Binc IMAP
- bincimap.conf(5) - Global configuration file for Binc IMAP
- bincimapd(1) - IMAP4rev1 server
- BINCLOCK(1) - prints time in binary format
- BINCOMP(1) - compare binary files
- Bind(3) - Bind variables to captured buffers
- BIND(2) - assign a local protocol address to a socket
- bind(n) - Arrange for X events to invoke Tcl scripts
- BIND::Conf_Parser(3) - Parser class for BIND configuration files
- BIND::Config::Parser(3) - Parse BIND Config file.
- BIND_TEXTDOMAIN_CODESET(3) - set encoding of message translations
- BINDAT(2) - assign a local protocol address to a socket
- BINDFS(1) - bindfs ‐ mount --bind in user-space
- BINDRESVPORT(3) - bind a socket to a privileged IP port
- bindtags(n) - Determine which bindings apply to a window, and order of evaluation
- BINDTEST(1) - test bind(2) behavior on IPv6 implementation
- BINDTEXTDOMAIN(3) - set directory containing message catalogs
- BINGO(1) - This is a console bingo game application. With bingo_print.pl from Games::Bingo::Print you can generate cards and then you are actually ready to play.
- BINGO_PRINT(1) - simple script to generate PDFs containing bingo cards
- BINHEX(1) - use Convert::BinHex to encode files as BinHex
- BINKD(8) - transfer files between two Fidonet systems over TCP/IP
- BINMISCCTL(8) - manage binary image activators
- Bino(1) - a 3D video player with multi-display support.
- BINSRCH(3WN) - bin_search, copyfile, replace_line, insert_line
- BINTRANS(1) - encode / decode a binary file
- Binutils(3) - no description
- BIO(3) - buffered input/output
- bio(3) - I/O abstraction
- BIO(7ossl) - Basic I/O abstraction
- Bio::Align::AlignI(3) - An interface for describing sequence alignments.
- Bio::Align::DNAStatistics(3) - Calculate some statistics for a DNA alignment
- Bio::Align::PairwiseStatistics(3) - Base statistic object for Pairwise Alignments
- Bio::Align::ProteinStatistics(3) - Calculate Protein Alignment statistics (mostly distances)
- Bio::Align::StatisticsI(3) - Calculate some statistics for an alignment
- Bio::Align::Utilities(3) - A collection of utilities regarding converting and manipulating alignment objects
- Bio::AlignIO(3) - Handler for AlignIO Formats
- Bio::AlignIO::arp(3) - ARP MSA Sequence input/output stream
- Bio::AlignIO::bl2seq(3) - bl2seq sequence input/output stream
- Bio::AlignIO::clustalw(3) - clustalw sequence input/output stream
- Bio::AlignIO::emboss(3) - Parse EMBOSS alignment output (from applications water and needle)
- Bio::AlignIO::fasta(3) - fasta MSA Sequence input/output stream
- Bio::AlignIO::Handler::GenericAlignHandler(3) - Bio::HandlerI-based generic data handler class for alignment-based data
- Bio::AlignIO::largemultifasta(3) - Largemultifasta MSA Sequence input/output stream
- Bio::AlignIO::maf(3) - Multiple Alignment Format sequence input stream
- Bio::AlignIO::mase(3) - mase sequence input/output stream
- Bio::AlignIO::mega(3) - Parse and Create MEGA format data files
- Bio::AlignIO::meme(3) - meme sequence input/output stream
- Bio::AlignIO::metafasta(3) - Metafasta MSA Sequence input/output stream
- Bio::AlignIO::msf(3) - msf sequence input/output stream
- Bio::AlignIO::nexus(3) - NEXUS format sequence input/output stream
- Bio::AlignIO::pfam(3) - pfam sequence input/output stream
- Bio::AlignIO::phylip(3) - PHYLIP format sequence input/output stream
- Bio::AlignIO::po(3) - po MSA Sequence input/output stream
- Bio::AlignIO::proda(3) - proda sequence input/output stream
- Bio::AlignIO::prodom(3) - prodom sequence input/output stream
- Bio::AlignIO::psi(3) - Read/Write PSI-BLAST profile alignment files
- Bio::AlignIO::selex(3) - selex sequence input/output stream
- Bio::AlignIO::xmfa(3) - XMFA MSA Sequence input/output stream
- Bio::AnalysisI(3) - An interface to any (local or remote) analysis tool
- Bio::AnalysisParserI(3) - Generic analysis output parser interface
- Bio::AnalysisResultI(3) - Interface for analysis result objects
- Bio::AnnotatableI(3) - the base interface an annotatable object must implement
- Bio::Annotation::AnnotationFactory(3) - Instantiates a new Bio::AnnotationI (or derived class) through a factory
- Bio::Annotation::Collection(3) - Default Perl implementation of AnnotationCollectionI
- Bio::Annotation::Comment(3) - A comment object, holding text
- Bio::Annotation::DBLink(3) - untyped links between databases
- Bio::Annotation::OntologyTerm(3) - An ontology term adapted to AnnotationI
- Bio::Annotation::Reference(3) - Specialised DBLink object for Literature References
- Bio::Annotation::Relation(3) - Relationship (pairwise) with other objects SeqI and NodeI;
- Bio::Annotation::SimpleValue(3) - A simple scalar
- Bio::Annotation::StructuredValue(3) - A scalar with embedded structured information
- Bio::Annotation::TagTree(3) - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
- Bio::Annotation::Target(3) - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
- Bio::Annotation::Tree(3) - Provide a tree as an annotation to a Bio::AnnotatableI object
- Bio::Annotation::TypeManager(3) - Manages types for annotation collections
- Bio::AnnotationCollectionI(3) - Interface for annotation collections
- Bio::AnnotationI(3) - Annotation interface
- Bio::ASN1::EntrezGene(3) - Regular expression-based Perl Parser for NCBI Entrez Gene.
- Bio::ASN1::EntrezGene::Indexer(3) - Indexes NCBI Sequence files.
- Bio::ASN1::Sequence(3) - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
- Bio::ASN1::Sequence::Indexer(3) - Indexes NCBI Sequence files.
- Bio::Cluster(3) - BioPerl cluster modules
- Bio::Cluster::ClusterFactory(3) - Instantiates a new Bio::ClusterI (or derived class) through a factory
- Bio::Cluster::FamilyI(3) - Family Interface
- Bio::Cluster::SequenceFamily(3) - Sequence Family object
- Bio::Cluster::UniGene(3) - UniGene object
- Bio::Cluster::UniGeneI(3) - abstract interface of UniGene object
- Bio::ClusterI(3) - Cluster Interface
- Bio::ClusterIO(3) - Handler for Cluster Formats
- Bio::ClusterIO::dbsnp(3) - dbSNP input stream
- Bio::ClusterIO::unigene(3) - UniGene input stream
- Bio::CodonUsage::IO(3) - for reading and writing codon usage tables to file
- Bio::CodonUsage::Table(3) - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
- Bio::Coordinate(3) - Modules for working with biological coordinates
- Bio::Coordinate::Chain(3) - Mapping locations through a chain of coordinate mappers.
- Bio::Coordinate::Collection(3) - Noncontinuous match between two coordinate sets.
- Bio::Coordinate::ExtrapolatingPair(3) - Continuous match between two coordinate sets.
- Bio::Coordinate::GeneMapper(3) - Transformations between gene related coordinate systems.
- Bio::Coordinate::Graph(3) - Finds shortest path between nodes in a graph.
- Bio::Coordinate::MapperI(3) - Interface describing coordinate mappers.
- Bio::Coordinate::Pair(3) - Continuous match between two coordinate sets.
- Bio::Coordinate::Result(3) - Results from coordinate transformation.
- Bio::Coordinate::Result::Gap(3) - Another name for Bio::Location::Simple.
- Bio::Coordinate::Result::Match(3) - Another name for Bio::Location::Simple.
- Bio::Coordinate::ResultI(3) - Interface to identify coordinate mapper results.
- Bio::Coordinate::Utils(3) - Additional methods to create Bio::Coordinate objects.
- Das(3) - Interface to Distributed Annotation System
- Das::AGPServer::Config(3)
- Das::AGPServer::Daemon(3)
- Das::AGPServer::Parser(3)
- Das::AGPServer::SQLStorage(3)
- Das::AGPServer::SQLStorage::CSV::DB(3)
- Das::AGPServer::SQLStorage::MySQL::DB(3)
- Das::DSN(3) - Object encapsulation of a DAS data source
- Das::Feature(3) - A genomic annotation
- Das::FeatureIterator(3) - Iterate over a set of Bio::Das::Features
- Bio::Das::FeatureTypeI(3) - Simple interface to Sequence Ontology feature types
- Das::HTTP::Fetch(3) - Manage the HTTP protocol for DAS transactions
- Bio::Das::Lite(3) - Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)
- Das::Map(3) - Resolve map coordinates
- Das::Request(3) - Base class for a request on a DAS server
- Das::Request::Dnas(3) - The DAS "dna" request
- Das::Request::Dsn(3) - The DAS "dsn" request
- Das::Request::Entry_points(3) - The DAS "entry_points" request
- Das::Request::Feature2Segments(3) - Translate feature names into segments
- Das::Request::Sequences(3) - The DAS "sequence" request
- Das::Request::Stylesheet(3) - The DAS "stylesheet" request
- Das::Request::Types(3) - The DAS "types" request
- Das::Segment(3) - Serial access to Bio::Das sequence "segments"
- Bio::Das::SegmentI(3) - DAS-style access to a feature database
- Das::Stylesheet(3) - Access to DAS stylesheets
- Das::Type(3) - A sequence annotation type
- Das::TypeHandler(3) - Utilities for handling types
- Das::Util(3) - Das Utilities
- Bio::DasI(3) - DAS-style access to a feature database
- Bio::DB::DBFetch(3) - Database object for retrieving using the dbfetch script
- Bio::DB::EMBL(3) - Database object interface for EMBL entry retrieval
- Bio::DB::EntrezGene(3) - Database object interface to Entrez Gene
- Bio::DB::ESoap(3) - Client for the NCBI Entrez EUtilities SOAP server
- Bio::DB::ESoap::WSDL(3) - WSDL parsing for Entrez SOAP EUtilities
- Bio::DB::Failover(3) - A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
- Bio::DB::Fasta(3) - Fast indexed access to fasta files
- Bio::DB::FileCache(3) - In file cache for BioSeq objects
- Bio::DB::Flat(3) - Interface for indexed flat files
- Bio::DB::Flat::BDB(3) - Interface for BioHackathon standard BDB-indexed flat file
- Bio::DB::Flat::BDB::embl(3) - embl adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::fasta(3) - fasta adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::genbank(3) - genbank adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::swiss(3) - swissprot adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BinarySearch(3) - BinarySearch search indexing system for sequence files
- Bio::DB::GenBank(3) - Database object interface to GenBank
- Bio::DB::GenericWebAgent(3) - helper base class for parameter-based remote server access and response retrieval.
- Bio::DB::GenPept(3) - Database object interface to GenPept
- Bio::DB::GFF::Util::Binning(3) - binning utility for Bio::DB::GFF index
- Bio::DB::GFF::Util::Rearrange(3) - rearrange utility
- Bio::DB::IndexedBase(3) - Base class for modules using indexed sequence files
- Bio::DB::InMemoryCache(3) - Abstract interface for a sequence database
- Bio::DB::LocationI(3) - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
- Bio::DB::NCBIHelper(3) - A collection of routines useful for queries to NCBI databases.
- Bio::DB::Qual(3) - Fast indexed access to quality files
- Bio::DB::Query::GenBank(3) - Build a GenBank Entrez Query
- Bio::DB::Query::WebQuery(3) - Helper class for web-based sequence queryies
- Bio::DB::QueryI(3) - Object Interface to queryable sequence databases
- Bio::DB::RandomAccessI(3) - Abstract interface for a sequence database
- Bio::DB::ReferenceI(3) - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
- Bio::DB::Registry(3) - Access to the Open Bio Database Access registry scheme
- Bio::DB::SeqI(3) - Abstract Interface for Sequence databases
- Bio::DB::SoapEUtilities(3) - Interface to the NCBI Entrez web service *BETA*
- Bio::DB::SoapEUtilities::DocSumAdaptor(3) - Handle for Entrez SOAP DocSums
- Bio::DB::SoapEUtilities::FetchAdaptor(3) - Conversion of Entrez SOAP messages to BioPerl objects
- Bio::DB::SoapEUtilities::FetchAdaptor::seq(3) - Fetch adaptor for 'seq' efetch SOAP messages
- Bio::DB::SoapEUtilities::FetchAdaptor::species(3) - Fetch adaptor for 'taxonomy' efetch SOAP messages
- Bio::DB::SoapEUtilities::GQueryAdaptor(3) - Handle for Entrez SOAP GlobalQuery items
- Bio::DB::SoapEUtilities::LinkAdaptor(3) - Handle for Entrez SOAP LinkSets
- Bio::DB::SoapEUtilities::Result(3) - Accessor object for SoapEUtilities results
- Bio::DB::Taxonomy(3) - Access to a taxonomy database
- Bio::DB::Taxonomy::entrez(3) - Taxonomy Entrez driver
- Bio::DB::Taxonomy::flatfile(3) - Use the NCBI taxonomy from local indexed flat files
- Bio::DB::Taxonomy::greengenes(3) - Use the Greengenes taxonomy
- Bio::DB::Taxonomy::list(3) - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
- Bio::DB::Taxonomy::silva(3) - Use the Silva taxonomy
- Bio::DB::UpdateableSeqI(3) - An interface for writing to a database of sequences.
- Bio::DB::WebDBSeqI(3) - Object Interface to generalize Web Databases for retrieving sequences
- Bio::DBLinkContainerI(3) - Abstract interface for any object wanting to use database cross references
- Bio::DescribableI(3) - interface for objects with human readable names and descriptions
- Bio::Event::EventGeneratorI(3) - This interface describes the basic event generator class.
- Bio::Event::EventHandlerI(3) - An Event Handler Interface
- Bio::Factory::AnalysisI(3) - An interface to analysis tool factory
- Bio::Factory::ApplicationFactoryI(3) - Interface class for Application Factories
- Bio::Factory::DriverFactory(3) - Base class for factory classes loading drivers
- Bio::Factory::EMBOSS(3) - EMBOSS application factory class
- Bio::Factory::FTLocationFactory(3) - A FeatureTable Location Parser
- Bio::Factory::LocationFactoryI(3) - A factory interface for generating locations from a string
- Bio::Factory::ObjectBuilderI(3) - Interface for an object builder
- Bio::Factory::ObjectFactory(3) - Instantiates a new Bio::Root::RootI (or derived class) through a factory
- Bio::Factory::ObjectFactoryI(3) - A General object creator factory
- Bio::Factory::SeqAnalysisParserFactory(3) - class capable of creating SeqAnalysisParserI compliant parsers
- Bio::Factory::SeqAnalysisParserFactoryI(3) - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
- Bio::Factory::SequenceFactoryI(3) - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
- Bio::Factory::SequenceProcessorI(3) - Interface for chained sequence processing algorithms
- Bio::Factory::SequenceStreamI(3) - Interface describing the basics of a Sequence Stream.
- Bio::Factory::TreeFactoryI(3) - Factory Interface for getting and writing trees from/to a data stream
- Bio::FeatureHolderI(3) - the base interface an object with features must implement
- Bio::FeatureIO(3) - Handler for FeatureIO
- Bio::FeatureIO::bed(3) - read/write features from UCSC BED format
- Bio::FeatureIO::gff(3) - read/write GFF feature files
- Bio::FeatureIO::gtf(3) - read write features in GTF format
- Bio::FeatureIO::interpro(3) - read features from InterPro XML
- Bio::FeatureIO::ptt(3) - read/write features in PTT format
- Bio::FeatureIO::vecscreen_simple(3) - read/write features from NCBI vecscreen -f 3 output
- Bio::GFF3::LowLevel(3) - fast, low-level functions for parsing and formatting GFF3
- Bio::GFF3::LowLevel::Parser(3) - a fast, low-level gff3 parser
- Bio::GFF3::LowLevel::Parser::1_0_backcompat(3) - compatibility layer to support Bio::GFF3::LowLevel::Parser 1.0 API
- Bio::GFF3::Transform::FromFasta(3) - make gff3 for the sequences in a fasta file
- Bio::GFF3::Transform::SyncDirectives(3) - insert sync (###) directives into an existing GFF3 file. WARNING: this module does not really work in the general case, read the DESCRIPTION section below.
- Bio::Glite(3) - G-language Genome Analysis Environment REST service interface module
- Bio::Graphics(3) - Generate GD images of Bio::Seq objects
- Bio::Graphics::ConfiguratorI(3) - A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation...
- Bio::Graphics::DrawTransmembrane(3) - draw a cartoon of an Alpha-helical transmembrane protein.
- Bio::Graphics::Feature(3) - A simple feature object for use with Bio::Graphics::Panel
- Bio::Graphics::FeatureBase(3) - Compatibility module
- Bio::Graphics::FeatureDir(3) - A directory of feature files and conf files
- Bio::Graphics::FeatureFile(3) - A set of Bio::Graphics features, stored in a file
- Bio::Graphics::FeatureFile::Iterator(3) - Iterator across a Bio::Graphics::FeatureFile
- Bio::Graphics::Glyph(3) - Base class for Bio::Graphics::Glyph objects
- Bio::Graphics::Glyph::alignment(3) - The "alignment" glyph
- Bio::Graphics::Glyph::allele_tower(3) - The "allele_tower" glyph
- Bio::Graphics::Glyph::anchored_arrow(3) - The "anchored_arrow" glyph
- Bio::Graphics::Glyph::arrow(3) - the "arrow" glyph
- Bio::Graphics::Glyph::box(3) - The "box" glyph
- Bio::Graphics::Glyph::broken_line(3) - The "broken line" glyph
- Bio::Graphics::Glyph::cds(3) - The "cds" glyph
- Bio::Graphics::Glyph::christmas_arrow(3) - The "christmas arrow" glyph
- Bio::Graphics::Glyph::crossbox(3) - The "crossbox" glyph
- Bio::Graphics::Glyph::dashed_line(3) - The "dashed line" glyph
- Bio::Graphics::Glyph::decorated_gene(3) - A GFF3-compatible gene glyph with protein decorations
- Bio::Graphics::Glyph::decorated_transcript(3) - draws processed transcript with protein decorations
- Bio::Graphics::Glyph::diamond(3) - The "diamond" glyph
- Bio::Graphics::Glyph::dna(3) - The "dna" glyph
- Bio::Graphics::Glyph::dot(3) - The "dot" glyph
- Bio::Graphics::Glyph::dumbbell(3) - A glyph that draws a "dumbbell" with the same shapes on both ends.
- Bio::Graphics::Glyph::ellipse(3) - The "ellipse" glyph
- Bio::Graphics::Glyph::ex(3) - the "ex", or "crossed box" glyph
- Bio::Graphics::Glyph::extending_arrow(3) - The "extending arrow" glyph
- Bio::Graphics::Glyph::Factory(3) - Factory for Bio::Graphics::Glyph objects
- Bio::Graphics::Glyph::fb_shmiggle(3)
- Bio::Graphics::Glyph::fixedwidth(3) - A base class fixed width glyphs
- Bio::Graphics::Glyph::flag(3) - the "flag" glyph
- Bio::Graphics::Glyph::gene(3) - A GFF3-compatible gene glyph
- Bio::Graphics::Glyph::generic(3) - The "generic" glyph
- Bio::Graphics::Glyph::graded_segments(3) - The "graded_segments" glyph
- Bio::Graphics::Glyph::group(3) - The "group" glyph
- Bio::Graphics::Glyph::hat(3) - The "hat" glyph
- Bio::Graphics::Glyph::heat_map(3) - The "heat_map" glyph
- Bio::Graphics::Glyph::heat_map_ideogram(3) - The "heat_map_ideogram" glyph
- Bio::Graphics::Glyph::heterogeneous_segments(3) - The "heterogeneous_segments" glyph
- Bio::Graphics::Glyph::hidden(3) - The "hidden" glyph
- Bio::Graphics::Glyph::hybrid_plot(3) - An xyplot plot drawing dual graph using data from two or more wiggle files per track
- Bio::Graphics::Glyph::ideogram(3) - The "ideogram" glyph
- Bio::Graphics::Glyph::image(3) - A glyph that draws photographs & other images
- Bio::Graphics::Glyph::lightning(3) - The "lightning" glyph
- Bio::Graphics::Glyph::line(3) - The "line" glyph
- Bio::Graphics::Glyph::merge_parts(3) - a base class which suppors semantic zooming of scored alignment features
- Bio::Graphics::Glyph::merged_alignment(3) - The "merged_alignment" glyph
- Bio::Graphics::Glyph::minmax(3) - The minmax glyph
- Bio::Graphics::Glyph::operon(3) - The "polycistronic operon" glyph
- Bio::Graphics::Glyph::oval(3) - The "oval" glyph
- Bio::Graphics::Glyph::pairplot(3) - The "pairwise plot" glyph
- Bio::Graphics::Glyph::pentagram(3) - The "pentagram" glyph
- Bio::Graphics::Glyph::phylo_align(3) - The "phylogenetic alignment" glyph
- Bio::Graphics::Glyph::pinsertion(3) - The "Drosophila P-element Insertion" glyph
- Bio::Graphics::Glyph::primers(3) - The "STS primers" glyph
- Bio::Graphics::Glyph::processed_transcript(3) - The sequence ontology transcript glyph
- Bio::Graphics::Glyph::protein(3) - The "protein" glyph
- Bio::Graphics::Glyph::ragged_ends(3) - The "ragged ends" glyph
- Bio::Graphics::Glyph::rainbow_gene(3) - A GFF3-compatible gene glyph
- Bio::Graphics::Glyph::redgreen_box(3) - The "redgreen_box" glyph
- Bio::Graphics::Glyph::redgreen_segment(3) - The "redgreen_segments" glyph
- Bio::Graphics::Glyph::repeating_shape(3) - A glyph that draws the same shape repeatedly.
- Bio::Graphics::Glyph::rndrect(3) - The "round rect" glyph
- Bio::Graphics::Glyph::ruler_arrow(3) - glyph for drawing an arrow as ruler (5' and 3' are marked as label)
- Bio::Graphics::Glyph::saw_teeth(3) - The "saw teeth" glyph
- Bio::Graphics::Glyph::scale(3) - The "scale" glyph
- Bio::Graphics::Glyph::segmented_keyglyph(3) - The "segmented_keyglyph" glyph
- Bio::Graphics::Glyph::segments(3) - The "segments" glyph
- Bio::Graphics::Glyph::so_transcript(3) - The sequence ontology transcript glyph
- Bio::Graphics::Glyph::span(3) - The "span" glyph
- Bio::Graphics::Glyph::spectrogram(3) - The "spectrogram" glyph
- Bio::Graphics::Glyph::splice_site(3) - The "splice_site" glyph
- Bio::Graphics::Glyph::stackedplot(3) - The stackedplot glyph
- Bio::Graphics::Glyph::ternary_plot(3) - Draw ternary plot data
- Bio::Graphics::Glyph::text_in_box(3) - The "text in box" glyph
- Bio::Graphics::Glyph::three_letters(3) - DAS-compatible package to use for drawing a line of groups of three letters
- Bio::Graphics::Glyph::tic_tac_toe(3) - The "tic-tac-toe" glyph
- Bio::Graphics::Glyph::toomany(3) - The "too many to show" glyph
- Bio::Graphics::Glyph::trace(3) - A glyph that visualizes a trace file
- Bio::Graphics::Glyph::track(3) - The "track" glyph
- Bio::Graphics::Glyph::transcript(3) - The "transcript" glyph
- Bio::Graphics::Glyph::transcript2(3) - The "transcript2" glyph
- Bio::Graphics::Glyph::translation(3) - The "6-frame translation" glyph
- Bio::Graphics::Glyph::triangle(3) - The "triangle" glyph
- Bio::Graphics::Glyph::two_bolts(3) - The "two bolts" glyph
- Bio::Graphics::Glyph::vista_plot(3) - The "vista_plot" glyph
- Bio::Graphics::Glyph::wave(3) - The "wave" glyph
- Bio::Graphics::Glyph::weighted_arrow(3) - The "weighted arrow" glyph
- Bio::Graphics::Glyph::whiskerplot(3) - The whiskerplot glyph
- Bio::Graphics::Glyph::wiggle_box(3) - A generic box glyph compatible with dense "wig"data
- Bio::Graphics::Glyph::wiggle_density(3) - A density plot compatible with dense "wig"data
- Bio::Graphics::Glyph::wiggle_xyplot(3) - An xyplot plot compatible with dense "wig"data
- Bio::Graphics::Glyph::xyplot(3) - The xyplot glyph
- Bio::Graphics::Panel(3) - Generate GD images of Bio::Seq objects
- Bio::Graphics::Pictogram(3) - generate SVG output of Pictogram display for consensus motifs
- Bio::Graphics::RendererI(3) - A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
- Bio::Graphics::Util(3) - non-object-oriented utilities used in Bio::Graphics modules
- Bio::Graphics::Wiggle(3) - Binary storage for dense genomic features
- Bio::Graphics::Wiggle::Loader(3)
- Bio::HandlerBaseI(3) - Interface class for handler methods which interact with any event-driven parsers (drivers).
- Bio::IdCollectionI(3) - interface for objects with multiple identifiers
- Bio::IdentifiableI(3) - interface for objects with identifiers
- Bio::Index::Abstract(3) - Abstract interface for indexing a flat file
- Bio::Index::AbstractSeq(3) - base class for AbstractSeq
- Bio::Index::Blast(3) - Indexes Blast reports and supports retrieval based on query accession(s)
- Bio::Index::BlastTable(3) - Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
- Bio::Index::EMBL(3) - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
- Bio::Index::Fasta(3) - Interface for indexing (multiple) fasta files
- Bio::Index::Fastq(3) - Interface for indexing (multiple) fastq files
- Bio::Index::GenBank(3) - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
- Bio::Index::Qual(3) - Interface for indexing (multiple) fasta qual files
- Bio::Index::SwissPfam(3) - Interface for indexing swisspfam files
- Bio::Index::Swissprot(3) - Interface for indexing one or more Swissprot files.
- Bio::LocatableSeq(3) - A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
- Bio::Location::Atomic(3) - Implementation of a Atomic Location on a Sequence
- Bio::Location::AvWithinCoordPolicy(3) - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
- Bio::Location::CoordinatePolicyI(3) - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
- Bio::Location::Fuzzy(3) - Implementation of a Location on a Sequence which has unclear start and/or end locations
- Bio::Location::FuzzyLocationI(3) - Abstract interface of a Location on a Sequence which has unclear start/end location
- Bio::Location::NarrowestCoordPolicy(3) - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
- Bio::Location::Simple(3) - Implementation of a Simple Location on a Sequence
- Bio::Location::Split(3) - Implementation of a Location on a Sequence which has multiple locations (start/end points)
- Bio::Location::SplitLocationI(3) - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
- Bio::Location::WidestCoordPolicy(3) - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
- Bio::LocationI(3) - Abstract interface of a Location on a Sequence
- Bio::MAGETAB(3) - A data model and utility API for the MAGE-TAB format.
- Bio::MAGETAB::ArrayDesign(3) - MAGE-TAB array design class
- Bio::MAGETAB::Assay(3) - MAGE-TAB assay class
- Bio::MAGETAB::BaseClass(3) - Abstract base class for all MAGE-TAB classes.
- Bio::MAGETAB::Comment(3) - MAGE-TAB user-defined comment class
- Bio::MAGETAB::CompositeElement(3) - MAGE-TAB composite element class
- Bio::MAGETAB::Contact(3) - MAGE-TAB contact class
- Bio::MAGETAB::ControlledTerm(3) - MAGE-TAB controlled term class
- Bio::MAGETAB::Data(3) - Abstract data class
- Bio::MAGETAB::DataAcquisition(3) - MAGE-TAB data acquisition class
- Bio::MAGETAB::DatabaseEntry(3) - MAGE-TAB database entry class
- Bio::MAGETAB::DataFile(3) - MAGE-TAB data file class
- Bio::MAGETAB::DataMatrix(3) - MAGE-TAB data matrix class
- Bio::MAGETAB::DesignElement(3) - Abstract design element class
- Bio::MAGETAB::Edge(3) - MAGE-TAB edge class
- Bio::MAGETAB::Event(3) - Abstract event class
- Bio::MAGETAB::Extract(3) - MAGE-TAB extract class
- Bio::MAGETAB::Factor(3) - MAGE-TAB experimental factor class
- Bio::MAGETAB::FactorValue(3) - MAGE-TAB experimental factor class
- Bio::MAGETAB::Feature(3) - MAGE-TAB feature class
- Bio::MAGETAB::Investigation(3) - MAGE-TAB investigation class
- Bio::MAGETAB::LabeledExtract(3) - MAGE-TAB labeled extract class
- Bio::MAGETAB::Material(3) - Abstract material class
- Bio::MAGETAB::MatrixColumn(3) - MAGE-TAB matrix column class
- Bio::MAGETAB::MatrixRow(3) - MAGE-TAB matrix row class
- Bio::MAGETAB::Measurement(3) - MAGE-TAB measurement class
- Bio::MAGETAB::Node(3) - Abstract node class
- Bio::MAGETAB::Normalization(3) - MAGE-TAB data acquisition class
- Bio::MAGETAB::ParameterValue(3) - MAGE-TAB parameter value class
- Bio::MAGETAB::Protocol(3) - MAGE-TAB protocol class
- Bio::MAGETAB::ProtocolApplication(3) - MAGE-TAB protocol application class
- Bio::MAGETAB::ProtocolParameter(3) - MAGE-TAB protocol parameter class
- Bio::MAGETAB::Publication(3) - MAGE-TAB publication class
- Bio::MAGETAB::Reporter(3) - MAGE-TAB reporter class
- Bio::MAGETAB::Sample(3) - MAGE-TAB sample class
- Bio::MAGETAB::SDRF(3) - MAGE-TAB SDRF class
- Bio::MAGETAB::SDRFRow(3) - MAGE-TAB SDRF row class
- Bio::MAGETAB::Source(3) - MAGE-TAB source class
- Bio::MAGETAB::TermSource(3) - MAGE-TAB term source class
- Bio::MAGETAB::Types(3) - custom data types for Bio::MAGETAB
- Bio::MAGETAB::Util::Builder(3) - A storage class used to track Bio::MAGETAB object creation.
- Bio::MAGETAB::Util::DBLoader(3) - A persistent storage class used to track Bio::MAGETAB object creation and insertion into a relational database.
- Bio::MAGETAB::Util::Persistence(3) - A Tangram-based object persistence class for MAGE-TAB.
- Bio::MAGETAB::Util::Reader(3) - A parser/validator for MAGE-TAB documents.
- Bio::MAGETAB::Util::Reader::ADF(3) - ADF parser class.
- Bio::MAGETAB::Util::Reader::DataMatrix(3) - Data matrix parser class.
- Bio::MAGETAB::Util::Reader::IDF(3) - IDF parser class.
- Bio::MAGETAB::Util::Reader::SDRF(3) - SDRF parser class.
- Bio::MAGETAB::Util::Reader::Tabfile(3) - An abstract class providing methods for handling tab-delimited files.
- Bio::MAGETAB::Util::Reader::TagValueFile(3) - An abstract class providing methods for handling tab-delimited files.
- Bio::MAGETAB::Util::RewriteAE(3) - A utility class providing methods to correct some common errors in ArrayExpress MAGE-TAB documents.
- Bio::MAGETAB::Util::Writer(3) - Export of MAGE-TAB objects.
- Bio::MAGETAB::Util::Writer::ADF(3) - Export of MAGE-TAB ArrayDesign objects.
- Bio::MAGETAB::Util::Writer::GraphViz(3) - Visualization of MAGE-TAB objects.
- Bio::MAGETAB::Util::Writer::IDF(3) - Export of MAGE-TAB Investigation objects.
- Bio::MAGETAB::Util::Writer::SDRF(3) - Export of MAGE-TAB SDRF objects.
- Bio::MAGETAB::Util::Writer::Tabfile(3) - Abstract MAGE-TAB exporter class.
- Bio::Matrix::Generic(3) - A generic matrix implementation
- Bio::Matrix::IO(3) - A factory for Matrix parsing
- Bio::Matrix::IO::mlagan(3) - A parser for the mlagan substitution matrix
- Bio::Matrix::IO::phylip(3) - A parser for PHYLIP distance matricies
- Bio::Matrix::IO::scoring(3) - A parser for PAM/BLOSUM matricies
- Bio::Matrix::MatrixI(3) - An interface for describing a Matrix
- Bio::Matrix::Mlagan(3) - A generic matrix with mlagan fields
- Bio::Matrix::PhylipDist(3) - A Phylip Distance Matrix object
- Bio::Matrix::PSM::InstanceSite(3) - A PSM site occurrence
- Bio::Matrix::PSM::InstanceSiteI(3) - InstanceSite interface, holds an instance of a PSM
- Bio::Matrix::PSM::IO(3) - PSM parser
- Bio::Matrix::PSM::IO::mast(3) - PSM mast parser implementation
- Bio::Matrix::PSM::IO::masta(3) - motif fasta format parser
- Bio::Matrix::PSM::IO::meme(3) - PSM meme parser implementation
- Bio::Matrix::PSM::IO::psiblast(3) - PSM psiblast parser
- Bio::Matrix::PSM::IO::transfac(3) - PSM transfac parser
- Bio::Matrix::PSM::ProtMatrix(3) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
- Bio::Matrix::PSM::ProtPsm(3) - handle combination of site matricies
- Bio::Matrix::PSM::Psm(3) - handle combination of site matricies
- Bio::Matrix::PSM::PsmHeader(3) - PSM mast parser implementation
- Bio::Matrix::PSM::PsmHeaderI(3) - handles the header data from a PSM file
- Bio::Matrix::PSM::PsmI(3) - abstract interface to handler of site matricies
- Bio::Matrix::PSM::SiteMatrix(3) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
- Bio::Matrix::PSM::SiteMatrixI(3) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
- Bio::Matrix::Scoring(3) - Object which can hold scoring matrix information
- Bio::NEXUS(3) - An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
- Bio::NEXUS::AssumptionsBlock(3) - Represents ASSUMPTIONS block of a NEXUS file
- Bio::NEXUS::Block(3) - Provides useful functions for blocks in NEXUS file (parent class).
- Bio::NEXUS::CharactersBlock(3) - Represents a CHARACTERS Block (Data or Characters) of a NEXUS file
- Bio::NEXUS::CodonsBlock(3) - Represents CODONS block in NEXUS file
- Bio::NEXUS::DataBlock(3) - Represents the deprecated DATA Block in NEXUS file.
- Bio::NEXUS::DistancesBlock(3) - Represents DISTANCES block in NEXUS file
- Bio::NEXUS::Functions(3) - Provides private utiliy functions for the module
- Bio::NEXUS::HistoryBlock(3) - Represents a HISTORY block of a NEXUS file
- Bio::NEXUS::Matrix(3) - Provides functions for handling blocks that have matrices
- Bio::NEXUS::NHXCmd(3) - Provides functions for manipulating nodes in trees
- Bio::NEXUS::Node(3) - Provides functions for manipulating nodes in trees
- Bio::NEXUS::NotesBlock(3) - Represents a NOTES block in a NEXUS file.
- Bio::NEXUS::SetsBlock(3) - Represents SETS block of a NEXUS file
- Bio::NEXUS::SpanBlock(3) - Represent SPAN block in a NEXUS file (contains meta data).
- Bio::NEXUS::TaxaBlock(3) - Represents TAXA block of a NEXUS file
- Bio::NEXUS::TaxUnit(3) - Represents a taxon unit in a NEXUS file
- Bio::NEXUS::TaxUnitSet(3) - Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file
- Bio::NEXUS::Tools::GraphicsParams(3) - represents a character block (Data or Characters) of a NEXUS file
- Bio::NEXUS::Tools::NexModifier(3) - NEXUS file content modifier ( exclude/select/rename options on OTUs).
- Bio::NEXUS::Tools::NexPlotter(3) - PostScript plot of tree + data table (from NEXUS infile)
- Bio::NEXUS::Tree(3) - Provides functions for manipulating trees
- Bio::NEXUS::TreesBlock(3) - Represents TREES block of a NEXUS file
- Bio::NEXUS::UnalignedBlock(3) - Represents an UNALIGNED block of a NEXUS file
- Bio::NEXUS::UnknownBlock(3) - Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module.
- Bio::NEXUS::Util::Exceptions(3) - Exception classes for Bio::NEXUS.
- Bio::NEXUS::Util::Logger(3) - Logging for Bio::NEXUS.
- Bio::NEXUS::WeightSet(3) - Represents column weights in alignment ( for each character)
- Bio::Ontology::DocumentRegistry(3) - Keep track of where to find ontologies. Allows lookups by name.
- Bio::Ontology::GOterm(3) - representation of GO terms
- Bio::Ontology::InterProTerm(3) - Implementation of InterProI term interface
- Bio::Ontology::OBOEngine(3) - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
- Bio::Ontology::OBOterm(3) - representation of OBO terms
- Bio::Ontology::Ontology(3) - standard implementation of an Ontology
- Bio::Ontology::OntologyEngineI(3) - Interface a minimal Ontology implementation should satisfy
- Bio::Ontology::OntologyI(3) - Interface for an ontology implementation
- Bio::Ontology::OntologyStore(3) - A repository of ontologies
- Bio::Ontology::Path(3) - a path for an ontology term graph
- Bio::Ontology::PathI(3) - Interface for a path between ontology terms
- Bio::Ontology::Relationship(3) - a relationship for an ontology
- Bio::Ontology::RelationshipFactory(3) - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
- Bio::Ontology::RelationshipI(3) - Interface for a relationship between ontology terms
- Bio::Ontology::RelationshipType(3) - a relationship type for an ontology
- Bio::Ontology::SimpleGOEngine::GraphAdaptor(3) - Graph adaptor for Bio::Ontology::SimpleGOEngine
- Bio::Ontology::SimpleOntologyEngine(3) - Implementation of OntologyEngineI interface
- Bio::Ontology::Term(3) - implementation of the interface for ontology terms
- Bio::Ontology::TermFactory(3) - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
- Bio::Ontology::TermI(3) - interface for ontology terms
- Bio::OntologyIO(3) - Parser factory for Ontology formats
- Bio::OntologyIO::dagflat(3) - a base class parser for GO flat-file type formats
- Bio::OntologyIO::goflat(3) - a parser for the Gene Ontology flat-file format
- Bio::OntologyIO::Handlers::BaseSAXHandler(3) - base class for SAX Handlers
- Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3) - parse an InterPro XML file and persist the resulting terms to a Biosql database
- Bio::OntologyIO::Handlers::InterProHandler(3) - XML handler class for InterProParser
- Bio::OntologyIO::InterProParser(3) - Parser for InterPro xml files.
- Bio::OntologyIO::obo(3) - parser for OBO flat-file format
- Bio::OntologyIO::simplehierarchy(3) - a base class parser for simple hierarchy-by-indentation type formats
- Bio::OntologyIO::soflat(3) - a parser for the Sequence Ontology flat-file format
- Bio::ParameterBaseI(3) - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
- Bio::Phylo(3) - Phylogenetic analysis using perl
- Bio::Phylo::EvolutionaryModels(3) - Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007
- Bio::Phylo::Factory(3) - Creator of objects, reduces hardcoded class names in code
- Bio::Phylo::Forest(3) - Container for tree objects
- Bio::Phylo::Forest::DrawNodeRole(3) - Tree node with extra methods for tree drawing
- Bio::Phylo::Forest::DrawTreeRole(3) - Tree with extra methods for tree drawing
- Bio::Phylo::Forest::Node(3) - Node in a phylogenetic tree
- Bio::Phylo::Forest::NodeRole(3) - Extra behaviours for a node in a phylogenetic tree
- Bio::Phylo::Forest::Tree(3) - Phylogenetic tree
- Bio::Phylo::Forest::TreeRole(3) - Extra behaviours for a phylogenetic tree
- Bio::Phylo::Generator(3) - Generator of tree topologies
- Bio::Phylo::Identifiable(3) - Objects with unique identifiers
- Bio::Phylo::IO(3) - Front end for parsers and serializers
- Bio::Phylo::Listable(3) - List of things, super class for many objects
- Bio::Phylo::ListableRole(3) - Extra functionality for things that are lists
- Bio::Phylo::Manual(3) - High-level user guide
- Bio::Phylo::Matrices(3) - Container of matrix objects
- Bio::Phylo::Matrices::Character(3) - A character (column) in a matrix
- Bio::Phylo::Matrices::Characters(3) - Container of character objects
- Bio::Phylo::Matrices::Datatype(3) - Validator of character state data
- Bio::Phylo::Matrices::Datatype::Continuous(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Custom(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Dna(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Illumina(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Mixed(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Protein(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Restriction(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Rna(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Sanger(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Solexa(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datatype::Standard(3) - Validator subclass, no serviceable parts inside
- Bio::Phylo::Matrices::Datum(3) - Character state sequence
- Bio::Phylo::Matrices::DatumRole(3) - Extra behaviours for a character state sequence
- Bio::Phylo::Matrices::Matrix(3) - Character state matrix
- Bio::Phylo::Matrices::MatrixRole(3) - Extra behaviours for a character state matrix
- Bio::Phylo::Matrices::TypeSafeData(3) - Superclass for objects that contain character data
- Bio::Phylo::Mediators::TaxaMediator(3) - Mediator for links between taxa and other objects
- Bio::Phylo::Models::Substitution::Binary(3) - Binary character substitution model
- Bio::Phylo::Models::Substitution::Dna(3) - DNA substitution model
- Bio::Phylo::Models::Substitution::Dna::F81(3) - Felsenstein (1981) model
- Bio::Phylo::Models::Substitution::Dna::GTR(3) - General Time Reversible model
- Bio::Phylo::Models::Substitution::Dna::HKY85(3) - Hasegawa, Kishino, Yano (1985) model
- Bio::Phylo::Models::Substitution::Dna::JC69(3) - Jukes, Cantor (1969)
- Bio::Phylo::Models::Substitution::Dna::K80(3) - Kimura 2-parameter
- Bio::Phylo::NeXML::DOM(3) - XML DOM support for Bio::Phylo
- Bio::Phylo::NeXML::DOM::Document(3) - XML DOM Abstract class for flexible document object model implementation
- Bio::Phylo::NeXML::DOM::Document::Libxml(3) - XML DOM document mappings to the "XML::LibXML" package
- Bio::Phylo::NeXML::DOM::Document::Twig(3) - XML DOM document mappings to the "XML::Twig" package
- Bio::Phylo::NeXML::DOM::Element(3) - XML DOM Abstract class for flexible document object model implementation
- Bio::Phylo::NeXML::DOM::Element::Libxml(3) - XML DOM element mappings to the "XML::LibXML" package
- Bio::Phylo::NeXML::DOM::Element::Twig(3) - XML DOM mappings to the XML::Twig package
- Bio::Phylo::NeXML::Entities(3) - Functions for dealing with XML entities
- Bio::Phylo::NeXML::Meta(3) - Single predicate/object annotation, attached to an xml-writable subject
- Bio::Phylo::NeXML::Meta::XMLLiteral(3) - Annotation value adaptor, no direct usage
- Bio::Phylo::NeXML::Writable(3) - Superclass for objects that serialize to NeXML
- Bio::Phylo::NeXML::XML2JSON(3) - Helps convert NeXML to JSON, no serviceable parts inside
- Bio::Phylo::Parsers::Abstract(3) - Superclass for parsers used by Bio::Phylo::IO
- Bio::Phylo::Parsers::Adjacency(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Cdao(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Dwca(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Fasta(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Fastq(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Figtree(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Json(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Newick(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Nexml(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Nexus(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Nhx(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Phylip(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Phyloxml(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Table(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Taxlist(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Tnrs(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Tolweb(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Ubiocbmeta(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Ubiometa(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Parsers::Ubiosearch(3) - Parser used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::PhyloWS(3) - Base class for phylogenetic web services
- Bio::Phylo::PhyloWS::Client(3) - Base class for phylogenetic web service clients
- Bio::Phylo::PhyloWS::Resource(3) - Represents a PhyloWS web resource
- Bio::Phylo::PhyloWS::Resource::Description(3) - Represents a PhyloWS resource description
- Bio::Phylo::PhyloWS::Service(3) - Base class for phylogenetic web services
- Bio::Phylo::PhyloWS::Service::Timetree(3) - PhyloWS service wrapper for Timetree
- Bio::Phylo::PhyloWS::Service::Tolweb(3) - PhyloWS service wrapper for Tree of Life
- Bio::Phylo::PhyloWS::Service::UbioClassificationBank(3) - PhyloWS service wrapper for uBio ClassificationBank records
- Bio::Phylo::PhyloWS::Service::UbioNameBank(3) - PhyloWS service wrapper for uBio NameBank records
- Bio::Phylo::Project(3) - Container for related data
- Bio::Phylo::Set(3) - Subset of the parts inside a container
- Bio::Phylo::Taxa(3) - Container of taxon objects
- Bio::Phylo::Taxa::TaxaLinker(3) - Superclass for objects that link to taxa objects
- Bio::Phylo::Taxa::Taxon(3) - Operational taxonomic unit
- Bio::Phylo::Taxa::TaxonLinker(3) - Superclass for objects that link to taxon objects
- Bio::Phylo::Treedrawer(3) - Visualizer of tree shapes
- Bio::Phylo::Treedrawer::Abstract(3) - Abstract graphics writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Canvas(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Gif(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Jpeg(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Pdf(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Png(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Processing(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Svg(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Treedrawer::Swf(3) - Graphics format writer used by treedrawer, no serviceable parts inside
- Bio::Phylo::Unparsers::Abstract(3) - Superclass for unparsers used by Bio::Phylo::IO
- Bio::Phylo::Unparsers::Adjacency(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Cdao(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Fasta(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Figtree(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Hennig86(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Html(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Json(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Mrp(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Newick(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Nexml(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Nexus(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Nhx(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Nwmsrdf(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Pagel(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Phylip(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Phyloxml(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Rss1(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Unparsers::Taxlist(3) - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::Phylo::Util::CONSTANT(3) - Global constants and utility functions
- Bio::Phylo::Util::CONSTANT::Int(3) - Integer constants, no serviceable parts inside
- Bio::Phylo::Util::Dependency(3) - Utility class for importing external dependencies. No serviceable parts inside.
- Bio::Phylo::Util::Exceptions(3) - Errors ($@) that are objects
- Bio::Phylo::Util::IDPool(3) - Utility class for generating object IDs. No serviceable parts inside.
- Bio::Phylo::Util::Logger(3) - Logger of internal messages of several severity levels
- Bio::Phylo::Util::Math(3) - Utility math functions
- Bio::Phylo::Util::MOP(3) - Meta-object programming, no serviceable parts inside
- Bio::Phylo::Util::OptionalInterface(3) - Utility class for managing optional superclasses. No serviceable parts inside.
- Bio::Phylo::Util::StackTrace(3) - Stack traces for exceptions
- Bio::PhyloRole(3) - Extra behaviours for the base class
- Bio::PrimarySeq(3) - Bioperl lightweight sequence object
- Bio::PrimarySeqI(3) - Interface definition for a Bio::PrimarySeq
- Bio::PullParserI(3) - A base module for fast 'pull' parsing
- Bio::Range(3) - Pure perl RangeI implementation
- Bio::RangeI(3) - Range interface
- Bio::Root::Exception(3) - BioPerl exceptions
- Bio::Root::HTTPget(3) - module for fallback HTTP get operations when LWP:: is unavailable
- Bio::Root::IO(3) - BioPerl base IO handling class
- Bio::Root::Root(3) - implementation of Bio::Root::RootI interface
- Bio::Root::RootI(3) - base interface for all BioPerl classes
- Bio::Root::Storable(3) - Safely store/retrieve objects from disk
- Bio::Root::Test(3) - common base for all BioPerl test scripts
- Bio::Root::TestObject(3) - An implementation of TestInterface
- Bio::Root::Utilities(3) - general-purpose utilities
- Bio::Root::Version(3) - don't use, get version from each module
- SCF(3) - Perl extension for reading and writting SCF sequence files
- Bio::Search::BlastStatistics(3) - An object for Blast statistics
- Bio::Search::BlastUtils(3) - Utility functions for Bio::Search:: BLAST objects
- Bio::Search::DatabaseI(3) - Interface for a database used in a sequence search
- Bio::Search::GenericDatabase(3) - Generic implementation of Bio::Search::DatabaseI
- Bio::Search::GenericStatistics(3) - An object for statistics
- Bio::Search::Hit::BlastHit(3) - Blast-specific subclass of Bio::Search::Hit::GenericHit
- Bio::Search::Hit::BlastPullHit(3) - A parser and hit object for BLASTN hits
- Bio::Search::Hit::Fasta(3) - Hit object specific for Fasta-generated hits
- Bio::Search::Hit::GenericHit(3) - A generic implementation of the Bio::Search::Hit::HitI interface
- Bio::Search::Hit::HitFactory(3) - A factory to create Bio::Search::Hit::HitI objects
- Bio::Search::Hit::HitI(3) - Interface for a hit in a similarity search result
- Bio::Search::Hit::ModelHit(3) - A model-based implementation of the Bio::Search::Hit::HitI interface
- Bio::Search::Hit::PsiBlastHit(3) - Bioperl BLAST Hit object
- Bio::Search::Hit::PullHitI(3) - Bio::Search::Hit::HitI interface for pull parsers.
- Bio::Search::HSP::BlastHSP(3) - Bioperl BLAST High-Scoring Pair object
- Bio::Search::HSP::BlastPullHSP(3) - A parser and HSP object for BlastN hsps
- Bio::Search::HSP::FastaHSP(3) - HSP object for FASTA specific data
- Bio::Search::HSP::GenericHSP(3) - A "Generic" implementation of a High Scoring Pair
- Bio::Search::HSP::HSPFactory(3) - A factory to create Bio::Search::HSP::HSPI objects
- Bio::Search::HSP::HSPI(3) - Interface for a High Scoring Pair in a similarity search result
- Bio::Search::HSP::ModelHSP(3) - A HSP object for model-based searches
- Bio::Search::HSP::PsiBlastHSP(3) - Bioperl BLAST High-Scoring Pair object
- Bio::Search::HSP::PSLHSP(3) - A HSP for PSL output
- Bio::Search::HSP::PullHSPI(3) - Bio::Search::HSP::HSPI interface for pull parsers.
- Bio::Search::HSP::WABAHSP(3) - HSP object suitable for describing WABA alignments
- Bio::Search::Iteration::GenericIteration(3) - A generic implementation of the Bio::Search::Iteration::IterationI interface.
- Bio::Search::Iteration::IterationI(3) - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
- Bio::Search::Processor(3) - DESCRIPTION of Object
- Bio::Search::Result::BlastPullResult(3) - A parser and result object for BLASTN results
- Bio::Search::Result::BlastResult(3) - Blast-specific subclass of Bio::Search::Result::GenericResult
- Bio::Search::Result::CrossMatchResult(3) - CrossMatch-specific subclass of Bio::Search::Result::GenericResult
- Bio::Search::Result::GenericResult(3) - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
- Bio::Search::Result::INFERNALResult(3) - A Result object for INFERNAL results
- Bio::Search::Result::PullResultI(3) - Bio::Search::Result::ResultI interface for 'pull' parsers
- Bio::Search::Result::ResultFactory(3) - A factory to create Bio::Search::Result::ResultI objects
- Bio::Search::Result::ResultI(3) - Abstract interface to Search Result objects
- Bio::Search::Result::WABAResult(3) - Result object for WABA alignment output
- Bio::Search::SearchUtils(3) - Utility functions for Bio::Search:: objects
- Bio::Search::StatisticsI(3) - A Base object for statistics
- Bio::Search::Tiling::MapTileUtils(3) - utilities for manipulating closed intervals for an HSP tiling algorithm
- Bio::Search::Tiling::MapTiling(3) - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
- Bio::Search::Tiling::TilingI(3) - Abstract interface for an HSP tiling module
- Bio::SearchIO(3) - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
- Bio::SearchIO::axt(3) - a parser for axt format reports
- Bio::SearchIO::blast(3) - Event generator for event based parsing of blast reports
- Bio::SearchIO::blast_pull(3) - A parser for BLAST output
- Bio::SearchIO::blasttable(3) - Driver module for SearchIO for parsing NCBI -m 8/9 format
- Bio::SearchIO::cross_match(3) - CrossMatch-specific subclass of Bio::SearchIO
- Bio::SearchIO::erpin(3) - SearchIO-based ERPIN parser
- Bio::SearchIO::EventHandlerI(3) - An abstract Event Handler for Search Result parsing
- Bio::SearchIO::exonerate(3) - parser for Exonerate
- Bio::SearchIO::fasta(3) - A SearchIO parser for FASTA results
- Bio::SearchIO::FastHitEventBuilder(3) - Event Handler for SearchIO events.
- Bio::SearchIO::gmap_f9(3) - Event generator for parsing gmap reports (Z format)
- Bio::SearchIO::infernal(3) - SearchIO-based Infernal parser
- Bio::SearchIO::IteratedSearchResultEventBuilder(3) - Event Handler for SearchIO events.
- Bio::SearchIO::megablast(3) - a driver module for Bio::SearchIO to parse megablast reports (format 0)
- Bio::SearchIO::psl(3) - A parser for PSL output (UCSC)
- Bio::SearchIO::rnamotif(3) - SearchIO-based RNAMotif parser
- Bio::SearchIO::SearchResultEventBuilder(3) - Event Handler for SearchIO events.
- Bio::SearchIO::SearchWriterI(3) - Interface for outputting parsed Search results
- Bio::SearchIO::sim4(3) - parser for Sim4 alignments
- Bio::SearchIO::waba(3) - SearchIO parser for Jim Kent WABA program alignment output
- Bio::SearchIO::wise(3) - Parsing of wise output as alignments
- Bio::SearchIO::Writer::GbrowseGFF(3) - Interface for outputting parsed search results in Gbrowse GFF format
- Bio::SearchIO::Writer::HitTableWriter(3) - Tab-delimited data for Bio::Search::Hit::HitI objects
- Bio::SearchIO::Writer::HSPTableWriter(3) - Tab-delimited data for Bio::Search::HSP::HSPI objects
- Bio::SearchIO::Writer::HTMLResultWriter(3) - write a Bio::Search::ResultI in HTML
- Bio::SearchIO::Writer::ResultTableWriter(3) - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
- Bio::SearchIO::Writer::TextResultWriter(3) - Object to implement writing a Bio::Search::ResultI in Text.
- Bio::Seq(3) - Sequence object, with features
- Bio::Seq::BaseSeqProcessor(3) - Base implementation for a SequenceProcessor
- Bio::Seq::EncodedSeq(3) - subtype of Bio::LocatableSeq to store DNA that encodes a protein
- Bio::Seq::LargeLocatableSeq(3) - LocatableSeq object that stores sequence as files in the tempdir
- Bio::Seq::LargePrimarySeq(3) - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
- Bio::Seq::LargeSeq(3) - SeqI compliant object that stores sequence as files in /tmp
- Bio::Seq::LargeSeqI(3) - Interface class for sequences that cache their residues in a temporary file
- Bio::Seq::Meta(3) - Generic superclass for sequence objects with residue-based meta information
- Bio::Seq::Meta::Array(3) - array-based generic implementation of a sequence class with residue-based meta information
- Bio::Seq::MetaI(3) - Interface for sequence objects with residue-based meta information
- Bio::Seq::PrimaryQual(3) - Bioperl lightweight Quality Object
- Bio::Seq::PrimedSeq(3) - A sequence and a pair of primers matching on it
- Bio::Seq::QualI(3) - Interface definition for a Bio::Seq::Qual
- Bio::Seq::Quality(3) - Implementation of sequence with residue quality and trace values
- Bio::Seq::RichSeq(3) - Module implementing a sequence created from a rich sequence database entry
- Bio::Seq::RichSeqI(3) - interface for sequences from rich data sources, mostly databases
- Bio::Seq::SeqBuilder(3) - Configurable object builder for sequence stream parsers
- Bio::Seq::SeqFactory(3) - Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory
- Bio::Seq::SeqFastaSpeedFactory(3) - Rapid creation of Bio::Seq objects through a factory
- Bio::Seq::SequenceTrace(3) - Bioperl object packaging a sequence with its trace
- Bio::Seq::SimulatedRead(3) - Read with sequencing errors taken from a reference sequence
- Bio::Seq::TraceI(3) - Interface definition for a Bio::Seq::Trace
- Bio::SeqAnalysisParserI(3) - Sequence analysis output parser interface
- Bio::SeqFeature::Amplicon(3) - Amplicon feature
- Bio::SeqFeature::Annotated(3) - PLEASE PUT SOMETHING HERE
- Bio::SeqFeature::AnnotationAdaptor(3) - integrates SeqFeatureIs annotation
- Bio::SeqFeature::Collection(3) - A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.
- Bio::SeqFeature::CollectionI(3) - An interface for a collection of SeqFeatureI objects.
- Bio::SeqFeature::Computation(3) - Computation SeqFeature
- Bio::SeqFeature::FeaturePair(3) - hold pair feature information e.g. blast hits
- Bio::SeqFeature::Gene::Exon(3) - a feature representing an exon
- Bio::SeqFeature::Gene::ExonI(3) - Interface for a feature representing an exon
- Bio::SeqFeature::Gene::GeneStructure(3) - A feature representing an arbitrarily complex structure of a gene
- Bio::SeqFeature::Gene::GeneStructureI(3) - A feature representing an arbitrarily complex structure of a gene
- Bio::SeqFeature::Gene::Intron(3) - An intron feature
- Bio::SeqFeature::Gene::NC_Feature(3) - superclass for non-coding features
- Bio::SeqFeature::Gene::Poly_A_site(3) - poly A feature
- Bio::SeqFeature::Gene::Promoter(3) - Describes a promoter
- Bio::SeqFeature::Gene::Transcript(3) - A feature representing a transcript
- Bio::SeqFeature::Gene::TranscriptI(3) - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
- Bio::SeqFeature::Gene::UTR(3) - A feature representing an untranslated region that is part of a transcriptional unit
- Bio::SeqFeature::Generic(3) - Generic SeqFeature
- Bio::SeqFeature::Lite(3) - Lightweight Bio::SeqFeatureI class
- Bio::SeqFeature::PositionProxy(3) - handle features when truncation/revcom sequences span a feature
- Bio::SeqFeature::Primer(3) - Primer Generic SeqFeature
- Bio::SeqFeature::Similarity(3) - A sequence feature based on similarity
- Bio::SeqFeature::SimilarityPair(3) - Sequence feature based on the similarity of two sequences.
- Bio::SeqFeature::SubSeq(3) - Feature representing a subsequence
- Bio::SeqFeature::Tools::FeatureNamer(3) - generates unique persistent names for features
- Bio::SeqFeature::Tools::IDHandler(3) - maps $seq_feature->primary_tag
- Bio::SeqFeature::Tools::TypeMapper(3) - maps $seq_feature->primary_tag
- Bio::SeqFeature::Tools::Unflattener(3) - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
- Bio::SeqFeature::TypedSeqFeatureI(3) - a strongly typed SeqFeature
- Bio::SeqFeatureI(3) - Abstract interface of a Sequence Feature
- Bio::SeqI(3) - [Developers] Abstract Interface of Sequence (with features)
- Bio::SeqIO(3) - Handler for SeqIO Formats
- Bio::SeqIO::ace(3) - ace sequence input/output stream
- Bio::SeqIO::asciitree(3) - asciitree sequence input/output stream
- Bio::SeqIO::bsml(3) - BSML sequence input/output stream
- Bio::SeqIO::bsml_sax(3) - BSML sequence input/output stream using SAX
- Bio::SeqIO::embl(3) - EMBL sequence input/output stream
- Bio::SeqIO::embldriver(3) - EMBL sequence input/output stream
- Bio::SeqIO::entrezgene(3) - Entrez Gene ASN1 parser
- Bio::SeqIO::fasta(3) - fasta sequence input/output stream
- Bio::SeqIO::fastq(3) - fastq sequence input/output stream
- Bio::SeqIO::FTHelper(3) - Helper class for EMBL/Genbank feature tables
- Bio::SeqIO::game(3) - a class for parsing and writing game-XML
- Bio::SeqIO::game::featHandler(3) - a class for handling feature elements
- Bio::SeqIO::game::gameHandler(3) - PerlSAX handler for game-XML
- Bio::SeqIO::game::gameSubs(3) - a base class for game-XML parsing
- Bio::SeqIO::game::gameWriter(3) - a class for writing game-XML
- Bio::SeqIO::game::seqHandler(3) - a class for handling game-XML sequences
- Bio::SeqIO::gbdriver(3) - GenBank handler-based push parser
- Bio::SeqIO::gbxml(3) - GenBank sequence input/output stream using SAX
- Bio::SeqIO::gcg(3) - GCG sequence input/output stream
- Bio::SeqIO::genbank(3) - GenBank sequence input/output stream
- Bio::SeqIO::Handler::GenericRichSeqHandler(3) - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
- Bio::SeqIO::kegg(3) - KEGG sequence input/output stream
- Bio::SeqIO::largefasta(3) - method i/o on very large fasta sequence files
- Bio::SeqIO::locuslink(3) - LocusLink input/output stream
- Bio::SeqIO::mbsout(3) - input stream for output by Teshima et al.'s mbs.
- Bio::SeqIO::metafasta(3) - metafasta sequence input/output stream
- Bio::SeqIO::msout(3) - input stream for output by Hudson's ms
- Bio::SeqIO::MultiFile(3) - Treating a set of files as a single input stream
- Bio::SeqIO::phd(3) - phd file input/output stream
- Bio::SeqIO::pir(3) - PIR sequence input/output stream
- Bio::SeqIO::qual(3) - .qual file input/output stream
- Bio::SeqIO::raw(3) - raw sequence file input/output stream
- Bio::SeqIO::scf(3) - .scf file input/output stream
- Bio::SeqIO::seqxml(3) - SeqXML sequence input/output stream
- Bio::SeqIO::swiss(3) - Swissprot sequence input/output stream
- Bio::SeqIO::swissdriver(3) - SwissProt/UniProt handler-based push parser
- Bio::SeqIO::tab(3) - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
- Bio::SeqIO::table(3) - sequence input/output stream from a delimited table
- Bio::SeqIO::tigr(3) - TIGR XML sequence input/output stream
- Bio::SeqIO::tigrxml(3) - Parse TIGR (new) XML
- Bio::SeqIO::tinyseq(3) - reading/writing sequences in NCBI TinySeq format
- Bio::SeqIO::tinyseq::tinyseqHandler(3) - XML event handlers to support NCBI TinySeq XML parsing
- Bio::SeqUtils(3) - Additional methods for PrimarySeq objects
- Bio::SimpleAlign(3) - Multiple alignments held as a set of sequences
- Bio::SimpleAnalysisI(3) - A simple interface to any (local or remote) analysis tool
- Bio::Species(3) - Generic species object.
- Bio::Taxon(3) - A node in a represented taxonomy
- Bio::Tools::Alignment::Consed(3) - A module to work with objects from consed .ace files
- Bio::Tools::Alignment::Trim(3) - A kludge to do specialized trimming of sequence based on quality.
- Bio::Tools::AmpliconSearch(3) - Find amplicons in a template using degenerate PCR primers
- Bio::Tools::Analysis::SimpleAnalysisBase(3) - abstract superclass for SimpleAnalysis implementations
- Bio::Tools::AnalysisResult(3) - Base class for analysis result objects and parsers
- Bio::Tools::Blat(3) - parser for Blat program
- Bio::Tools::CodonTable(3) - Codon table object
- Bio::Tools::Coil(3) - parser for Coil output
- Bio::Tools::ECnumber(3) - representation of EC numbers (Enzyme Classification)
- Bio::Tools::EMBOSS::Palindrome(3) - parse EMBOSS palindrome output
- Bio::Tools::EPCR(3) - Parse ePCR output and make features
- Bio::Tools::Eponine(3) - Results of one Eponine run
- Bio::Tools::Est2Genome(3) - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
- Bio::Tools::ESTScan(3) - Results of one ESTScan run
- Bio::Tools::Fgenesh(3) - parse results of one Fgenesh run
- Bio::Tools::FootPrinter(3) - write sequence features in FootPrinter format
- Bio::Tools::Geneid(3) - Results of one geneid run
- Bio::Tools::Genemark(3) - Results of one Genemark run
- Bio::Tools::Genewise(3) - Results of one Genewise run
- Bio::Tools::Genomewise(3) - Results of one Genomewise run
- Bio::Tools::Genscan(3) - Results of one Genscan run
- Bio::Tools::GFF(3) - A Bio::SeqAnalysisParserI compliant GFF format parser
- Bio::Tools::Glimmer(3) - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
- Bio::Tools::Grail(3) - Results of one Grail run
- Bio::Tools::GuessSeqFormat(3) - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
- Bio::Tools::ipcress(3) - Parse ipcress output and make features
- Bio::Tools::isPcr(3) - Parse isPcr output and make features
- Bio::Tools::IUPAC(3) - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
- Bio::Tools::Lucy(3) - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
- Bio::Tools::Match(3) - Parses output from Transfac's match(TM)
- Bio::Tools::MZEF(3) - Results of one MZEF run
- Bio::Tools::OddCodes(3) - Object holding alternative alphabet coding for one protein sequence
- Bio::Tools::Phylo::Gerp(3) - Parses output from GERP
- Bio::Tools::Phylo::Molphy(3) - parser for Molphy output
- Bio::Tools::Phylo::Molphy::Result(3) - container for data parsed from a ProtML run
- Bio::Tools::Phylo::Phylip::ProtDist(3) - parser for ProtDist output
- Bio::Tools::pICalculator(3) - calculate the isoelectric point of a protein
- Bio::Tools::Prediction::Exon(3) - A predicted exon feature
- Bio::Tools::Prediction::Gene(3) - a predicted gene structure feature
- Bio::Tools::Primer3(3) - Create input for and work with the output from the program primer3
- Bio::Tools::Primer::Assessor::Base(3) - base class for common assessor things
- Bio::Tools::Primer::AssessorI(3) - interface for assessing primer pairs
- Bio::Tools::Primer::Feature(3) - position of a single primer
- Bio::Tools::Primer::Pair(3) - two primers on left and right side
- Bio::Tools::Prints(3) - Parser for FingerPRINTScanII program
- Bio::Tools::Profile(3) - parse Profile output
- Bio::Tools::Promoterwise(3) - parser for Promoterwise tab format output
- Bio::Tools::PrositeScan(3) - Parser for ps_scan result
- Bio::Tools::Pseudowise(3) - Results of one Pseudowise run
- Bio::Tools::QRNA(3) - A Parser for qrna output
- Bio::Tools::RandomDistFunctions(3) - A set of routines useful for generating random data in different distributions
- Bio::Tools::RepeatMasker(3) - a parser for RepeatMasker output
- Bio::Tools::Run::Alignment::Amap(3) - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program
- Bio::Tools::Run::Alignment::Blat(3) - Wrapper module for Blat program. This newer version allows for all parameters to be set by passing them as an option to new().
- Bio::Tools::Run::Alignment::DBA(3) - Object for the alignment of two sequences using the DNA Block Aligner program.
- Bio::Tools::Run::Alignment::Exonerate(3) - Wrapper for Exonerate alignment program. You can get exonerate at http://www.ebi.ac.uk/~guy/exonerate/. This wrapper is written without parameter checking. All parameters are passed via the arugment...
- Bio::Tools::Run::Alignment::Gmap(3) - Wrapper for running gmap.
- Bio::Tools::Run::Alignment::Kalign(3) - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program
- Bio::Tools::Run::Alignment::Lagan(3) - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
- Bio::Tools::Run::Alignment::MAFFT(3) - run the MAFFT alignment tools
- Bio::Tools::Run::Alignment::MSAProbs(3) - Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program
- Bio::Tools::Run::Alignment::Muscle(3) - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
- Bio::Tools::Run::Alignment::Pal2Nal(3) - Wrapper for Pal2Nal
- Bio::Tools::Run::Alignment::Probalign(3) - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program
- Bio::Tools::Run::Alignment::Probcons(3) - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program
- Bio::Tools::Run::Alignment::Proda(3) - Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program.
- Bio::Tools::Run::Alignment::Sim4(3) - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
- Bio::Tools::Run::Alignment::StandAloneFasta(3) - Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)
- Bio::Tools::Run::Analysis(3) - Module representing any (remote or local) analysis tool
- Bio::Tools::Run::Analysis::soap(3) - A SOAP-based access to the analysis tools
- Bio::Tools::Run::AnalysisFactory(3) - A directory of analysis tools
- Bio::Tools::Run::AnalysisFactory::soap(3) - A SOAP-based access to the list of analysis tools
- Bio::Tools::Run::BEDTools(3) - Run wrapper for the BEDTools suite of programs *BETA*
- Bio::Tools::Run::BEDTools::Config(3) - Configuration data for bowtie commands
- Bio::Tools::Run::BlastPlus(3) - A wrapper for NCBI's blast+ suite
- Bio::Tools::Run::Coil(3) - wrapper for ncoils program
- Bio::Tools::Run::EMBOSSacd(3) - class for EMBOSS Application qualifiers
- Bio::Tools::Run::EMBOSSApplication(3) - class for EMBOSS Applications
- Bio::Tools::Run::Ensembl(3) - A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API.
- Bio::Tools::Run::Eponine(3) - Object for execution of the Eponine which is a mammalian TSS predictor
- Bio::Tools::Run::ERPIN(3) - Wrapper for local execution of the ERPIN suite of programs.
- Bio::Tools::Run::FootPrinter(3) - wrapper for the FootPrinter program
- Bio::Tools::Run::Genemark(3) - Wrapper for local execution of the GeneMark family of programs.
- Bio::Tools::Run::GenericParameters(3) - An object for the parameters used to run programs
- Bio::Tools::Run::Genewise(3) - Object for predicting genes in a given sequence given a protein
- Bio::Tools::Run::Genscan(3) - Object for identifying genes in a given sequence given a matrix(for appropriate organisms).
- Bio::Tools::Run::Glimmer(3) - Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.
- Bio::Tools::Run::Hmmer(3) - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
- Bio::Tools::Run::Infernal(3) - Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore
- Bio::Tools::Run::Match(3) - Wrapper for Transfac's match(TM)
- Bio::Tools::Run::MCS(3) - Wrapper for MCS
- Bio::Tools::Run::Mdust(3) - Perl extension for Mdust nucleotide filtering
- Bio::Tools::Run::ParametersI(3) - A Base object for the parameters used to run programs
- Bio::Tools::Run::Phylo::FastTree(3) - Get a Bio::Tree object given a protein or DNA alignment.
- Bio::Tools::Run::Phylo::Gerp(3) - Wrapper for GERP
- Bio::Tools::Run::Phylo::Hyphy::Base(3) - Hyphy wrapping base methods
- Bio::Tools::Run::Phylo::Hyphy::BatchFile(3) - Wrapper for custom execution of Hyphy batch files
- Bio::Tools::Run::Phylo::Hyphy::FEL(3) - Wrapper around the Hyphy FEL analysis
- Bio::Tools::Run::Phylo::Hyphy::Modeltest(3) - Wrapper around the Hyphy Modeltest analysis
- Bio::Tools::Run::Phylo::Hyphy::REL(3) - Wrapper around the Hyphy REL analysis
- Bio::Tools::Run::Phylo::Hyphy::SLAC(3) - Wrapper around the Hyphy SLAC analysis
- Bio::Tools::Run::Phylo::LVB(3) - Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1.
- Bio::Tools::Run::Phylo::Molphy::ProtML(3) - A wrapper for the Molphy pkg app ProtML
- Bio::Tools::Run::Phylo::Njtree::Best(3) - Wrapper around the Njtree (Njtree/phyml) best program.
- Bio::Tools::Run::Phylo::Phast::PhastCons(3) - Wrapper for footprinting using phastCons
- Bio::Tools::Run::Phylo::Phast::PhyloFit(3) - Wrapper for phyloFit
- Bio::Tools::Run::Phylo::Phylip::Base(3) - Base object for Phylip modules
- Bio::Tools::Run::Phylo::Phylip::Consense(3) - Wrapper for the phylip program Consense
- Bio::Tools::Run::Phylo::Phylip::DrawGram(3) - use Phylip DrawTree program to draw phylograms or phenograms
- Bio::Tools::Run::Phylo::Phylip::DrawTree(3) - use Phylip DrawTree program to draw trees
- Bio::Tools::Run::Phylo::Phylip::Neighbor(3) - Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate.
- Bio::Tools::Run::Phylo::Phylip::PhylipConf(3) - A configuration for managing menu configuration differences between version 3.5 and 3.6
- Bio::Tools::Run::Phylo::Phylip::ProtDist(3) - Wrapper for the phylip program protdist
- Bio::Tools::Run::Phylo::Phylip::ProtPars(3) - Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
- Bio::Tools::Run::Phylo::Phylip::SeqBoot(3) - Wrapper for the phylip program SeqBoot
- Bio::Tools::Run::Phylo::PhyloBase(3) - Bio::Tools::Run::Phylo::PhyloBase- base module for phylo wrappers
- Bio::Tools::Run::Phylo::Phyml(3) - Wrapper for rapid reconstruction of phylogenies using Phyml
- Bio::Tools::Run::Phylo::QuickTree(3) - Wrapper for rapid reconstruction of phylogenies using QuickTree
- Bio::Tools::Run::Phylo::Raxml(3) - Get a Bio::Tree object using raxml given a protein or DNA alignment.
- Bio::Tools::Run::Phylo::Semphy(3) - Wrapper for Semphy
- Bio::Tools::Run::Phylo::SLR(3) - Wrapper around the SLR program
- Bio::Tools::Run::Primate(3) - Wrapper for Primate, Guy Slater's near exact match finder for short sequence tags.
- Bio::Tools::Run::Primer3(3) - Create input for and work with the output from the program primer3
- Bio::Tools::Run::Prints(3) - Bio::Tools::Run::Prints
- Bio::Tools::Run::Profile(3) - Bio::Tools::Run::Profile
- Bio::Tools::Run::Promoterwise(3) - Wrapper for aligning two sequences using promoterwise
- Bio::Tools::Run::Pseudowise(3) - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence
- Bio::Tools::Run::RepeatMasker(3) - Wrapper for RepeatMasker Program
- Bio::Tools::Run::RNAMotif(3) - Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune
- Bio::Tools::Run::Samtools(3) - a run wrapper for the samtools suite *BETA*
- Bio::Tools::Run::Samtools::Config(3) - configurator for Bio::Tools::Run::Samtools
- Bio::Tools::Run::Seg(3) - Object for identifying low complexity regions in a given protein seequence.
- Bio::Tools::Run::Signalp(3) - Bio::Tools::Run::Signalp
- Bio::Tools::Run::Simprot(3) - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
- Bio::Tools::Run::StandAloneBlast(3) - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
- Bio::Tools::Run::StandAloneBlastPlus(3) - Compute with NCBI's blast+ suite *ALPHA*
- Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3) - Provides BLAST methods to StandAloneBlastPlus
- Bio::Tools::Run::StandAloneNCBIBlast(3) - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
- Bio::Tools::Run::StandAloneWUBlast(3) - Object for the local execution of WU-Blast.
- Bio::Tools::Run::Tmhmm(3) - Object for identifying transmembrane helixes in a given protein seequence.
- Bio::Tools::Run::TribeMCL(3) - TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. This clustering is achieved by analysing similarity patterns between proteins in a given...
- Bio::Tools::Run::tRNAscanSE(3) - Wrapper for local execution of tRNAscan-SE
- Bio::Tools::Run::Vista(3) - Pls see Vista documentation for plotfile options
- Bio::Tools::Run::WrapperBase(3) - A Base object for wrappers around executables
- Bio::Tools::Run::WrapperBase::CommandExts(3) - Extensions to WrapperBase for handling programs with commands *ALPHA*
- Bio::Tools::Seg(3) - parse "seg" output
- Bio::Tools::SeqPattern(3) - represent a sequence pattern or motif
- Bio::Tools::SeqPattern::Backtranslate(3) - reverse translate protein patterns
- Bio::Tools::SeqStats(3) - Object holding statistics for one particular sequence
- Bio::Tools::SeqWords(3) - Object holding n-mer statistics for a sequence
- Bio::Tools::Sigcleave(3) - Bioperl object for sigcleave analysis
- Bio::Tools::Signalp(3) - parser for Signalp output
- Bio::Tools::Signalp::ExtendedSignalp(3) - enhanced parser for Signalp output
- Bio::Tools::Sim4::Exon(3) - A single exon determined by an alignment
- Bio::Tools::Sim4::Results(3) - Results of one Sim4 run
- Bio::Tools::Spidey::Exon(3) - A single exon determined by an alignment
- Bio::Tools::Spidey::Results(3) - Results of a Spidey run
- Bio::Tools::TandemRepeatsFinder(3) - a parser for Tandem Repeats Finder output
- Bio::Tools::TargetP(3) - Results of one TargetP run
- Bio::Tools::Tmhmm(3) - parse TMHMM output (TransMembrane HMM)
- Bio::Tools::tRNAscanSE(3) - A parser for tRNAscan-SE output
- Bio::Tree::AnnotatableNode(3) - A Tree Node with support for annotation
- Bio::Tree::Compatible(3) - Testing compatibility of phylogenetic trees with nested taxa.
- Bio::Tree::DistanceFactory(3) - Construct a tree using distance based methods
- Bio::Tree::Node(3) - A Simple Tree Node
- Bio::Tree::NodeI(3) - Interface describing a Tree Node
- Bio::Tree::NodeNHX(3) - A Simple Tree Node with support for NHX tags
- Bio::Tree::RandomFactory(3) - TreeFactory for generating Random Trees
- Bio::Tree::Statistics(3) - Calculate certain statistics for a Tree
- Bio::Tree::Tree(3) - An implementation of the TreeI interface.
- Bio::Tree::TreeFunctionsI(3) - Decorated Interface implementing basic Tree exploration methods
- Bio::Tree::TreeI(3) - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
- Bio::TreeIO(3) - Parser for Tree files
- Bio::TreeIO::cluster(3) - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
- Bio::TreeIO::lintree(3) - Parser for lintree output trees
- Bio::TreeIO::newick(3) - parsing and writing of Newick/PHYLIP/New Hampshire format
- Bio::TreeIO::NewickParser(3) - newick string parser
- Bio::TreeIO::nexus(3) - A TreeIO driver module for parsing Nexus tree output from PAUP
- Bio::TreeIO::nhx(3) - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
- Bio::TreeIO::pag(3) - Bio::TreeIO driver for Pagel format
- Bio::TreeIO::phyloxml(3) - TreeIO implementation for parsing PhyloXML format.
- Bio::TreeIO::tabtree(3) - A simple output format which displays a tree as an ASCII drawing
- Bio::TreeIO::TreeEventBuilder(3) - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
- Bio::UpdateableSeqI(3) - Descendant of Bio::SeqI that allows updates
- Bio::Variation(3) - These classes are part of "Computational Mutation Expression Toolkit" project at European Bioinformatics Institute <http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to...
- Bio::Variation::AAChange(3) - Sequence change class for polypeptides
- Bio::Variation::AAReverseMutate(3) - point mutation and codon information from single amino acid changes
- Bio::Variation::Allele(3) - Sequence object with allele-specific attributes
- Bio::Variation::DNAMutation(3) - DNA level mutation class
- Bio::Variation::IO(3) - Handler for sequence variation IO Formats
- Bio::Variation::IO::flat(3) - flat file sequence variation input/output stream
- Bio::Variation::IO::xml(3) - XML sequence variation input/output stream
- Bio::Variation::RNAChange(3) - Sequence change class for RNA level
- Bio::Variation::SeqDiff(3) - Container class for mutation/variant descriptions
- Bio::Variation::SNP(3) - submitted SNP
- Bio::Variation::VariantI(3) - Sequence Change SeqFeature abstract class
- Bio::WebAgent(3) - A base class for Web (any protocol) access
- BIO_ACCEPT(3) - wrappers for socket operations
- BIO_ADDR(3ossl) - BIO_ADDR routines
- BIO_ADDRINFO(3ossl) - BIO_ADDRINFO type and routines
- BIO_CONNECT(3ossl) - BIO socket communication setup routines
- BIO_ctrl(3) - BIO control operations
- BIO_CTRL(3ossl) - BIO control operations
- BIO_S_DATAGRAM(3) - datagram socket BIO
- BIO_DUMP(3) - hexadecimal printout of arbitrary byte arrays
- BIO_DUP_CHAIN(3) - copy a BIO chain
- BIO_f_base64(3) - base64 BIO filter
- BIO_F_BASE64(3ossl) - base64 BIO filter
- BIO_f_buffer(3) - buffering BIO
- BIO_F_BUFFER(3ossl) - buffering BIO
- BIO_f_cipher(3) - cipher BIO filter
- BIO_F_CIPHER(3ossl) - cipher BIO filter
- BIO_f_md(3) - message digest BIO filter
- BIO_F_MD(3ossl) - message digest BIO filter
- BIO_f_null(3) - null filter
- BIO_F_NULL(3ossl) - null filter
- BIO_F_PREFIX(3ossl) - prefix BIO filter
- BIO_F_READBUFFER(3ossl) - read only buffering BIO that supports BIO_tell() and BIO_seek()
- BIO_f_ssl(3) - SSL BIO
- BIO_F_SSL(3ossl) - SSL BIO
- BIO_S_FD(3) - file descriptor BIO
- BIO_find_type(3) - BIO chain traversal
- BIO_FIND_TYPE(3ossl) - BIO chain traversal
- BIO_S_CONNECT(3) - connect BIO
- BIO_GET_DATA(3ossl) - functions for managing BIO state information
- BIO_GET_EX_NEW_INDEX(3ossl) - application-specific data
- BIO_GET_EX_NEW_INDEX(3) - application-specific data
- BIO_GET_DATA(3) - manage BIO state information
- BIO_GET_RPOLL_DESCRIPTOR(3ossl) - obtain a structure which can be used to determine when a BIO object can next be read or written
- BIO_READ(3) - BIO I/O functions
- BIO_CTRL(3) - BIO control operations
- BIO_METH_NEW(3ossl) - Routines to build up BIO methods
- BIO_FIND_TYPE(3) - BIO chain traversal
- BIO_new(3) - BIO allocation and freeing functions
- BIO_NEW(3ossl) - BIO allocation and freeing functions
- BIO_new_CMS(3) - CMS streaming filter BIO
- BIO_NEW_CMS(3ossl) - CMS streaming filter BIO
- BIO_PARSE_HOSTSERV(3ossl) - utility routines to parse a standard host and service string
- BIO_PRINTF(3ossl) - formatted output to a BIO
- BIO_push(3) - add and remove BIOs from a chain.
- BIO_PUSH(3ossl) - add and remove BIOs from a chain
- BIO_read(3) - BIO I/O functions
- BIO_READ(3ossl) - BIO I/O functions
- BIO_s_accept(3) - accept BIO
- BIO_S_ACCEPT(3ossl) - accept BIO
- BIO_s_bio(3) - BIO pair BIO
- BIO_S_BIO(3ossl) - BIO pair BIO
- BIO_s_connect(3) - connect BIO
- BIO_S_CONNECT(3ossl) - connect BIO
- BIO_S_CORE(3ossl) - OSSL_CORE_BIO functions
- BIO_S_DATAGRAM(3ossl) - Network BIO with datagram semantics
- BIO_S_DGRAM_PAIR(3ossl) - datagram pair BIO
- BIO_s_fd(3) - file descriptor BIO
- BIO_S_FD(3ossl) - file descriptor BIO
- BIO_s_file(3) - FILE bio
- BIO_S_FILE(3ossl) - FILE bio
- BIO_s_mem(3) - memory BIO
- BIO_S_MEM(3ossl) - memory BIO
- BIO_s_null(3) - null data sink
- BIO_S_NULL(3ossl) - null data sink
- BIO_s_socket(3) - socket BIO
- BIO_S_SOCKET(3ossl) - socket BIO
- BIO_SENDMMSG(3ossl) - send and receive multiple datagrams in a single call
- BIO_NEW(3) - construct and destruct I/O abstraction objects
- BIO_set_callback(3) - BIO callback functions
- BIO_SET_CALLBACK(3ossl) - BIO callback functions
- BIO_SET_FLAGS(3ossl) - manipulate and interpret BIO flags
- BIO_F_MD(3) - message digest BIO filter
- BIO_should_retry(3) - BIO retry functions
- BIO_SHOULD_RETRY(3ossl) - BIO retry functions
- BIO_SOCKET_WAIT(3ossl) - BIO connection utility functions
- RSS Other Screensaver(1) - rotating stack of quads.
- BIOLIBC(3) - Library of high-performance low-level functions for bioinformatics programming
- BioPerl(3) - Perl modules for biology
- BIORYTHM(6) - simple biorythm calculation program
- BIOS(9) - interact with PC BIOS
- BIOSDECODE(8) - BIOS information decoder
- BIOSFONT(4) - retrieve font bitmaps from BIOS memory
- BIOSIG2GDF(1) - converts different biomedical signal file formats into a simplified version of GDF, and can stream the result to stdout. This is useful for reading the data by an unnamed pipe into different...
- BIOSIG_FHIR(1) - provides fhir binary template for biosignal data
- BIP(1) - BIP IRC Proxy
- BIP.CONF(5) - Configuration file for BIP IRC Proxy
- BIPMKPW(1) - Password hasher for BIP
- BIRDFONT(1) - font editor
- BIRDFONT-AUTOTRACE(1) - Convert raster image to vector graphics
- BIRDFONT-EXPORT(1) - generate TTF, EOT and SVG files from BIRDFONT files
- BIRDFONT-IMPORT(1) - Create a font from SVG files
- birthday(1) - warn about upcoming birthdays and other events
- BISON(1) - GNU Project parser generator (yacc replacement)
- ShiftReg(3) - Bit Shift Registers with Rotate / Shift Operations
- Vector(3) - Efficient bit vector, set of integers and "big int" math library
- Bit::Vector::Minimal(3) - Object-oriented wrapper around vec()
- Bit::Vector::Overload(3) - Overloaded operators add-on for Bit::Vector
- Bit::Vector::String(3) - Generic string import/export for Bit::Vector
- BitchX(1) - The Ultimate IRC Client
- BITCOIN(1) - manual page for bitcoin v30.2.0
- BITCOIN-CLI(1) - manual page for bitcoin-cli v30.2.0
- BITCOIN-QT(1) - manual page for bitcoin-qt v30.2.0
- BITCOIN-TX(1) - manual page for bitcoin-tx v30.2.0
- BITCOIN-UTIL(1) - manual page for bitcoin-util v30.2.0
- BITCOIN-WALLET(1) - manual page for bitcoin-wallet v30.2.0
- BITCOIND(1) - manual page for bitcoind v30.2.0
- bitesize.d(1m) - analyse disk I/O size by process. Uses DTrace.
- bitlbee(8) - IRC gateway to IM chat networks
- BITLBEE.CONF(5) - configuration file for bitlbee(8)
- BITLY_URL(1) - Command-line interface to WWW::Shorten::Bitly
- BITMAP(3) - Stores the contents of a bitmap. Allegro game programming library.
- BITMAP(1) - bitmap editor and converter utilities for the X Window System
- bitmap(n) - Images that display two colors
- bitmap2pp(1) - Bitmap to PDF/PS converter
- bitmap_color_depth(3) - Returns the color depth of the specified bitmap. Allegro game programming library.
- bitmap_mask_color(3) - Returns the mask color of the specified bitmap. Allegro game programming library.
- BITS(1) - convert bit masks from/to various formats
- bitset(3m) - functions for manipulating memory as sets of bits
- BITSET(9) - bitset manipulation macros
- BITSTRING(3) - bit-string manipulation functions and macros
- BITTWIST(1) - pcap based ethernet packet generator
- BITTWISTE(1) - pcap capture file editor
- BITWISE(1) - Terminal based bit manipulator in ncurses
- bk alias(5.4.3) - manage aliases for lists of components
- BKPUPSD(8) - Simple UPS daemon for APC BK-Pro series
- BKT(1) - Subprocess caching utility
- bl_align_map_seq_exact(3) - Locate little sequence in big sequence
- bl_align_map_seq_sub(3) - Locate little sequence in big sequence
- BL_ALIGN_MAX_MISMATCH_PERCENT(3) - Accessor macro for max_mismatch_percent. Use this macro to reference max_mismatch_percent in a bl_align_t structure from functions that are not members of the class. This allows separation of...
- BL_ALIGN_MIN_MATCH(3) - Accessor macro for min_match. Use this macro to reference min_match in a bl_align_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_align_set_max_mismatch_percent(3) - Mutator for max_mismatch_percent member in a bl_align_t structure. Use this function to set max_mismatch_percent in a bl_align_t object from non-member functions. This function performs a direct...
- bl_align_set_min_match(3) - Mutator for min_match member in a bl_align_t structure. Use this function to set min_match in a bl_align_t object from non-member functions. This function performs a direct assignment for scalar or...
- BL_BED_BLOCK_COUNT(3) - Accessor macro for block_count. Use this macro to reference block_count in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_BED_BLOCK_SIZES(3) - Accessor macro for block_sizes. Use this macro to reference block_sizes in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_BED_BLOCK_SIZES_AE(3) - Accessor macro for block_sizes array elements. Use this macro to reference an element of block_sizes in a bl_bed_t structure from functions that are not members of the class. This allows separation...
- BL_BED_BLOCK_STARTS(3) - Accessor macro for block_starts. Use this macro to reference block_starts in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_BED_BLOCK_STARTS_AE(3) - Accessor macro for block_starts array elements. Use this macro to reference an element of block_starts in a bl_bed_t structure from functions that are not members of the class. This allows separation...
- bl_bed_check_order(3) - Compare positions of two bed records
- BL_BED_CHROM(3) - Accessor macro for chrom. Use this macro to reference chrom in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_BED_CHROM_AE(3) - Accessor macro for chrom array elements. Use this macro to reference an element of chrom in a bl_bed_t structure from functions that are not members of the class. This allows separation of...
- BL_BED_CHROM_END(3) - Accessor macro for chrom_end. Use this macro to reference chrom_end in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_BED_CHROM_START(3) - Accessor macro for chrom_start. Use this macro to reference chrom_start in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_BED_FIELDS(3) - Accessor macro for fields. Use this macro to reference fields in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- bl_bed_gff3_cmp(3) - Compare positions of BED and GFF3 objects
- bl_bed_gff_cmp(3) - Compare the position of a BED feature to that of a GFF feature. Return 0 if the features overlap, < 0 if the BED feature is upstream of the GFF feature, > 0 if the BED feature is downstream of...
- BL_BED_ITEM_RGB(3) - Accessor macro for item_rgb. Use this macro to reference item_rgb in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_BED_ITEM_RGB_AE(3) - Accessor macro for item_rgb array elements. Use this macro to reference an element of item_rgb in a bl_bed_t structure from functions that are not members of the class. This allows separation of...
- BL_BED_NAME(3) - Accessor macro for name. Use this macro to reference name in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_BED_NAME_AE(3) - Accessor macro for name array elements. Use this macro to reference an element of name in a bl_bed_t structure from functions that are not members of the class. This allows separation of...
- bl_bed_read(3) - Read a BED record
- BL_BED_SCORE(3) - Accessor macro for score. Use this macro to reference score in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- bl_bed_set_block_count(3) - Mutator for block_count member in a bl_bed_t structure. Use this function to set block_count in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_block_sizes(3) - Mutator for block_sizes member in a bl_bed_t structure. Use this function to set block_sizes in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_block_sizes_ae(3) - Mutator for an array element of block_sizes member in a bl_bed_t structure. Use this function to set bl_bed_ptr->block_sizes[c] in a bl_bed_t object from non-member functions.
- bl_bed_set_block_sizes_cpy(3) - Mutator for block_sizes member in a bl_bed_t structure. Use this function to set block_sizes in a bl_bed_t object from non-member functions. This function copies the array pointed to by...
- bl_bed_set_block_starts(3) - Mutator for block_starts member in a bl_bed_t structure. Use this function to set block_starts in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_block_starts_ae(3) - Mutator for an array element of block_starts member in a bl_bed_t structure. Use this function to set bl_bed_ptr->block_starts[c] in a bl_bed_t object from non-member functions.
- bl_bed_set_block_starts_cpy(3) - Mutator for block_starts member in a bl_bed_t structure. Use this function to set block_starts in a bl_bed_t object from non-member functions. This function copies the array pointed to by...
- bl_bed_set_chrom_ae(3) - Mutator for an array element of chrom member in a bl_bed_t structure. Use this function to set bl_bed_ptr->chrom[c] in a bl_bed_t object from non-member functions.
- bl_bed_set_chrom_cpy(3) - Mutator for chrom member in a bl_bed_t structure. Use this function to set chrom in a bl_bed_t object from non-member functions. This function copies the array pointed to by new_chrom to...
- bl_bed_set_chrom_end(3) - Mutator for chrom_end member in a bl_bed_t structure. Use this function to set chrom_end in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_chrom_start(3) - Mutator for chrom_start member in a bl_bed_t structure. Use this function to set chrom_start in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_fields(3) - Mutator for fields member in a bl_bed_t structure. Use this function to set fields in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_bed_set_item_rgb_ae(3) - Mutator for an array element of item_rgb member in a bl_bed_t structure. Use this function to set bl_bed_ptr->item_rgb[c] in a bl_bed_t object from non-member functions.
- bl_bed_set_item_rgb_cpy(3) - Mutator for item_rgb member in a bl_bed_t structure. Use this function to set item_rgb in a bl_bed_t object from non-member functions. This function copies the array pointed to by new_item_rgb to...
- bl_bed_set_name_ae(3) - Mutator for an array element of name member in a bl_bed_t structure. Use this function to set bl_bed_ptr->name[c] in a bl_bed_t object from non-member functions.
- bl_bed_set_name_cpy(3) - Mutator for name member in a bl_bed_t structure. Use this function to set name in a bl_bed_t object from non-member functions. This function copies the array pointed to by new_name to...
- bl_bed_set_score(3) - Mutator for score member in a bl_bed_t structure. Use this function to set score in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_bed_set_strand(3) - Mutator for strand member in a bl_bed_t structure. Use this function to set strand in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_bed_set_thick_end(3) - Mutator for thick_end member in a bl_bed_t structure. Use this function to set thick_end in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_set_thick_start(3) - Mutator for thick_start member in a bl_bed_t structure. Use this function to set thick_start in a bl_bed_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_bed_skip_header(3) - Read past BED header
- BL_BED_STRAND(3) - Accessor macro for strand. Use this macro to reference strand in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_BED_THICK_END(3) - Accessor macro for thick_end. Use this macro to reference thick_end in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_BED_THICK_START(3) - Accessor macro for thick_start. Use this macro to reference thick_start in a bl_bed_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_bed_write(3) - Write a BED record
- bl_chrom_name_cmp(3) - Compare chromosome names numerically or lexically
- BL_FASTA_DESC(3) - Accessor macro for desc. Use this macro to reference desc in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTA_DESC_AE(3) - Accessor macro for desc array elements. Use this macro to reference an element of desc in a bl_fasta_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTA_DESC_ARRAY_SIZE(3) - Accessor macro for desc_array_size. Use this macro to reference desc_array_size in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_FASTA_DESC_LEN(3) - Accessor macro for desc_len. Use this macro to reference desc_len in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fasta_free(3) - Free memory for a FASTA object
- bl_fasta_init(3) - Initialize all fields of a FASTA object
- bl_fasta_read(3) - Read a FASTA record
- BL_FASTA_SEQ(3) - Accessor macro for seq. Use this macro to reference seq in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_FASTA_SEQ_AE(3) - Accessor macro for seq array elements. Use this macro to reference an element of seq in a bl_fasta_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTA_SEQ_ARRAY_SIZE(3) - Accessor macro for seq_array_size. Use this macro to reference seq_array_size in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_FASTA_SEQ_LEN(3) - Accessor macro for seq_len. Use this macro to reference seq_len in a bl_fasta_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fasta_set_desc(3) - Mutator for desc member in a bl_fasta_t structure. Use this function to set desc in a bl_fasta_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fasta_set_desc_ae(3) - Mutator for an array element of desc member in a bl_fasta_t structure. Use this function to set bl_fasta_ptr->desc[c] in a bl_fasta_t object from non-member functions.
- bl_fasta_set_desc_array_size(3) - Mutator for desc_array_size member in a bl_fasta_t structure. Use this function to set desc_array_size in a bl_fasta_t object from non-member functions. This function performs a direct assignment for...
- bl_fasta_set_desc_cpy(3) - Mutator for desc member in a bl_fasta_t structure. Use this function to set desc in a bl_fasta_t object from non-member functions. This function copies the array pointed to by new_desc to...
- bl_fasta_set_desc_len(3) - Mutator for desc_len member in a bl_fasta_t structure. Use this function to set desc_len in a bl_fasta_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fasta_set_seq(3) - Mutator for seq member in a bl_fasta_t structure. Use this function to set seq in a bl_fasta_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fasta_set_seq_ae(3) - Mutator for an array element of seq member in a bl_fasta_t structure. Use this function to set bl_fasta_ptr->seq[c] in a bl_fasta_t object from non-member functions.
- bl_fasta_set_seq_array_size(3) - Mutator for seq_array_size member in a bl_fasta_t structure. Use this function to set seq_array_size in a bl_fasta_t object from non-member functions. This function performs a direct assignment for...
- bl_fasta_set_seq_cpy(3) - Mutator for seq member in a bl_fasta_t structure. Use this function to set seq in a bl_fasta_t object from non-member functions. This function copies the array pointed to by new_seq to...
- bl_fasta_set_seq_len(3) - Mutator for seq_len member in a bl_fasta_t structure. Use this function to set seq_len in a bl_fasta_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fasta_write(3) - Write a FASTA object
- bl_fastq_3p_trim(3) - Trim 3' end of a FASTQ object
- bl_fastq_5p_trim(3) - Trim 5' end of a FASTQ object
- BL_FASTQ_DESC(3) - Accessor macro for desc. Use this macro to reference desc in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTQ_DESC_AE(3) - Accessor macro for desc array elements. Use this macro to reference an element of desc in a bl_fastq_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTQ_DESC_ARRAY_SIZE(3) - Accessor macro for desc_array_size. Use this macro to reference desc_array_size in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_FASTQ_DESC_LEN(3) - Accessor macro for desc_len. Use this macro to reference desc_len in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fastq_find_3p_low_qual(3) - Find start of low-quality 3' end
- bl_fastq_find_5p_low_qual(3) - Find start of low-quality 5' end
- bl_fastq_free(3) - Free memory for a FASTQ object
- bl_fastq_init(3) - Initialize all fields in a FASTQ object
- bl_fastq_name_cmp(3) - Compare read names of two FASTQ objects
- BL_FASTQ_PLUS(3) - Accessor macro for plus. Use this macro to reference plus in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTQ_PLUS_AE(3) - Accessor macro for plus array elements. Use this macro to reference an element of plus in a bl_fastq_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTQ_PLUS_ARRAY_SIZE(3) - Accessor macro for plus_array_size. Use this macro to reference plus_array_size in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_FASTQ_PLUS_LEN(3) - Accessor macro for plus_len. Use this macro to reference plus_len in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_FASTQ_QUAL(3) - Accessor macro for qual. Use this macro to reference qual in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTQ_QUAL_AE(3) - Accessor macro for qual array elements. Use this macro to reference an element of qual in a bl_fastq_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTQ_QUAL_ARRAY_SIZE(3) - Accessor macro for qual_array_size. Use this macro to reference qual_array_size in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_FASTQ_QUAL_LEN(3) - Accessor macro for qual_len. Use this macro to reference qual_len in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fastq_read(3) - Read a FASTQ record
- BL_FASTQ_SEQ(3) - Accessor macro for seq. Use this macro to reference seq in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_FASTQ_SEQ_AE(3) - Accessor macro for seq array elements. Use this macro to reference an element of seq in a bl_fastq_t structure from functions that are not members of the class. This allows separation of...
- BL_FASTQ_SEQ_ARRAY_SIZE(3) - Accessor macro for seq_array_size. Use this macro to reference seq_array_size in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_FASTQ_SEQ_LEN(3) - Accessor macro for seq_len. Use this macro to reference seq_len in a bl_fastq_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fastq_set_desc(3) - Mutator for desc member in a bl_fastq_t structure. Use this function to set desc in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastq_set_desc_ae(3) - Mutator for an array element of desc member in a bl_fastq_t structure. Use this function to set bl_fastq_ptr->desc[c] in a bl_fastq_t object from non-member functions.
- bl_fastq_set_desc_array_size(3) - Mutator for desc_array_size member in a bl_fastq_t structure. Use this function to set desc_array_size in a bl_fastq_t object from non-member functions. This function performs a direct assignment for...
- bl_fastq_set_desc_cpy(3) - Mutator for desc member in a bl_fastq_t structure. Use this function to set desc in a bl_fastq_t object from non-member functions. This function copies the array pointed to by new_desc to...
- bl_fastq_set_desc_len(3) - Mutator for desc_len member in a bl_fastq_t structure. Use this function to set desc_len in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fastq_set_plus(3) - Mutator for plus member in a bl_fastq_t structure. Use this function to set plus in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastq_set_plus_ae(3) - Mutator for an array element of plus member in a bl_fastq_t structure. Use this function to set bl_fastq_ptr->plus[c] in a bl_fastq_t object from non-member functions.
- bl_fastq_set_plus_array_size(3) - Mutator for plus_array_size member in a bl_fastq_t structure. Use this function to set plus_array_size in a bl_fastq_t object from non-member functions. This function performs a direct assignment for...
- bl_fastq_set_plus_cpy(3) - Mutator for plus member in a bl_fastq_t structure. Use this function to set plus in a bl_fastq_t object from non-member functions. This function copies the array pointed to by new_plus to...
- bl_fastq_set_plus_len(3) - Mutator for plus_len member in a bl_fastq_t structure. Use this function to set plus_len in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fastq_set_qual(3) - Mutator for qual member in a bl_fastq_t structure. Use this function to set qual in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastq_set_qual_ae(3) - Mutator for an array element of qual member in a bl_fastq_t structure. Use this function to set bl_fastq_ptr->qual[c] in a bl_fastq_t object from non-member functions.
- bl_fastq_set_qual_array_size(3) - Mutator for qual_array_size member in a bl_fastq_t structure. Use this function to set qual_array_size in a bl_fastq_t object from non-member functions. This function performs a direct assignment for...
- bl_fastq_set_qual_cpy(3) - Mutator for qual member in a bl_fastq_t structure. Use this function to set qual in a bl_fastq_t object from non-member functions. This function copies the array pointed to by new_qual to...
- bl_fastq_set_qual_len(3) - Mutator for qual_len member in a bl_fastq_t structure. Use this function to set qual_len in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fastq_set_seq(3) - Mutator for seq member in a bl_fastq_t structure. Use this function to set seq in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastq_set_seq_ae(3) - Mutator for an array element of seq member in a bl_fastq_t structure. Use this function to set bl_fastq_ptr->seq[c] in a bl_fastq_t object from non-member functions.
- bl_fastq_set_seq_array_size(3) - Mutator for seq_array_size member in a bl_fastq_t structure. Use this function to set seq_array_size in a bl_fastq_t object from non-member functions. This function performs a direct assignment for...
- bl_fastq_set_seq_cpy(3) - Mutator for seq member in a bl_fastq_t structure. Use this function to set seq in a bl_fastq_t object from non-member functions. This function copies the array pointed to by new_seq to...
- bl_fastq_set_seq_len(3) - Mutator for seq_len member in a bl_fastq_t structure. Use this function to set seq_len in a bl_fastq_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_fastq_write(3) - Write a FASTQ record
- BL_FASTX_}(3) - Accessor macro for }. Use this macro to reference } in a bl_fastx_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- bl_fastx_desc(3) - Return description of a FASTX object
- bl_fastx_desc_len(3) - Return length of FASTX description
- BL_FASTX_FASTA(3) - Accessor macro for fasta. Use this macro to reference fasta in a bl_fastx_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTX_FASTQ(3) - Accessor macro for fastq. Use this macro to reference fastq in a bl_fastx_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_FASTX_FORMAT(3) - Accessor macro for format. Use this macro to reference format in a bl_fastx_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_fastx_free(3) - Free memory for a FASTX object
- bl_fastx_init(3) - Initialize a FASTX object
- bl_fastx_plus(3) - Return '+' line of a FASTQ object, NULL if FASTA
- bl_fastx_plus_len(3) - Return length of FASTQ '+' line, 0 if FASTA
- bl_fastx_qual(3) - Return FASTQ quality line, NULL if FASTA
- bl_fastx_qual_len(3) - Return length of FASTQ quality line, 0 if FASTA
- bl_fastx_read(3) - Read a FASTX record
- bl_fastx_seq(3) - Return sequence of a FASTX object
- bl_fastx_seq_len(3) - Return length of a FASTX sequence object
- bl_fastx_set_fasta(3) - Mutator for fasta member in a bl_fastx_t structure. Use this function to set fasta in a bl_fastx_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastx_set_fastq(3) - Mutator for fastq member in a bl_fastx_t structure. Use this function to set fastq in a bl_fastx_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_fastx_set_format(3) - Mutator for format member in a bl_fastx_t structure. Use this function to set format in a bl_fastx_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- BL_FASTX_UNION(3) - Accessor macro for union. Use this macro to reference union in a bl_fastx_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- bl_fastx_write(3) - Write a FASTX record
- bl_gff3_copy(3) - Copy a GFF3 object
- bl_gff3_copy_header(3) - Read and copy a GFF3 header
- bl_gff3_dup(3) - Duplicate a GFF3 object
- bl_gff3_extract_attribute(3) - Extract GFF3 attribute by name
- bl_gff3_free(3) - Free memory for a GFF3 object
- bl_gff3_index_add(3) - Add a GFF3 feature to an in-memory index
- bl_gff3_index_seek_reverse(3) - Search backward through GFF3 index
- bl_gff3_index_set_array_size(3) - Mutator for array_size member in a bl_gff3_index_t structure. Use this function to set array_size in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for...
- bl_gff3_index_set_count(3) - Mutator for count member in a bl_gff3_index_t structure. Use this function to set count in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_index_set_end(3) - Mutator for end member in a bl_gff3_index_t structure. Use this function to set end in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_index_set_end_ae(3) - Mutator for an array element of end member in a bl_gff3_index_t structure. Use this function to set bl_gff3_index_ptr->end[c] in a bl_gff3_index_t object from non-member functions.
- bl_gff3_index_set_end_cpy(3) - Mutator for end member in a bl_gff3_index_t structure. Use this function to set end in a bl_gff3_index_t object from non-member functions. This function copies the array pointed to by new_end to...
- bl_gff3_index_set_file_pos(3) - Mutator for file_pos member in a bl_gff3_index_t structure. Use this function to set file_pos in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for...
- bl_gff3_index_set_file_pos_ae(3) - Mutator for an array element of file_pos member in a bl_gff3_index_t structure. Use this function to set bl_gff3_index_ptr->file_pos[c] in a bl_gff3_index_t object from non-member functions.
- bl_gff3_index_set_file_pos_cpy(3) - Mutator for file_pos member in a bl_gff3_index_t structure. Use this function to set file_pos in a bl_gff3_index_t object from non-member functions. This function copies the array pointed to by...
- bl_gff3_index_set_seqid(3) - Mutator for seqid member in a bl_gff3_index_t structure. Use this function to set seqid in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_index_set_seqid_ae(3) - Mutator for an array element of seqid member in a bl_gff3_index_t structure. Use this function to set bl_gff3_index_ptr->seqid[c] in a bl_gff3_index_t object from non-member functions.
- bl_gff3_index_set_seqid_cpy(3) - Mutator for seqid member in a bl_gff3_index_t structure. Use this function to set seqid in a bl_gff3_index_t object from non-member functions. This function copies the array pointed to by new_seqid...
- bl_gff3_index_set_start(3) - Mutator for start member in a bl_gff3_index_t structure. Use this function to set start in a bl_gff3_index_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_index_set_start_ae(3) - Mutator for an array element of start member in a bl_gff3_index_t structure. Use this function to set bl_gff3_index_ptr->start[c] in a bl_gff3_index_t object from non-member functions.
- bl_gff3_index_set_start_cpy(3) - Mutator for start member in a bl_gff3_index_t structure. Use this function to set start in a bl_gff3_index_t object from non-member functions. This function copies the array pointed to by new_start...
- bl_gff3_init(3) - Initialize all fields in a GFF3 object
- bl_gff3_read(3) - Read a GFF3 feature
- bl_gff3_sam_cmp(3) - Compare SAM/GFF3 positions
- bl_gff3_sam_overlap(3) - Compute SAM/GFF3 overlap
- bl_gff3_set_attributes(3) - Mutator for attributes member in a bl_gff3_t structure. Use this function to set attributes in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_set_attributes_ae(3) - Mutator for an array element of attributes member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->attributes[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_attributes_array_size(3) - Mutator for attributes_array_size member in a bl_gff3_t structure. Use this function to set attributes_array_size in a bl_gff3_t object from non-member functions. This function performs a direct...
- bl_gff3_set_attributes_cpy(3) - Mutator for attributes member in a bl_gff3_t structure. Use this function to set attributes in a bl_gff3_t object from non-member functions. This function copies the array pointed to by...
- bl_gff3_set_attributes_len(3) - Mutator for attributes_len member in a bl_gff3_t structure. Use this function to set attributes_len in a bl_gff3_t object from non-member functions. This function performs a direct assignment for...
- bl_gff3_set_end(3) - Mutator for end member in a bl_gff3_t structure. Use this function to set end in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_gff3_set_feature_id(3) - Mutator for feature_id member in a bl_gff3_t structure. Use this function to set feature_id in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_set_feature_id_ae(3) - Mutator for an array element of feature_id member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->feature_id[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_feature_id_cpy(3) - Mutator for feature_id member in a bl_gff3_t structure. Use this function to set feature_id in a bl_gff3_t object from non-member functions. This function copies the array pointed to by...
- bl_gff3_set_feature_name(3) - Mutator for feature_name member in a bl_gff3_t structure. Use this function to set feature_name in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_gff3_set_feature_name_ae(3) - Mutator for an array element of feature_name member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->feature_name[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_feature_name_cpy(3) - Mutator for feature_name member in a bl_gff3_t structure. Use this function to set feature_name in a bl_gff3_t object from non-member functions. This function copies the array pointed to by...
- bl_gff3_set_feature_parent(3) - Mutator for feature_parent member in a bl_gff3_t structure. Use this function to set feature_parent in a bl_gff3_t object from non-member functions. This function performs a direct assignment for...
- bl_gff3_set_feature_parent_ae(3) - Mutator for an array element of feature_parent member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->feature_parent[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_feature_parent_cpy(3) - Mutator for feature_parent member in a bl_gff3_t structure. Use this function to set feature_parent in a bl_gff3_t object from non-member functions. This function copies the array pointed to by...
- bl_gff3_set_file_pos(3) - Mutator for file_pos member in a bl_gff3_t structure. Use this function to set file_pos in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_gff3_set_gene_name_cpy(3) - Mutator for gene_name member in a bl_gff3_t structure. Use this function to set gene_name in a bl_gff3_t variable from non-member functions. This function copies the array pointed to by new_gene_name...
- bl_gff3_set_phase(3) - Mutator for phase member in a bl_gff3_t structure. Use this function to set phase in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_gff3_set_score(3) - Mutator for score member in a bl_gff3_t structure. Use this function to set score in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_gff3_set_seqid_ae(3) - Mutator for an array element of seqid member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->seqid[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_seqid_cpy(3) - Mutator for seqid member in a bl_gff3_t structure. Use this function to set seqid in a bl_gff3_t object from non-member functions. This function copies the array pointed to by new_seqid to...
- bl_gff3_set_source_ae(3) - Mutator for an array element of source member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->source[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_source_cpy(3) - Mutator for source member in a bl_gff3_t structure. Use this function to set source in a bl_gff3_t object from non-member functions. This function copies the array pointed to by new_source to...
- bl_gff3_set_start(3) - Mutator for start member in a bl_gff3_t structure. Use this function to set start in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_gff3_set_strand(3) - Mutator for strand member in a bl_gff3_t structure. Use this function to set strand in a bl_gff3_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_gff3_set_type_ae(3) - Mutator for an array element of type member in a bl_gff3_t structure. Use this function to set bl_gff3_ptr->type[c] in a bl_gff3_t object from non-member functions.
- bl_gff3_set_type_cpy(3) - Mutator for type member in a bl_gff3_t structure. Use this function to set type in a bl_gff3_t object from non-member functions. This function copies the array pointed to by new_type to...
- bl_gff3_skip_header(3) - Read past header in a GFF3 file
- bl_gff3_to_bed(3) - Convert a GFF3 featuer to a BED object
- bl_gff3_write(3) - Write a GFF3 feature
- BL_GFF_ATTRIBUTES(3) - Accessor macro for attributes. Use this macro to reference attributes in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_ATTRIBUTES_AE(3) - Accessor macro for attributes array elements. Use this macro to reference an element of attributes in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_ATTRIBUTES_ARRAY_SIZE(3) - Accessor macro for attributes_array_size. Use this macro to reference attributes_array_size in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_ATTRIBUTES_LEN(3) - Accessor macro for attributes_len. Use this macro to reference attributes_len in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_END(3) - Accessor macro for end. Use this macro to reference end in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_GFF_FEATURE_ID(3) - Accessor macro for feature_id. Use this macro to reference feature_id in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_FEATURE_ID_AE(3) - Accessor macro for feature_id array elements. Use this macro to reference an element of feature_id in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_FEATURE_NAME(3) - Accessor macro for feature_name. Use this macro to reference feature_name in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_FEATURE_NAME_AE(3) - Accessor macro for feature_name array elements. Use this macro to reference an element of feature_name in a bl_gff_t structure from functions that are not members of the class. This allows separation...
- BL_GFF_FEATURE_PARENT(3) - Accessor macro for feature_parent. Use this macro to reference feature_parent in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_FEATURE_PARENT_AE(3) - Accessor macro for feature_parent array elements. Use this macro to reference an element of feature_parent in a bl_gff_t structure from functions that are not members of the class. This allows...
- BL_GFF_FILE_POS(3) - Accessor macro for file_pos. Use this macro to reference file_pos in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_GFF_INDEX_ARRAY_SIZE(3) - Accessor macro for array_size. Use this macro to reference array_size in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_INDEX_COUNT(3) - Accessor macro for count. Use this macro to reference count in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_GFF_INDEX_END(3) - Accessor macro for end. Use this macro to reference end in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_INDEX_END_AE(3) - Accessor macro for end array elements. Use this macro to reference an element of end in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_INDEX_FILE_POS(3) - Accessor macro for file_pos. Use this macro to reference file_pos in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_GFF_INDEX_FILE_POS_AE(3) - Accessor macro for file_pos array elements. Use this macro to reference an element of file_pos in a bl_gff_index_t structure from functions that are not members of the class. This allows separation...
- BL_GFF_INDEX_SEQID(3) - Accessor macro for seqid. Use this macro to reference seqid in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_GFF_INDEX_SEQID_AE(3) - Accessor macro for seqid array elements. Use this macro to reference an element of seqid in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_INDEX_START(3) - Accessor macro for start. Use this macro to reference start in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_GFF_INDEX_START_AE(3) - Accessor macro for start array elements. Use this macro to reference an element of start in a bl_gff_index_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_PHASE(3) - Accessor macro for phase. Use this macro to reference phase in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_SCORE(3) - Accessor macro for score. Use this macro to reference score in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_SEQID(3) - Accessor macro for seqid. Use this macro to reference seqid in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_SEQID_AE(3) - Accessor macro for seqid array elements. Use this macro to reference an element of seqid in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_SOURCE(3) - Accessor macro for source. Use this macro to reference source in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_SOURCE_AE(3) - Accessor macro for source array elements. Use this macro to reference an element of source in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- BL_GFF_START(3) - Accessor macro for start. Use this macro to reference start in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_STRAND(3) - Accessor macro for strand. Use this macro to reference strand in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_GFF_TYPE(3) - Accessor macro for type. Use this macro to reference type in a bl_gff_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_GFF_TYPE_AE(3) - Accessor macro for type array elements. Use this macro to reference an element of type in a bl_gff_t structure from functions that are not members of the class. This allows separation of...
- bl_next_start_codon(3) - Find next start codon
- bl_next_stop_codon(3) - Find next stop codon
- BL_OVERLAP_FEATURE1_LEN(3) - Accessor macro for feature1_len. Use this macro to reference feature1_len in a bl_overlap_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_OVERLAP_FEATURE2_LEN(3) - Accessor macro for feature2_len. Use this macro to reference feature2_len in a bl_overlap_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_OVERLAP_OVERLAP_END(3) - Accessor macro for overlap_end. Use this macro to reference overlap_end in a bl_overlap_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_OVERLAP_OVERLAP_LEN(3) - Accessor macro for overlap_len. Use this macro to reference overlap_len in a bl_overlap_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_OVERLAP_OVERLAP_START(3) - Accessor macro for overlap_start. Use this macro to reference overlap_start in a bl_overlap_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_overlap_print(3) - Print overlap summary for two features
- bl_overlap_set_all(3) - Set overlap fields for two features
- bl_overlap_set_feature1_len(3) - Mutator for feature1_len member in a bl_overlap_t structure. Use this function to set feature1_len in a bl_overlap_t object from non-member functions. This function performs a direct assignment for...
- bl_overlap_set_feature2_len(3) - Mutator for feature2_len member in a bl_overlap_t structure. Use this function to set feature2_len in a bl_overlap_t object from non-member functions. This function performs a direct assignment for...
- bl_overlap_set_overlap_end(3) - Mutator for overlap_end member in a bl_overlap_t structure. Use this function to set overlap_end in a bl_overlap_t object from non-member functions. This function performs a direct assignment for...
- bl_overlap_set_overlap_len(3) - Mutator for overlap_len member in a bl_overlap_t structure. Use this function to set overlap_len in a bl_overlap_t object from non-member functions. This function performs a direct assignment for...
- bl_overlap_set_overlap_start(3) - Mutator for overlap_start member in a bl_overlap_t structure. Use this function to set overlap_start in a bl_overlap_t object from non-member functions. This function performs a direct assignment for...
- bl_pos_list_add_position(3) - Add a position to a list
- bl_pos_list_allocate(3) - Initialize position list object
- BL_POS_LIST_ARRAY_SIZE(3) - Accessor macro for array_size. Use this macro to reference array_size in a bl_pos_list_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_POS_LIST_COUNT(3) - Accessor macro for count. Use this macro to reference count in a bl_pos_list_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_pos_list_free(3) - Free a position list object
- bl_pos_list_from_csv(3) - Convert comma-separated data to position list
- BL_POS_LIST_POSITIONS(3) - Accessor macro for positions. Use this macro to reference positions in a bl_pos_list_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_POS_LIST_POSITIONS_AE(3) - Accessor macro for positions array elements. Use this macro to reference an element of positions in a bl_pos_list_t structure from functions that are not members of the class. This allows separation...
- bl_pos_list_set_array_size(3) - Mutator for array_size member in a bl_pos_list_t structure. Use this function to set array_size in a bl_pos_list_t object from non-member functions. This function performs a direct assignment for...
- bl_pos_list_set_count(3) - Mutator for count member in a bl_pos_list_t structure. Use this function to set count in a bl_pos_list_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_pos_list_set_positions(3) - Mutator for positions member in a bl_pos_list_t structure. Use this function to set positions in a bl_pos_list_t object from non-member functions. This function performs a direct assignment for...
- bl_pos_list_set_positions_ae(3) - Mutator for an array element of positions member in a bl_pos_list_t structure. Use this function to set bl_pos_list_ptr->positions[c] in a bl_pos_list_t object from non-member functions.
- bl_pos_list_set_positions_cpy(3) - Mutator for positions member in a bl_pos_list_t structure. Use this function to set positions in a bl_pos_list_t object from non-member functions. This function copies the array pointed to by...
- bl_pos_list_sort(3) - Sort a position list
- bl_sam_buff_add_alignment(3) - Add alignment to SAM buffer
- bl_sam_buff_alignment_ok(3) - Verify alignment quality
- BL_SAM_BUFF_ALIGNMENTS(3) - Accessor macro for alignments. Use this macro to reference alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_ALIGNMENTS_AE(3) - Accessor macro for alignments array elements. Use this macro to reference an element of alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows...
- BL_SAM_BUFF_BUFF_SIZE(3) - Accessor macro for buff_size. Use this macro to reference buff_size in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_BUFFERED_COUNT(3) - Accessor macro for buffered_count. Use this macro to reference buffered_count in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation...
- bl_sam_buff_check_order(3) - Check sort order of SAM records
- BL_SAM_BUFF_DISCARDED_ALIGNMENTS(3) - Accessor macro for discarded_alignments. Use this macro to reference discarded_alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_DISCARDED_SCORE_SUM(3) - Accessor macro for discarded_score_sum. Use this macro to reference discarded_score_sum in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_DISCARDED_TRAILING(3) - Accessor macro for discarded_trailing. Use this macro to reference discarded_trailing in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- bl_sam_buff_free_alignment(3) - Free an alignment in a SAM buffer
- BL_SAM_BUFF_INC_DISCARDED_TRAILING(3) - Increment discarded_trailing. Use this macro to increment the discarded_trailing of a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS(3) - Increment total_alignments. Use this macro to increment the total_alignments of a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS(3) - Increment trailing_alignments. Use this macro to increment the trailing_alignments of a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- bl_sam_buff_init(3) - Initialize a SAM buffer object
- BL_SAM_BUFF_MAPQ_HIGH(3) - Accessor macro for mapq_high. Use this macro to reference mapq_high in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_MAPQ_LOW(3) - Accessor macro for mapq_low. Use this macro to reference mapq_low in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_MAPQ_MIN(3) - Accessor macro for mapq_min. Use this macro to reference mapq_min in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_MAPQ_SUM(3) - Accessor macro for mapq_sum. Use this macro to reference mapq_sum in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_MAX_ALIGNMENTS(3) - Accessor macro for max_alignments. Use this macro to reference max_alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_SAM_BUFF_MAX_COUNT(3) - Accessor macro for max_count. Use this macro to reference max_count in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_MAX_DISCARDED_SCORE(3) - Accessor macro for max_discarded_score. Use this macro to reference max_discarded_score in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_MIN_DISCARDED_SCORE(3) - Accessor macro for min_discarded_score. Use this macro to reference min_discarded_score in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- bl_sam_buff_out_of_order(3) - Print sort order message and exit
- BL_SAM_BUFF_PREVIOUS_POS(3) - Accessor macro for previous_pos. Use this macro to reference previous_pos in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_BUFF_PREVIOUS_RNAME(3) - Accessor macro for previous_rname. Use this macro to reference previous_rname in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_SAM_BUFF_PREVIOUS_RNAME_AE(3) - Accessor macro for previous_rname array elements. Use this macro to reference an element of previous_rname in a bl_sam_buff_t structure from functions that are not members of the class. This allows...
- BL_SAM_BUFF_READS_USED(3) - Accessor macro for reads_used. Use this macro to reference reads_used in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_sam_buff_set_alignments(3) - Mutator for alignments member in a bl_sam_buff_t structure. Use this function to set alignments in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_alignments_ae(3) - Mutator for an array element of alignments member in a bl_sam_buff_t structure. Use this function to set bl_sam_buff_ptr->alignments[c] in a bl_sam_buff_t object from non-member functions.
- bl_sam_buff_set_alignments_cpy(3) - Mutator for alignments member in a bl_sam_buff_t structure. Use this function to set alignments in a bl_sam_buff_t object from non-member functions. This function copies the array pointed to by...
- bl_sam_buff_set_buff_size(3) - Mutator for buff_size member in a bl_sam_buff_t structure. Use this function to set buff_size in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_buffered_count(3) - Mutator for buffered_count member in a bl_sam_buff_t structure. Use this function to set buffered_count in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment...
- bl_sam_buff_set_discarded_alignments(3) - Mutator for discarded_alignments member in a bl_sam_buff_t structure. Use this function to set discarded_alignments in a bl_sam_buff_t object from non-member functions. This function performs a...
- bl_sam_buff_set_discarded_score_sum(3) - Mutator for discarded_score_sum member in a bl_sam_buff_t structure. Use this function to set discarded_score_sum in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_discarded_trailing(3) - Mutator for discarded_trailing member in a bl_sam_buff_t structure. Use this function to set discarded_trailing in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_mapq_high(3) - Mutator for mapq_high member in a bl_sam_buff_t structure. Use this function to set mapq_high in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_mapq_low(3) - Mutator for mapq_low member in a bl_sam_buff_t structure. Use this function to set mapq_low in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_sam_buff_set_mapq_min(3) - Mutator for mapq_min member in a bl_sam_buff_t structure. Use this function to set mapq_min in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_sam_buff_set_mapq_sum(3) - Mutator for mapq_sum member in a bl_sam_buff_t structure. Use this function to set mapq_sum in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_sam_buff_set_max_alignments(3) - Mutator for max_alignments member in a bl_sam_buff_t structure. Use this function to set max_alignments in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment...
- bl_sam_buff_set_max_count(3) - Mutator for max_count member in a bl_sam_buff_t structure. Use this function to set max_count in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_max_discarded_score(3) - Mutator for max_discarded_score member in a bl_sam_buff_t structure. Use this function to set max_discarded_score in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_min_discarded_score(3) - Mutator for min_discarded_score member in a bl_sam_buff_t structure. Use this function to set min_discarded_score in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_previous_pos(3) - Mutator for previous_pos member in a bl_sam_buff_t structure. Use this function to set previous_pos in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_previous_rname_ae(3) - Mutator for an array element of previous_rname member in a bl_sam_buff_t structure. Use this function to set bl_sam_buff_ptr->previous_rname[c] in a bl_sam_buff_t object from non-member functions.
- bl_sam_buff_set_previous_rname_cpy(3) - Mutator for previous_rname member in a bl_sam_buff_t structure. Use this function to set previous_rname in a bl_sam_buff_t object from non-member functions. This function copies the array pointed to...
- bl_sam_buff_set_reads_used(3) - Mutator for reads_used member in a bl_sam_buff_t structure. Use this function to set reads_used in a bl_sam_buff_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_buff_set_total_alignments(3) - Mutator for total_alignments member in a bl_sam_buff_t structure. Use this function to set total_alignments in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_trailing_alignments(3) - Mutator for trailing_alignments member in a bl_sam_buff_t structure. Use this function to set trailing_alignments in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_set_unmapped_alignments(3) - Mutator for unmapped_alignments member in a bl_sam_buff_t structure. Use this function to set unmapped_alignments in a bl_sam_buff_t object from non-member functions. This function performs a direct...
- bl_sam_buff_shift(3) - Close gap after removing a SAM alignment
- BL_SAM_BUFF_TOTAL_ALIGNMENTS(3) - Accessor macro for total_alignments. Use this macro to reference total_alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_TRAILING_ALIGNMENTS(3) - Accessor macro for trailing_alignments. Use this macro to reference trailing_alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_BUFF_UNMAPPED_ALIGNMENTS(3) - Accessor macro for unmapped_alignments. Use this macro to reference unmapped_alignments in a bl_sam_buff_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_CIGAR(3) - Accessor macro for cigar. Use this macro to reference cigar in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_SAM_CIGAR_AE(3) - Accessor macro for cigar array elements. Use this macro to reference an element of cigar in a bl_sam_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_CIGAR_ARRAY_SIZE(3) - Accessor macro for cigar_array_size. Use this macro to reference cigar_array_size in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_SAM_CIGAR_LEN(3) - Accessor macro for cigar_len. Use this macro to reference cigar_len in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_sam_copy(3) - Copy a SAM object
- bl_sam_copy_header(3) - Copy SAM header to another stream
- bl_sam_fclose(3) - Close a stream opened by bl_sam_fopen(3)
- BL_SAM_FLAG(3) - Accessor macro for flag. Use this macro to reference flag in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- bl_sam_fopen(3) - Open a SAM/BAM/CRAM file
- bl_sam_free(3) - Destroy a SAM object
- bl_sam_gff3_cmp(3) - Compare positions of SAM and GFF3 records
- bl_sam_gff3_overlap(3) - Compute SAM/GFF3 overlap
- bl_sam_gff_cmp(3) - Compare the positions of a SAM alignment and a GFF feature and return a status value much like strcmp(). 0 is returned if the alignment and feature overlap. A value < 0 is returned if the...
- bl_sam_gff_overlap(3) - Return the amount of overlap between a GFF feature and a SAM alignment.
- bl_sam_init(3) - Initialize all fields of a SAM object
- BL_SAM_MAPQ(3) - Accessor macro for mapq. Use this macro to reference mapq in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_SAM_PNEXT(3) - Accessor macro for pnext. Use this macro to reference pnext in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_SAM_POS(3) - Accessor macro for pos. Use this macro to reference pos in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_SAM_QNAME(3) - Accessor macro for qname. Use this macro to reference qname in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_SAM_QNAME_AE(3) - Accessor macro for qname array elements. Use this macro to reference an element of qname in a bl_sam_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_QUAL(3) - Accessor macro for qual. Use this macro to reference qual in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_SAM_QUAL_AE(3) - Accessor macro for qual array elements. Use this macro to reference an element of qual in a bl_sam_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_QUAL_ARRAY_SIZE(3) - Accessor macro for qual_array_size. Use this macro to reference qual_array_size in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_QUAL_LEN(3) - Accessor macro for qual_len. Use this macro to reference qual_len in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_sam_read(3) - Read one SAM record
- BL_SAM_RNAME(3) - Accessor macro for rname. Use this macro to reference rname in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_SAM_RNAME_AE(3) - Accessor macro for rname array elements. Use this macro to reference an element of rname in a bl_sam_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_RNEXT(3) - Accessor macro for rnext. Use this macro to reference rnext in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_SAM_RNEXT_AE(3) - Accessor macro for rnext array elements. Use this macro to reference an element of rnext in a bl_sam_t structure from functions that are not members of the class. This allows separation of...
- BL_SAM_SEQ(3) - Accessor macro for seq. Use this macro to reference seq in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_SAM_SEQ_AE(3) - Accessor macro for seq array elements. Use this macro to reference an element of seq in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_SAM_SEQ_ARRAY_SIZE(3) - Accessor macro for seq_array_size. Use this macro to reference seq_array_size in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_SAM_SEQ_LEN(3) - Accessor macro for seq_len. Use this macro to reference seq_len in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_sam_set_cigar(3) - Mutator for cigar member in a bl_sam_t structure. Use this function to set cigar in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_cigar_ae(3) - Mutator for an array element of cigar member in a bl_sam_t structure. Use this function to set bl_sam_ptr->cigar[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_cigar_array_size(3) - Mutator for cigar_array_size member in a bl_sam_t structure. Use this function to set cigar_array_size in a bl_sam_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_set_cigar_cpy(3) - Mutator for cigar member in a bl_sam_t structure. Use this function to set cigar in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_cigar to...
- bl_sam_set_cigar_len(3) - Mutator for cigar_len member in a bl_sam_t structure. Use this function to set cigar_len in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_sam_set_flag(3) - Mutator for flag member in a bl_sam_t structure. Use this function to set flag in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_mapq(3) - Mutator for mapq member in a bl_sam_t structure. Use this function to set mapq in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_pnext(3) - Mutator for pnext member in a bl_sam_t structure. Use this function to set pnext in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_pos(3) - Mutator for pos member in a bl_sam_t structure. Use this function to set pos in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer structure...
- bl_sam_set_qname_ae(3) - Mutator for an array element of qname member in a bl_sam_t structure. Use this function to set bl_sam_ptr->qname[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_qname_cpy(3) - Mutator for qname member in a bl_sam_t structure. Use this function to set qname in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_qname to...
- bl_sam_set_qual(3) - Mutator for qual member in a bl_sam_t structure. Use this function to set qual in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_qual_ae(3) - Mutator for an array element of qual member in a bl_sam_t structure. Use this function to set bl_sam_ptr->qual[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_qual_array_size(3) - Mutator for qual_array_size member in a bl_sam_t structure. Use this function to set qual_array_size in a bl_sam_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_set_qual_cpy(3) - Mutator for qual member in a bl_sam_t structure. Use this function to set qual in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_qual to...
- bl_sam_set_qual_len(3) - Mutator for qual_len member in a bl_sam_t structure. Use this function to set qual_len in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_rname_ae(3) - Mutator for an array element of rname member in a bl_sam_t structure. Use this function to set bl_sam_ptr->rname[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_rname_cpy(3) - Mutator for rname member in a bl_sam_t structure. Use this function to set rname in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_rname to...
- bl_sam_set_rnext_ae(3) - Mutator for an array element of rnext member in a bl_sam_t structure. Use this function to set bl_sam_ptr->rnext[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_rnext_cpy(3) - Mutator for rnext member in a bl_sam_t structure. Use this function to set rnext in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_rnext to...
- bl_sam_set_seq(3) - Mutator for seq member in a bl_sam_t structure. Use this function to set seq in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer structure...
- bl_sam_set_seq_ae(3) - Mutator for an array element of seq member in a bl_sam_t structure. Use this function to set bl_sam_ptr->seq[c] in a bl_sam_t object from non-member functions.
- bl_sam_set_seq_array_size(3) - Mutator for seq_array_size member in a bl_sam_t structure. Use this function to set seq_array_size in a bl_sam_t object from non-member functions. This function performs a direct assignment for...
- bl_sam_set_seq_cpy(3) - Mutator for seq member in a bl_sam_t structure. Use this function to set seq in a bl_sam_t object from non-member functions. This function copies the array pointed to by new_seq to bl_sam_ptr->seq.
- bl_sam_set_seq_len(3) - Mutator for seq_len member in a bl_sam_t structure. Use this function to set seq_len in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_set_tlen(3) - Mutator for tlen member in a bl_sam_t structure. Use this function to set tlen in a bl_sam_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_sam_skip_header(3) - Read past SAM header
- BL_SAM_TLEN(3) - Accessor macro for tlen. Use this macro to reference tlen in a bl_sam_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- bl_sam_write(3) - Write a SAM object to a file stream
- BL_VCF_ALT(3) - Accessor macro for alt. Use this macro to reference alt in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_ALT_AE(3) - Accessor macro for alt array elements. Use this macro to reference an element of alt in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_ALT_COUNT(3) - Accessor macro for alt_count. Use this macro to reference alt_count in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_vcf_call_downstream_of_alignment(3) - Return true if VCF call is downstream of alignment
- bl_vcf_call_in_alignment(3) - Return true if VCF call is within alignment
- bl_vcf_call_out_of_order(3) - Terminate with VCF sort error message
- BL_VCF_CHROM(3) - Accessor macro for chrom. Use this macro to reference chrom in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_VCF_CHROM_AE(3) - Accessor macro for chrom array elements. Use this macro to reference an element of chrom in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_FILTER(3) - Accessor macro for filter. Use this macro to reference filter in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_VCF_FILTER_AE(3) - Accessor macro for filter array elements. Use this macro to reference an element of filter in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_FORMAT(3) - Accessor macro for format. Use this macro to reference format in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_VCF_FORMAT_AE(3) - Accessor macro for format array elements. Use this macro to reference an element of format in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_FORMAT_ARRAY_SIZE(3) - Accessor macro for format_array_size. Use this macro to reference format_array_size in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_FORMAT_LEN(3) - Accessor macro for format_len. Use this macro to reference format_len in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_vcf_free(3) - Destroy a VCF object
- bl_vcf_get_sample_ids(3) - Extract sample IDs from a VCF header
- BL_VCF_ID(3) - Accessor macro for id. Use this macro to reference id in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_ID_AE(3) - Accessor macro for id array elements. Use this macro to reference an element of id in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_INFO(3) - Accessor macro for info. Use this macro to reference info in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_INFO_AE(3) - Accessor macro for info array elements. Use this macro to reference an element of info in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_INFO_ARRAY_SIZE(3) - Accessor macro for info_array_size. Use this macro to reference info_array_size in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_INFO_LEN(3) - Accessor macro for info_len. Use this macro to reference info_len in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- bl_vcf_init(3) - Initialize fields in a VCF object
- BL_VCF_MULTI_SAMPLE_ARRAY_SIZES(3) - Accessor macro for multi_sample_array_sizes. Use this macro to reference multi_sample_array_sizes in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_MULTI_SAMPLE_ARRAY_SIZES_AE(3) - Accessor macro for multi_sample_array_sizes array elements. Use this macro to reference an element of multi_sample_array_sizes in a bl_vcf_t structure from functions that are not members of the...
- BL_VCF_MULTI_SAMPLE_COUNT(3) - Accessor macro for multi_sample_count. Use this macro to reference multi_sample_count in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_MULTI_SAMPLE_LENS(3) - Accessor macro for multi_sample_lens. Use this macro to reference multi_sample_lens in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_MULTI_SAMPLE_LENS_AE(3) - Accessor macro for multi_sample_lens array elements. Use this macro to reference an element of multi_sample_lens in a bl_vcf_t structure from functions that are not members of the class. This allows...
- BL_VCF_MULTI_SAMPLE_POINTER_ARRAY_SIZE(3) - Accessor macro for multi_sample_pointer_array_size. Use this macro to reference multi_sample_pointer_array_size in a bl_vcf_t structure from functions that are not members of the class. This allows...
- BL_VCF_MULTI_SAMPLES(3) - Accessor macro for multi_samples. Use this macro to reference multi_samples in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_MULTI_SAMPLES_AE(3) - Accessor macro for multi_samples array elements. Use this macro to reference an element of multi_samples in a bl_vcf_t structure from functions that are not members of the class. This allows...
- BL_VCF_OTHER_COUNT(3) - Accessor macro for other_count. Use this macro to reference other_count in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_vcf_parse_field_spec(3) - Convert comma-separated fields to bitmask
- BL_VCF_PHRED_BUFF_SIZE(3) - Accessor macro for phred_buff_size. Use this macro to reference phred_buff_size in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_PHRED_COUNT(3) - Accessor macro for phred_count. Use this macro to reference phred_count in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_PHREDS(3) - Accessor macro for phreds. Use this macro to reference phreds in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While...
- BL_VCF_PHREDS_AE(3) - Accessor macro for phreds array elements. Use this macro to reference an element of phreds in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_POS(3) - Accessor macro for pos. Use this macro to reference pos in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_QUAL(3) - Accessor macro for qual. Use this macro to reference qual in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_QUAL_AE(3) - Accessor macro for qual array elements. Use this macro to reference an element of qual in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- bl_vcf_read_ss_call(3) - Read a single-sample VCF call
- bl_vcf_read_static_fields(3) - Read static VCF fields
- BL_VCF_REF(3) - Accessor macro for ref. Use this macro to reference ref in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface. While the...
- BL_VCF_REF_AE(3) - Accessor macro for ref array elements. Use this macro to reference an element of ref in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_REF_COUNT(3) - Accessor macro for ref_count. Use this macro to reference ref_count in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from interface....
- BL_VCF_SAMPLE_ARRAY_SIZE(3) - Accessor macro for sample_array_size. Use this macro to reference sample_array_size in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- BL_VCF_SAMPLE_LEN(3) - Accessor macro for sample_len. Use this macro to reference sample_len in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_SAMPLE_MAX(3) - Accessor macro for sample_max. Use this macro to reference sample_max in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- bl_vcf_set_alt_ae(3) - Mutator for an array element of alt member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->alt[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_alt_count(3) - Mutator for alt_count member in a bl_vcf_t structure. Use this function to set alt_count in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_vcf_set_alt_cpy(3) - Mutator for alt member in a bl_vcf_t structure. Use this function to set alt in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_alt to bl_vcf_ptr->alt.
- bl_vcf_set_chrom_ae(3) - Mutator for an array element of chrom member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->chrom[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_chrom_cpy(3) - Mutator for chrom member in a bl_vcf_t structure. Use this function to set chrom in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_chrom to...
- bl_vcf_set_filter_ae(3) - Mutator for an array element of filter member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->filter[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_filter_cpy(3) - Mutator for filter member in a bl_vcf_t structure. Use this function to set filter in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_filter to...
- bl_vcf_set_format(3) - Mutator for format member in a bl_vcf_t structure. Use this function to set format in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_vcf_set_format_ae(3) - Mutator for an array element of format member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->format[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_format_array_size(3) - Mutator for format_array_size member in a bl_vcf_t structure. Use this function to set format_array_size in a bl_vcf_t object from non-member functions. This function performs a direct assignment for...
- bl_vcf_set_format_cpy(3) - Mutator for format member in a bl_vcf_t structure. Use this function to set format in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_format to...
- bl_vcf_set_format_len(3) - Mutator for format_len member in a bl_vcf_t structure. Use this function to set format_len in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_vcf_set_id_ae(3) - Mutator for an array element of id member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->id[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_id_cpy(3) - Mutator for id member in a bl_vcf_t structure. Use this function to set id in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_id to bl_vcf_ptr->id.
- bl_vcf_set_info(3) - Mutator for info member in a bl_vcf_t structure. Use this function to set info in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_vcf_set_info_ae(3) - Mutator for an array element of info member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->info[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_info_array_size(3) - Mutator for info_array_size member in a bl_vcf_t structure. Use this function to set info_array_size in a bl_vcf_t object from non-member functions. This function performs a direct assignment for...
- bl_vcf_set_info_cpy(3) - Mutator for info member in a bl_vcf_t structure. Use this function to set info in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_info to...
- bl_vcf_set_info_len(3) - Mutator for info_len member in a bl_vcf_t structure. Use this function to set info_len in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_vcf_set_multi_sample_array_sizes(3) - Mutator for multi_sample_array_sizes member in a bl_vcf_t structure. Use this function to set multi_sample_array_sizes in a bl_vcf_t object from non-member functions. This function performs a direct...
- bl_vcf_set_multi_sample_array_sizes_ae(3) - Mutator for an array element of multi_sample_array_sizes member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->multi_sample_array_sizes[c] in a bl_vcf_t object from non-member...
- bl_vcf_set_multi_sample_array_sizes_cpy(3) - Mutator for multi_sample_array_sizes member in a bl_vcf_t structure. Use this function to set multi_sample_array_sizes in a bl_vcf_t object from non-member functions. This function copies the array...
- bl_vcf_set_multi_sample_count(3) - Mutator for multi_sample_count member in a bl_vcf_t structure. Use this function to set multi_sample_count in a bl_vcf_t object from non-member functions. This function performs a direct assignment...
- bl_vcf_set_multi_sample_lens(3) - Mutator for multi_sample_lens member in a bl_vcf_t structure. Use this function to set multi_sample_lens in a bl_vcf_t object from non-member functions. This function performs a direct assignment for...
- bl_vcf_set_multi_sample_lens_ae(3) - Mutator for an array element of multi_sample_lens member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->multi_sample_lens[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_multi_sample_lens_cpy(3) - Mutator for multi_sample_lens member in a bl_vcf_t structure. Use this function to set multi_sample_lens in a bl_vcf_t object from non-member functions. This function copies the array pointed to by...
- bl_vcf_set_multi_sample_pointer_array_size(3) - Mutator for multi_sample_pointer_array_size member in a bl_vcf_t structure. Use this function to set multi_sample_pointer_array_size in a bl_vcf_t object from non-member functions. This function...
- bl_vcf_set_multi_samples(3) - Mutator for multi_samples member in a bl_vcf_t structure. Use this function to set multi_samples in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_vcf_set_multi_samples_ae(3) - Mutator for an array element of multi_samples member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->multi_samples[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_multi_samples_cpy(3) - Mutator for multi_samples member in a bl_vcf_t structure. Use this function to set multi_samples in a bl_vcf_t object from non-member functions. This function copies the array pointed to by...
- bl_vcf_set_other_count(3) - Mutator for other_count member in a bl_vcf_t structure. Use this function to set other_count in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_vcf_set_phred_buff_size(3) - Mutator for phred_buff_size member in a bl_vcf_t structure. Use this function to set phred_buff_size in a bl_vcf_t object from non-member functions. This function performs a direct assignment for...
- bl_vcf_set_phred_count(3) - Mutator for phred_count member in a bl_vcf_t structure. Use this function to set phred_count in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_vcf_set_phreds(3) - Mutator for phreds member in a bl_vcf_t structure. Use this function to set phreds in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or pointer...
- bl_vcf_set_phreds_ae(3) - Mutator for an array element of phreds member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->phreds[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_phreds_cpy(3) - Mutator for phreds member in a bl_vcf_t structure. Use this function to set phreds in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_phreds to...
- bl_vcf_set_pos(3) - Mutator for pos member in a bl_vcf_t structure. Use this function to set pos in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or pointer structure...
- bl_vcf_set_qual_ae(3) - Mutator for an array element of qual member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->qual[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_qual_cpy(3) - Mutator for qual member in a bl_vcf_t structure. Use this function to set qual in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_qual to...
- bl_vcf_set_ref_ae(3) - Mutator for an array element of ref member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->ref[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_ref_count(3) - Mutator for ref_count member in a bl_vcf_t structure. Use this function to set ref_count in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar or...
- bl_vcf_set_ref_cpy(3) - Mutator for ref member in a bl_vcf_t structure. Use this function to set ref in a bl_vcf_t object from non-member functions. This function copies the array pointed to by new_ref to bl_vcf_ptr->ref.
- bl_vcf_set_single_sample(3) - Mutator for single_sample member in a bl_vcf_t structure. Use this function to set single_sample in a bl_vcf_t object from non-member functions. This function performs a direct assignment for scalar...
- bl_vcf_set_single_sample_ae(3) - Mutator for an array element of single_sample member in a bl_vcf_t structure. Use this function to set bl_vcf_ptr->single_sample[c] in a bl_vcf_t object from non-member functions.
- bl_vcf_set_single_sample_array_size(3) - Mutator for single_sample_array_size member in a bl_vcf_t structure. Use this function to set single_sample_array_size in a bl_vcf_t object from non-member functions. This function performs a direct...
- bl_vcf_set_single_sample_cpy(3) - Mutator for single_sample member in a bl_vcf_t structure. Use this function to set single_sample in a bl_vcf_t object from non-member functions. This function copies the array pointed to by...
- bl_vcf_set_single_sample_len(3) - Mutator for single_sample_len member in a bl_vcf_t structure. Use this function to set single_sample_len in a bl_vcf_t object from non-member functions. This function performs a direct assignment for...
- BL_VCF_SINGLE_SAMPLE(3) - Accessor macro for single_sample. Use this macro to reference single_sample in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation from...
- BL_VCF_SINGLE_SAMPLE_AE(3) - Accessor macro for single_sample array elements. Use this macro to reference an element of single_sample in a bl_vcf_t structure from functions that are not members of the class. This allows...
- BL_VCF_SINGLE_SAMPLE_ARRAY_SIZE(3) - Accessor macro for single_sample_array_size. Use this macro to reference single_sample_array_size in a bl_vcf_t structure from functions that are not members of the class. This allows separation of...
- BL_VCF_SINGLE_SAMPLE_LEN(3) - Accessor macro for single_sample_len. Use this macro to reference single_sample_len in a bl_vcf_t structure from functions that are not members of the class. This allows separation of implementation...
- bl_vcf_skip_header(3) - Read past VCF header
- bl_vcf_skip_meta_data(3) - Read past VCF metadata
- bl_vcf_write_ss_call(3) - Write a single-sample VCF call
- bl_vcf_write_static_fields(3) - Write VCF static fields
- black_palette(3) - A palette containing solid black colors. Allegro game programming library.
- blackbox(1) - a window manager for X11
- BLACKHOLE(4) - quietly drop refused SCTP, TCP, or UDP packets
- BLACKHOLE6(1) - A tool to find IPv6 blackholes
- BLACKLISTCTL(8) - display and change the state of the blacklistd database
- BLACKLISTD(8) - block and release ports on demand to avoid DoS abuse
- BLACKLISTD.CONF(5) - configuration file format for blacklistd
- BlackPixelOfScreen(3) - screen information functions and macros
- BLAME(1) - annotate RCS files
- blas0_like_grp(3) - Scalar operations
- blas1_grp(3) - Level 1 BLAS: vector ops
- blas1_like_grp(3) - Level 1 BLAS-like vector ops
- blas2_banded(3) - --- banded ---
- blas2_full(3) - --- full ---
- blas2_grp(3) - Level 2 BLAS: matrix-vector ops
- blas2_like_grp(3) - Level 2 BLAS-like matrix-vector ops
- blas2_packed(3) - --- packed ---
- blas3_grp(3) - Level 3 BLAS: matrix-matrix ops
- blas3_like_grp(3) - Level 3 BLAS-like matrix-matrix ops
- blas_like_top(3) - BLAS-like
- blas_top(3) - BLAS
- blast_aux(3) - --- BLAST constants ---
- BLASTCL3(1) - Basic Local Alignment Search Tool client
- blaster(6) - simulation of space combat
- BLAZER_SER(8) - Driver for Megatec/Q1 protocol serial based UPS equipment
- BLAZER_USB(8) - Driver for Megatec/Q1 protocol USB based UPS equipment
- blend_image(3) - Change image opacity.
- BLENDER(1) - a full-featured 3D application
- blib(3) - Use MakeMaker's uninstalled version of a package
- BLIND(7) - Collection of command line video editing utilities
- BLIND-ARITHM(1) - Perform simple arithmetic on a video
- BLIND-COLOUR-CIEXYZ(1) - Convert CIE XYZ for use with blind-single-colour(1)
- BLIND-COLOUR-SRGB(1) - Convert sRGB for use with blind-single-colour(1)
- BLIND-COMPRESS(1) - Compress a video for network transmission
- BLIND-CONCAT(1) - Concatenate videos
- BLIND-CROP(1) - Extract subframes for all frames
- BLIND-CUT(1) - Retain consecutive frames
- BLIND-DECOMPRESS(1) - Decompress a video compressed by blind-compress(1)
- BLIND-DISSOLVE(1) - Fade a video by chaning it's alpha channel
- BLIND-EXTEND(1) - Add margins to a video
- BLIND-FLIP(1) - Mirror a video vertically
- BLIND-FLOP(1) - Mirror a video horizontally
- BLIND-FROM-IMAGE(1) - Convert an image to a frame
- BLIND-FROM-TEXT(1) - Convert text to a video
- BLIND-FROM-VIDEO(1) - Converts a regular, cooked video to a blind video
- BLIND-GAUSS-BLUR(1) - Apply Gaussian blur to a video
- BLIND-INVERT-LUMA(1) - Invert the luminosity of a video
- BLIND-NEXT-FRAME(1) - Extracts the next frame from a video
- BLIND-READ-HEAD(1) - Reads the head from a video
- BLIND-REPEAT(1) - Repeat a video
- BLIND-REVERSE(1) - Reverse a video
- BLIND-REWRITE-HEAD(1) - Rewrite the head of a video
- BLIND-ROTATE-180(1) - Rotate a video 180 degrees
- BLIND-ROTATE-270(1) - Rotate a video 270 degrees clockwise
- BLIND-ROTATE-90(1) - Rotate a video 90 degrees clockwise
- BLIND-SET-ALPHA(1) - Multiply the alpha channel of a video
- BLIND-SET-LUMA(1) - Multiply the luminosity of a video
- BLIND-SET-SATURATION(1) - Multiply the saturation of a video
- BLIND-SINGLE-COLOUR(1) - Generate a single-colour video
- BLIND-SKIP-PATTERN(1) - Skips frames in a video according to pattern
- BLIND-SPLIT(1) - Split a video, by frame, into multiple videos
- BLIND-STACK(1) - Overlay videos
- BLIND-TIME-BLUR(1) - Draw new frames on top of old frames with partial alpha
- BLIND-TO-IMAGE(1) - Convert a frame to an image
- BLIND-TO-TEXT(1) - Convert a video to text
- BLIND-TO-VIDEO(1) - Converts blind video to a regular video
- BLIND-TRANSLATE(1) - Perform framewise translation of a video
- BLIND-TRANSPOSE(1) - Transpose a video
- BLIND-WRITE-HEAD(1) - Writes the head of a video
- blinkbox(6) - shows a ball inside a box.
- blit(3) - Copies a rectangular area from one bitmap to another. Allegro game programming library.
- blitspin(6) - rotate a bitmap in an interesting way
- BLITZ(1) - Securely transfer files between two workstations through NAT/Firewall.
- BLKCALC(1) - Converts between unallocated disk unit numbers and regular disk unit numbers.
- BLKCAT(1) - Display the contents of file system data unit in a disk image.
- BLKDISCARD(8) - discard sectors on a device
- BLKID(8) - locate/print block device attributes
- BLKLS(1) - List or output file system data units.
- BLKSTAT(1) - Display details of a file system data unit (i.e. block or sector)
- BLKZONE(8) - run zone command on a device
- BLOCK(1) - temporarily block delivery of events
- BLOCK(6) - a small text based maze game
- BLOCKATTACK(6) - a puzzle game inspired by Tetris Attack
- BLOCKDEV(8) - call block device ioctls from the command line
- BLOCKDIAG(1) - generate block-diagram image file from spec-text file.
- BLOCKLISTCTL(8) - display and change the state of the blocklistd database
- BLOCKLISTD(8) - block and release ports on demand to avoid DoS abuse
- BLOCKLISTD.CONF(5) - configuration file format for blocklistd
- BLOCKRAGE(6) - a falling-blocks arcade game
- blocktube(6) - draws a swirling, falling tunnel of reflective slabs
- Blog::Spam::API(3) - A description of Blog-Spam API.
- Blog::Spam::Plugin::00blacklist(3) - Reject comments from known-bad IP addresses.
- Blog::Spam::Plugin::00whitelist(3) - Always permit comments from some IP addresses.
- Blog::Spam::Plugin::badip(3) - Reject comments from known-bad IP addresses.
- Blog::Spam::Plugin::bayesian(3) - Bayesian analysis of submitted comments.
- Blog::Spam::Plugin::bogusip(3) - Reject comments from bogus IP addresses.
- Blog::Spam::Plugin::drone(3) - Lookup comment submissions in dronebl.org
- Blog::Spam::Plugin::dropme(3) - A plugin for self-dropping comments.
- Blog::Spam::Plugin::emailtests(3) - Reject email addresses which are bogus.
- Blog::Spam::Plugin::hashcash(3) - Block comments which have bogus Wordpress values
- Blog::Spam::Plugin::httpbl(3) - Lookup submitters in the HTTP;bl list
- Blog::Spam::Plugin::logger(3) - Log the contents of our messages.
- Blog::Spam::Plugin::lotsaurls(3) - Reject comments containing multiple URLs.
- Blog::Spam::Plugin::multilinks(3) - Reject opportunistic use of URLs.
- Blog::Spam::Plugin::rdns(3) - Reject content from hosts with no RDNS.
- Blog::Spam::Plugin::requiremx(3) - Reject email addresses to have an MX record.
- Blog::Spam::Plugin::Sample(3) - A sample plugin.
- Blog::Spam::Plugin::sfs(3) - Lookup comment submissions in stopforumspam.com
- Blog::Spam::Plugin::size(3) - Size-Test submitted comments.
- Blog::Spam::Plugin::stopwords(3) - Reject comments which contain known-bad words.
- Blog::Spam::Plugin::strong(3) - Block comments which have undue strong tags.
- Blog::Spam::Plugin::surbl(3) - Discard comments with surbl-listed URLs.
- Blog::Spam::Plugin::wordcount(3) - Discard comments with too few words.
- Blog::Spam::Server(3) - An RPC server which detects comment spam.
- blogbench(8) - a realistic filesystem benchmark
- BLOGSPAM(1) - An RPC server for testing blog comments
- Bloom::Filter(3) - Sample Perl Bloom filter implementation
- blow(1) - transfer data over a TCP connection
- BLOWFISH(3) - blowfish encryption
- blowfish(3) - Blowfish encryption
- BLS(8) - Bareos's 'Volume LS'
- intro(n) - Introduction to the BLT library
- blt(1) - Wrapper for all biolibc-tools subcommands
- blt chrom-lens(1) - blt chrom-lens Generates TSV (tab separated values) output containing chromosome names and lengths as required by kallisto and other tools. Since the lengths are taken directly from the FASTA...
- blt deromanize(1) - It was once a common practice to represent chromosome numbers as Roman numerals. This is no longer common, but files containing Roman numerals still exist. blt deromanize converts a column of Roman...
- blt ensemblid2gene(1) - blt ensemblid2gene reads a list of Ensembl IDs, one per line, and outputs them along with their associated gene name, in TSV (tab-separated-values) format. IDs should be genes, transcripts, or other...
- blt extract-seq(1) - blt extract-seq searches a GFF3 file for a feature of feature-type (e.g. gene, CDS, exon) and a substring of the attributes field. If found, extracts the sequence for that feature and all subfeatures...
- blt fasta2seq(1) - blt fasta2seq Converts fasta input to a raw sequence stream. I.e., it removes header lines and concatenates the sequence lines.
- blt fastq-derep.sh(1) - blt fastq-derep.sh removes replicates from a fastq file using fastq2tsv to reformat to tab-separated data for easier sorting, then using Unix sort and an awk script to remove adjacent entries with...
- blt fastx-derep(1) - blt fastx-derep remove replicates from a FASTA or FASTQ file by hashing each sequence and printing only records for which the hash has not previously been encountered.
- blt fastx2tsv(1) - Convert FASTA and FASTQ streams to TSV format
- blt find-orfs(1) - blt find-orfs locates start and stop codon sequences within a raw DNA or RNA sequence.
- blt gff3-to-bed(1) - blt gff3-to-bed converts GFF3 input to BED output. Currently it generates 6-column BED output with scores set to 0.
- blt vcf-downsample(1) - blt vcf-downsample Outputs a uniformly random sample of roughly desired-count VCF calls from the input. The strategy involves generating a random number which is compared to desired-count /...
- blt vcf-search(1) - blt vcf-search locates a given chromosome and position within a VCF file.
- Blt_Tree(3) - Tree data object.
- Blt_TreeCreate(3) - Create tree data object.
- Blt_TreeCreateNode(3) - Creates a node in a tree data object.
- Blt_TreeDeleteNode(3) - Deletes a node and its descendants.
- Blt_TreeExists(3) - Indicates if a tree exists.
- Blt_TreeGetNode(3) - Finds the node from the ID.
- Blt_TreeGetToken(3) - Grabs a token associated with existing tree data object.
- Blt_TreeName(3) - Returns the name of the tree data object.
- Blt_TreeNodeId(3) - Returns the node serial number.
- Blt_TreeReleaseToken(3) - Releases token associated with tree object.
- bltdebug(n) - print Tcl commands before execution
- bluecloth(1) - convert Markdown input to HTML
- BLUEFISH(1) - editor for experienced web designers and programmers
- BLUEGPS(1) - datalog download tool for Royaltek RBT-3000 GPS
- BLUETOOTH(3) - Bluetooth routines
- BLUETOOTH-CONFIG(8) - a script to manage config files for the bluetooth sub system
- BLUETOOTH.DEVICE.CONF(5) - Bluetooth device configuration file
- BLUETOOTH.HOSTS(5) - Bluetooth host name database
- BLUETOOTH.PROTOCOLS(5) - Bluetooth Protocol Service Multiplexor database
- BMC-DEVICE(8) - perform advanced BMC commands
- BMC-INFO(8) - display BMC information
- bmc-watchdog(8) - BMC watchdog timer daemon and control utility
- BMD(8) - bhyve management daemon
- BMD-PLUGIN-AVAHI(8) - publishes VM's vnc port via mDNS
- BMD-PLUGIN-HOOKCMD(8) - Spawns command when VM state is changed.
- BMD.CONF(5) - configuration file for bmd(8)
- bmdctl(8) - control utility for bhyve management daemon (bmd)
- BMF(1) - efficient Bayesian mail filter
- BMFCONV(1) - Database converter for bmf
- bmon(8) - bandwidth monitor and rate estimator
- BMORE(1) - browse through a binary file
- bmp_read_line(3) - Direct access bank switching line selection for reading. Allegro game programming library.
- bmp_unwrite_line(3) - Direct access bank switching line release. Allegro game programming library.
- bmp_write_line(3) - Direct access bank switching line selection for writing. Allegro game programming library.
- bmptopnm(1) - convert a BMP(DIB) file into a portable anymap
- bn(3) - multiprecision integer arithmetics
- BN_add(3) - arithmetic operations on BIGNUMs
- BN_ADD(3ossl) - arithmetic operations on BIGNUMs
- BN_add_word(3) - arithmetic functions on BIGNUMs with integers
- BN_ADD_WORD(3ossl) - arithmetic functions on BIGNUMs with integers
- BN_BN2BIN(3) - format conversions
- BN_BLINDING_new(3) - blinding related BIGNUM functions.
- BN_BLINDING_NEW(3ossl) - blinding related BIGNUM functions
- BN_bn2bin(3) - format conversions
- BN_BN2BIN(3ossl) - format conversions
- BN_cmp(3) - BIGNUM comparison and test functions
- BN_CMP(3ossl) - BIGNUM comparison and test functions
- BN_SWAP(3) - exchange BIGNUMs
- BN_copy(3) - copy BIGNUMs
- BN_COPY(3ossl) - copy BIGNUMs
- BN_CTX_new(3) - allocate and free BN_CTX structures
- BN_CTX_NEW(3ossl) - allocate and free BN_CTX structures
- BN_CTX_start(3) - use temporary BIGNUM variables
- BN_CTX_START(3ossl) - use temporary BIGNUM variables
- BN_generate_prime(3) - generate primes and test for primality
- BN_GENERATE_PRIME(3ossl) - generate primes and test for primality
- bn_internal(3) - BIGNUM library internal functions
- BN_KRONECKER(3) - Kronecker symbol
- BN_MOD_EXP_MONT(3ossl) - Montgomery exponentiation
- BN_mod_inverse(3) - compute inverse modulo n
- BN_MOD_INVERSE(3ossl) - compute inverse modulo n
- BN_mod_mul_montgomery(3) - Montgomery multiplication
- BN_MOD_MUL_MONTGOMERY(3ossl) - Montgomery multiplication
- BN_mod_mul_reciprocal(3) - modular multiplication using reciprocal
- BN_MOD_MUL_RECIPROCAL(3ossl) - modular multiplication using reciprocal
- BN_MOD_MUL_MONTGOMERY(3) - Montgomery multiplication
- BN_new(3) - allocate and free BIGNUMs
- BN_NEW(3ossl) - allocate and free BIGNUMs
- BN_num_bytes(3) - get BIGNUM size
- BN_NUM_BYTES(3ossl) - get BIGNUM size
- BN_rand(3) - generate pseudo-random number
- BN_RAND(3ossl) - generate pseudo-random number
- BN_SECURITY_BITS(3ossl) - returns bits of security based on given numbers
- BN_set_bit(3) - bit operations on BIGNUMs
- BN_SET_BIT(3ossl) - bit operations on BIGNUMs
- BN_SET_FLAGS(3) - enable and inspect flags on BIGNUM objects
- BN_SET_NEGATIVE(3) - change and inspect the sign of a BIGNUM
- BN_swap(3) - exchange BIGNUMs
- BN_SWAP(3ossl) - exchange BIGNUMs
- BN_ADD(3) - arithmetic operations on BIGNUMs
- BN_zero(3) - BIGNUM assignment operations
- BN_ZERO(3ossl) - BIGNUM assignment operations
- BNBOT(1) - Battle.net text-based chat bot client
- BNCFREQ(1) - Compute Information Content based on British National Corpus (World Edition)
- BNCHAT(1) - Battle.net text-based chat client
- BNETD(1) - Unix Battle.net daemon
- BNETD.CONF(5) - configuration for the Unix Battle.net daemon
- BNFTP(1) - Battle.net file transfer client
- BNI2TGA(1) - convert a Battle.net icon file to a Targa file
- BNIBUILD(1) - build a Battle.net icon file from a directory of Targa icon files
- BNIEXTRACT(1) - extract a directory of Targa icon files from a Battle.net icon file
- BNILIST(1) - list contents of a Battle.net icon file
- BNPASS(1) - bnetd password utility
- BNSTAT(1) - Battle.net statisics client
- bntext(5) - messages for the Unix Battle.net daemon
- BNPROXY(1) - bnetd tracking daemon
- BNXT(4) - Broadcom NetXtreme family 10Gb to 400Gb Ethernet driver
- bochs(1) - Portable x86 Emulator.
- bochs-dlx(1) - Runs DLX-Linux under the Bochs x86 Emulator
- bochsrc(5) - Configuration file for Bochs.
- body(n) - change the body for a class method/proc
- BOGGLE(6) - word search game
- BOGOFILTER(1) - fast Bayesian spam filter
- BOGOLEXER(1) - Utility program for separating email messages into tokens
- BOGOM(8) - simple sendmail milter to interface bogofilter
- BOGOSORT(1) - sorts or doesn't sort files or standard input
- BOGOTUNE(1) - find optimum parameter settings for bogofilter
- BOGOUPGRADE(1) - upgrades bogofilter database to current version
- BOGOUTIL(1) - Dumps, loads, and maintains bogofilter database files
- BOINCTUI(1) - Fullscreen text mode manager for BOINC client
- boing(6) - draws a bouncing ball like the ancient Amiga demo
- bombadillo(1) - a non-web browser
- BOMBARDMENT(1) - Run siege with an ever-increasing number of users
- bon_csv2html(1) - bon_csv2html program to convert CSV format Bonnie++ data to a HTML form using tables suitable for display on a web page. NB Lynx can't display this properly, and due to the size it probably requires...
- bond_target(3) - Setup a state transfer pipe between two targets.
- Bonds(1) - Example of bond pricing
- BONNIE(1) - Performance Test of Filesystem I/O
- bonnie++(8) - program to test hard drive performance.
- BOOG(1) - See the file man1/alc_origin.1.
- bookman(1) - Generate a book from man pages
- Bool(3) - Boolean values.
- boolean(3) - Boolean support for Perl
- BOOM(1) - See the file man1/alc_origin.1.
- BOOT(8) - system bootstrapping procedures
- BOOT.CONFIG(5) - Configuration file for the legacy boot blocks
- BOOT0CFG(8) - boot manager installation/configuration utility
- BOOT1.EFI(8) - UEFI chain loader
- BOOTPARAMD(8) - boot parameter server
- BOOTPARAMS(5) - boot parameter database
- BOOTPD(8) - Internet Boot Protocol server/gateway
- BOOTPEF(8) - BOOTP Extension File compiler
- BOOTPTAB(5) - Internet Bootstrap Protocol server database
- BOOTPTEST(8) - send BOOTP queries and print responses
- BOOTTRACE(4) - Boot-time, run-time, and shutdown-time tracing facility
- BOOTTRACE(8) - trace command execution with boottrace(4)
- Border::Style(3) - Border style structure
- Border::Style::Role(3) - Role for class wanting to support border styles
- BorderStyle(3) - Border styles
- BorderStyle::ASCII::None(3) - No borders, but row separator is still drawn using dashes
- BorderStyle::ASCII::SingleLine(3) - Single line border with ASCII characters
- BorderStyle::ASCII::SingleLineDoubleAfterHeader(3) - Just like ASCII::SingleLine but uses double line to separate header row and first data row
- BorderStyle::ASCII::SingleLineHorizontalOnly(3) - Single line border with ASCII characters, horizontal only
- BorderStyle::ASCII::SingleLineInnerOnly(3) - Single line border with ASCII characters, between columns only
- BorderStyle::ASCII::SingleLineOuterOnly(3) - Single line border with ASCII characters, outer borders only
- BorderStyle::ASCII::SingleLineVerticalOnly(3) - Single line border with ASCII characters, vertical only
- BorderStyle::ASCII::Space(3) - Space as borders, but data row separator is still drawn using dashes
- BorderStyle::ASCII::SpaceInnerOnly(3) - No borders, but columns are still separated using spaces and data row separator is still drawn using dashes
- BorderStyle::BoxChar::None(3) - No borders, but data row separator is still drawn using horizontal line
- BorderStyle::BoxChar::SingleLine(3) - Single line border with box-drawing characters
- BorderStyle::BoxChar::SingleLineHorizontalOnly(3) - Single line border with box-drawing characters, horizontal only
- BorderStyle::BoxChar::SingleLineInnerOnly(3) - Single line border with box-drawing characters, between columns only
- BorderStyle::BoxChar::SingleLineOuterOnly(3) - Single line border with box-drawing characters, outer borders only
- BorderStyle::BoxChar::SingleLineVerticalOnly(3) - Single line border with box-drawing characters, vertical only
- BorderStyle::BoxChar::Space(3) - Space as borders, but data row separator is still drawn using horizontal line
- BorderStyle::BoxChar::SpaceInnerOnly(3) - No borders, but columns are still separated using spaces and data row separator is still drawn using horizontal line
- BorderStyle::Test::CustomChar(3) - A border style that uses a single custom character
- BorderStyle::Test::Labeled(3) - A border style that uses labeled characters
- BorderStyle::Text::ANSITable::OldCompat::Default::bold(3) - UTF8::SingleLineBold border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::brick(3) - UTF8::Brick border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::bricko(3) - UTF8::BrickOuterOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::csingle(3) - UTF8::SingleLineCurved border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::double(3) - UTF8::DoubleLine border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::none_ascii(3) - ASCII::None border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::none_boxchar(3) - BoxChar::None border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::none_utf8(3) - UTF8::None border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::single_ascii(3) - ASCII::SingleLine border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::single_boxchar(3) - BoxChar::SingleLine border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::single_utf8(3) - UTF8::SingleLine border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleh_ascii(3) - ASCII::SingleLineHorizontalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleh_boxchar(3) - BoxChar::SingleLineHorizontalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleh_utf8(3) - UTF8::SingleLineHorizontalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlei_ascii(3) - ASCII::SingleLineInnerOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlei_boxchar(3) - BoxChar::SingleLineInnerOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlei_utf8(3) - UTF8::SingleLineInnerOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleo_ascii(3) - ASCII::SingleLineOuterOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleo_boxchar(3) - BoxChar::SingleLineOuterOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singleo_utf8(3) - UTF8::SingleLineOuterOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlev_ascii(3) - ASCII::SingleLineVerticalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlev_boxchar(3) - BoxChar::SingleLineVerticalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::singlev_utf8(3) - UTF8::SingleLineVerticalOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::space_ascii(3) - ASCII::Space border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::space_boxchar(3) - BoxChar::Space border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::space_utf8(3) - UTF8::Space border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::spacei_ascii(3) - ASCII::SpaceInnerOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::spacei_boxchar(3) - BoxChar::SpaceInnerOnly border style (with old name)
- BorderStyle::Text::ANSITable::OldCompat::Default::spacei_utf8(3) - UTF8::SpaceInnerOnly border style (with old name)
- BorderStyle::UTF8::Brick(3) - Single-line, bold on bottom right to give illusion of depth
- BorderStyle::UTF8::BrickOuterOnly(3) - Single-line (outer only), bold on bottom right to give illusion of depth
- BorderStyle::UTF8::DoubleLine(3) - Double-line border with UTF8 characters
- BorderStyle::UTF8::None(3) - No borders, but data row separator is still drawn using horizontal line
- BorderStyle::UTF8::SingleLine(3) - Single-line border with UTF8 characters
- BorderStyle::UTF8::SingleLineBold(3) - Bold single-line border with UTF8 characters
- BorderStyle::UTF8::SingleLineBoldHeader(3) - Single-line border (header box bold) with UTF8 characters
- BorderStyle::UTF8::SingleLineCurved(3) - Single-line border with UTF8 characters, curved edges
- BorderStyle::UTF8::SingleLineDoubleAfterHeader(3) - Just like UTF8::SingleLine but uses double line to separate header row and first data row
- BorderStyle::UTF8::SingleLineHorizontalOnly(3) - Single line border with box-drawing characters, horizontal only
- BorderStyle::UTF8::SingleLineInnerOnly(3) - Single line border with UTF8 characters, between columns only
- BorderStyle::UTF8::SingleLineOuterOnly(3) - Single line border with UTF8 characters, outer borders only
- BorderStyle::UTF8::SingleLineVerticalOnly(3) - Single line border with UTF8 characters, vertical only
- BorderStyle::UTF8::Space(3) - Space as borders, but data row separator is still drawn using horizontal line
- BorderStyle::UTF8::SpaceInnerOnly(3) - No borders, but columns are still separated using spaces and data row separator is still drawn using horizontal line
- BorderStyleBase(3) - A suitable base class for most BorderStyle::* modules
- BorderStyleBase::Constructor(3) - Provide new()
- BorderStyleRole::Source::ASCIIArt(3) - Get border characters from ASCII art
- BorderStyleRole::Source::Hash(3) - Get border characters from %CHARS (or @MULTI_CHARS) package variable
- BorderStyleRole::Spec::Basic(3) - Required methods for all BorderStyle::* modules
- BorderStyleRole::Transform::BoxChar(3) - Emit proper escape code to display box characters
- BorderStyleRole::Transform::InnerOnly(3) - Strip outer border characters
- BorderStyleRole::Transform::OuterOnly(3) - Strip inner border characters
- BorderStyles::Standard(3) - A standard collection of border styles
- BORG(1) - deduplicating and encrypting backup tool
- BORG-BENCHMARK(1) - benchmark command
- BORG-BENCHMARK-CRUD(1) - Benchmark Create, Read, Update, Delete for archives.
- BORG-BREAK-LOCK(1) - Break the repository lock (e.g. in case it was left by a dead borg.
- BORG-CHANGE-PASSPHRASE(1) - Change repository key file passphrase
- BORG-CHECK(1) - Check repository consistency
- BORG-COMMON(1) - Common options of Borg commands
- BORG-COMPACT(1) - compact segment files in the repository
- BORG-COMPRESSION(1) - Details regarding compression
- BORG-CONFIG(1) - get, set, and delete values in a repository or cache config file
- BORG-CREATE(1) - Create new archive
- BORG-DELETE(1) - Delete an existing repository or archives
- BORG-DIFF(1) - Diff contents of two archives
- BORG-EXPORT-TAR(1) - Export archive contents as a tarball
- BORG-EXTRACT(1) - Extract archive contents
- BORG-IMPORT-TAR(1) - Create a backup archive from a tarball
- BORG-INFO(1) - Show archive details such as disk space used
- BORG-INIT(1) - Initialize an empty repository
- BORG-KEY(1) - Manage a keyfile or repokey of a repository
- BORG-KEY-CHANGE-PASSPHRASE(1) - Change repository key file passphrase
- BORG-KEY-EXPORT(1) - Export the repository key for backup
- BORG-KEY-IMPORT(1) - Import the repository key from backup
- BORG-KEY-MIGRATE-TO-REPOKEY(1) - Migrate passphrase -> repokey
- BORG-LIST(1) - List archive or repository contents
- BORG-MOUNT(1) - Mount archive or an entire repository as a FUSE filesystem
- BORG-PATTERNS(1) - Details regarding patterns
- BORG-PLACEHOLDERS(1) - Details regarding placeholders
- BORG-PRUNE(1) - Prune repository archives according to specified rules
- BORG-RECREATE(1) - Re-create archives
- BORG-RENAME(1) - Rename an existing archive
- BORG-SERVE(1) - Start in server mode. This command is usually not used manually.
- BORG-UMOUNT(1) - un-mount the FUSE filesystem
- BORG-UPGRADE(1) - upgrade a repository from a previous version
- BORG-VERSION(1) - Display the borg client / borg server version
- BORG-WITH-LOCK(1) - run a user specified command with the repository lock held
- BORGFS(1) - Mount archive or an entire repository as a FUSE filesystem
- sh(1) - standard and job control shell and command interpreter
- BOSSKILL(8) - send a signal to your boss, or terminate your boss
- BOT-TRAINING(1) - Command-line interface Bot::Training
- Bot::BasicBot(3) - simple irc bot baseclass
- Bot::Training(3) - Plain text training material for bots like Hailo and AI::MegaHAL
- Bot::Training::MegaHAL(3) - Provide megahal.trn via Bot::Training
- Bot::Training::StarCraft(3) - Provide starcraft.trn via Bot::Training
- BOTAN(1) - Botan command line util
- bouboule(6) - draws spinning 3D blobs
- Boulder(3) - An API for hierarchical tag/value structures
- Boulder::Blast(3) - Parse and read BLAST files
- Boulder::Blast::NCBI(3) - Parse and read NCBI BLAST files
- Boulder::Blast::WU(3) - Parse and read WU-BLAST files
- Boulder::Genbank(3) - Fetch Genbank data records as parsed Boulder Stones
- Boulder::LocusLink(3) - Fetch LocusLink data records as parsed Boulder Stones
- Boulder::Medline(3) - Fetch Medline data records as parsed Boulder Stones
- Boulder::Omim(3) - Fetch Omim data records as parsed Boulder Stones
- Boulder::Store(3) - Simple persistent storage for Stone tag/value objects
- Boulder::Stream(3) - Read and write tag/value data from an input stream
- Boulder::String(3) - Read and write tag/value data from a string.
- Boulder::Swissprot(3) - Fetch SwissProt data records as parsed Boulder Stones
- Boulder::Unigene(3) - Fetch Unigene data records as parsed Boulder Stones
- Boulder::XML(3) - XML format input/output for Boulder streams
- BOUNCE(5) - Postfix bounce message template format
- BOUNCE(8) - Postfix delivery status reports
- BOUNCED(8) - Mailing List Bounce Processing Daemon for Sympa
- bouncesaying(1) - perhaps bounce each incoming message
- bouncingcow(6) - a happy cow on a trampoline in 3D. Moo.
- BOUNDARY_FOPEN(3) - read from a stream until a boundary string is matched
- BOX(1) - A language to create figures and graphics.
- boxed(6) - draws a box full of 3D bouncing balls that explode.
- boxes(1) - text mode box and comment drawing filter
- boxfit(6) - fills space with a gradient of growing boxes or circles.
- BOXRUN(1) - sandboxed command execution using FreeBSD jails
- boxsym-rnd(1) - generate box shaped symbol(s)
- boxsym-rnd(5) - boxsym description syntax
- BOZOHTTPD(8) - hyper text transfer protocol version 1.1 daemon
- BP_AACOMP(1) - amino acid composition of protein sequences
- BP_BIOFETCH_GENBANK_PROXY(1) - Caching BioFetch-compatible web proxy for GenBank
- BP_BIOFLAT_INDEX(1) - index sequence files using Bio::DB::Flat
- BP_BIOGETSEQ(1) - sequence retrieval using OBDA registry
- BP_DBSPLIT(1) - script to split an input set of database(s) into smaller pieces
- BP_DOWNLOAD_QUERY_GENBANK(1) - script to query Genbank and retrieve records
- BP_EXTRACT_FEATURE_SEQ(1) - extract the corresponding sequence for a specified feature type
- BP_FASTAM9_TO_TABLE(1) - turn FASTA -m 9 output into NCBI -m 9 tabular output
- BP_FETCH(1) - fetches sequences from bioperl indexed databases
- BP_FILTER_SEARCH(1) - filters searchio results, outputting a tab delimited summary
- BP_FIND-BLAST-MATCHES(1) - extract DNA sequences based on BLAST hits
- BP_FLANKS(1) - finding flanking sequences for a variant in a sequence position
- BP_GCCALC(1) - GC content of nucleotide sequences
- BP_GENBANK2GFF3(1) - Genbank->gbrowse-friendly GFF3
- BP_INDEX(1) - indexes files for use by bp_fetch.pl
- BP_LOCAL_TAXONOMYDB_QUERY(1) - query a local TaxonomyDB for species or taxonid
- BP_MAKE_MRNA_PROTEIN(1) - Convert an input mRNA/cDNA sequence into protein
- BP_MASK_BY_SEARCH(1) - mask sequence(s) based on its alignment results
- BP_MRTRANS(1) - implement a transformer of alignments from protein to mrna coordinates
- BP_MUTATE(1) - randomly mutagenize a single protein or DNA sequence
- BP_NEXUS2NH(1) - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
- BP_NRDB(1) - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
- BP_OLIGO_COUNT(1) - oligo count and frequency
- BP_PROCESS_GADFLY(1) - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
- BP_PROCESS_SGD(1) - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
- BP_QUERY_ENTREZ_TAXA(1) - query Entrez taxonomy database and print out information
- BP_REVTRANS-MOTIF(1) - Reverse translate a Profam-like protein motif
- BP_SEARCH2ALNBLOCKS(1) - Turn SearchIO parseable reports(s) into a set of aligned blocks
- BP_SEARCH2GFF(1) - turn a SearchIO report into GFF
- BP_SEARCH2TABLE(1) - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
- BP_SEARCH2TRIBE(1) - Turn SearchIO parseable reports(s) into TRIBE matrix
- BP_SEQ_LENGTH(1) - lists the number of bases and number of sequences in specified sequence database files
- BP_SEQCONVERT(1) - generic BioPerl sequence format converter
- BP_SEQCUT(1) - cut FASTA sequences with a given range
- BP_SEQPART(1) - Takes one or more sequence files and splits them into a number of load balanced files.
- BP_SEQRET(1) - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
- BP_SEQRETSPLIT(1) - split a sequence (or stream) into a single file per sequence
- BP_SPLIT_SEQ(1) - splits a sequence into equal sized chunks with an optional overlapping range
- BP_SREFORMAT(1) - convert sequence formats
- BP_TAXID4SPECIES(1) - simple script which returns the NCBI Taxonomic id for a requested species
- BP_TAXONOMY2TREE(1) - Building a taxonomic tree based on the full lineages of a set of species names
- BP_TRANSLATE_SEQ(1) - translates a sequence
- BP_TREE2PAG(1) - convert Bio::TreeIO parseable format trees to pagel format
- BP_UNFLATTEN_SEQ(1) - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
- bpatch(1) - binary patch and dump file utility
- BPF(4) - Berkeley Packet Filter
- BPF(9) - Berkeley Packet Filter
- bpkg(1) - package dependency manager
- bpkg-argument-grouping(1) - argument grouping facility
- bpkg-cfg-create(1) - create configuration
- bpkg-cfg-info(1) - print configuration information
- bpkg-cfg-link(1) - link configuration
- bpkg-cfg-unlink(1) - unlink configuration
- bpkg-common-options(1) - details on common options
- bpkg-default-options-files(1) - specifying default options
- bpkg-help(1) - show help for a command or help topic
- bpkg-pkg-build(1) - build package
- bpkg-pkg-checkout(1) - check out package version
- bpkg-pkg-clean(1) - clean package
- bpkg-pkg-configure(1) - configure package
- bpkg-pkg-disfigure(1) - disfigure package
- bpkg-pkg-drop(1) - drop package
- bpkg-pkg-fetch(1) - fetch package archive
- bpkg-pkg-install(1) - install package
- bpkg-pkg-purge(1) - purge package
- bpkg-pkg-status(1) - print package status
- bpkg-pkg-test(1) - test package
- bpkg-pkg-uninstall(1) - uninstall package
- bpkg-pkg-unpack(1) - unpack package archive
- bpkg-pkg-update(1) - update package
- bpkg-pkg-verify(1) - verify package archive
- bpkg-rep-add(1) - add repository to configuration
- bpkg-rep-create(1) - create repository
- bpkg-rep-fetch(1) - fetch list of available packages
- bpkg-rep-info(1) - print repository information
- bpkg-rep-list(1) - list repositories in configuration
- bpkg-rep-remove(1) - remove repository from configuration
- bpkg-repository-signing(1) - how to sign repository
- bpkg-repository-types(1) - repository types, structure, and URLs
- bpluginfo(8) - Bareos Plugin information utility
- BPRINTF(1) - formatted output with named arguments
- BPYTHON(1) - a fancy {curtsies, curses, urwid} interface to the Python interactive interpreter
- BPYTHON-CONFIG(5) - user configuration file for bpython
- Brackup(3) - Flexible backup tool. Slices, dices, encrypts, and sprays across the net.
- BRACKUP(1) - do a backup using Brackup
- BRACKUP-MOUNT(1) - mount a backup as a filesystem using FUSE
- BRACKUP-RESTORE(1) - The brackup restore tool.
- BRACKUP-TARGET(1) - Manage your backup targets
- BRACKUP-VERIFY-INVENTORY(1) - utility to validate brackup inventory entries against the target
- Brackup::Chunker::MP3(3) - an mp3-aware file chunker
- Brackup::Config(3) - configuration parsing/etc
- Brackup::Dict::Null(3) - noop key-value dictionary implementation, discarding everything it receives
- Brackup::Dict::SQLite(3) - key-value dictionary implementation, using a SQLite database for storage
- Brackup::Dict::SQLite2(3) - key-value dictionary implementation, using a SQLite database for storage (lighter/slower version of Brackup::Dict::SQLite)
- Brackup::DigestCache(3) - cache digests of file and chunk contents
- Brackup::InventoryDatabase(3) - track what chunks are already on a target
- Brackup::Manual::Overview(3) - how Brackup works, and how to use it
- Brackup::Mount(3) - Mount a backup as a usable filesystem using FUSE
- Brackup::Root(3) - describes the source directory (and options) for a backup
- Brackup::Target(3) - describes the destination for a backup
- Brackup::Target::Amazon(3) - backup to Amazon's S3 service
- Brackup::Target::CloudFiles(3) - backup to Rackspace's CloudFiles Service
- Brackup::Target::Filesystem(3) - backup to a locally mounted filesystem
- Brackup::Target::Ftp(3) - backup to an FTP server
- Brackup::Target::GoogleAppEngine(3) - backup to the App Engine target server
- Brackup::Target::Riak(3) - backup to a Riak key-value store
- Brackup::Target::Sftp(3) - backup to an SSH/SFTP server
- braid(6) - draws random color-cycling braids around a circle
- BRAND.4TH(8) - FreeBSD ASCII art boot module
- BRANDELF(1) - mark an ELF binary for a specific ABI
- Brannigan(3) - Comprehensive, flexible system for validating and parsing input, mainly targeted at web applications.
- Brannigan::Examples(3) - Example schemes, input and output for Brannigan.
- Brannigan::Tree(3) - A Brannigan validation/parsing scheme tree, possibly built from a series of inherited schemes.
- Brannigan::Validations(3) - Built-in validation methods for Brannigan.
- BRASERO(1) - Simple and easy to use CD/DVD burning application for the Gnome Desktop
- brave-browser(1) - Brave Browser
- BREAD(3) - read and write blocks of a UFS file system
- Bread::Board(3) - A solderless way to wire up your application components
- Bread::Board::BlockInjection(3) - service instantiated via custom subroutine
- Bread::Board::ConstructorInjection(3) - service instantiating objects via a constructor
- Bread::Board::Container(3) - A container for services and other containers
- Bread::Board::Container::FromParameterized(3) - container with weak parent reference
- Bread::Board::Container::Parameterized(3) - A parameterized container
- Bread::Board::Declare(3) - create Bread::Board containers as normal Moose objects
- Bread::Board::Declare::BlockInjection(3) - subclass of Bread::Board::BlockInjection for Bread::Board::Declare
- Bread::Board::Declare::ConstructorInjection(3) - subclass of Bread::Board::ConstructorInjection for Bread::Board::Declare
- Bread::Board::Declare::Literal(3) - subclass of Bread::Board::Literal for Bread::Board::Declare
- Bread::Board::Declare::Meta::Role::Attribute(3) - base attribute metarole for Bread::Board::Declare
- Bread::Board::Declare::Meta::Role::Attribute::Container(3) - attribute metarole for container attributes in Bread::Board::Declare
- Bread::Board::Declare::Meta::Role::Attribute::Service(3) - attribute metarole for service attributes in Bread::Board::Declare
- Bread::Board::Declare::Meta::Role::Class(3) - class metarole for Bread::Board::Declare
- Bread::Board::Declare::Meta::Role::Instance(3) - Bread::Board::Declare::Meta::Role::Instance
- Bread::Board::Declare::Role::Object(3) - Bread::Board::Declare::Role::Object
- Bread::Board::Declare::Role::Service(3) - role for Bread::Board::Service objects
- Bread::Board::Dependency(3) - dependency for a service
- Bread::Board::Dumper(3) - Pretty printer for visualizing the layout of your Bread::Board
- Bread::Board::LifeCycle(3) - base lifecycle role
- Bread::Board::LifeCycle::Singleton(3) - service role for singleton lifecycle
- Bread::Board::LifeCycle::Singleton::WithParameters(3) - singleton lifecycle role for a parameterized service
- Bread::Board::Literal(3) - service providing a literal value
- Bread::Board::Manual(3) - A manual for Bread::Board
- Bread::Board::Manual::Concepts(3) - An overview of the concepts in Bread::Board
- Bread::Board::Manual::Concepts::Advanced(3) - An overview of some of the more advanced Bread::Board concepts
- Bread::Board::Manual::Concepts::Typemap(3) - An overview of the typemapping feature
- Bread::Board::Manual::Example(3) - A set of examples of Bread::Board usage
- Bread::Board::Manual::Example::FormSensible(3) - A Form::Sensible and Catalyst example.
- Bread::Board::Manual::Example::LogDispatch(3) - An example of composing a dynamic Log::Dispatch object.
- Bread::Board::Service(3) - Base service role
- Bread::Board::Service::Alias(3) - aliases another service
- Bread::Board::Service::Deferred(3) - Helper for holding a service that is not quite constructed yet
- Bread::Board::Service::Deferred::Thunk(3) - Helper for using services with incomplete parameters
- Bread::Board::Service::Inferred(3) - Helper for inferring a service from a Moose object
- Bread::Board::Service::WithClass(3) - role for services returning instances of a given class
- Bread::Board::Service::WithConstructor(3) - Bread::Board::Service::WithConstructor
- Bread::Board::Service::WithDependencies(3) - Services with dependencies
- Bread::Board::Service::WithParameters(3) - Services with parameters
- Bread::Board::SetterInjection(3) - service instantiating objects via setter functions
- Bread::Board::Traversable(3) - role for traversing a container service tree
- Bread::Board::Types(3) - types and coercions for Bread::Board
- break(n) - Abort looping command
- BREAKPOINT(1) - launch debug mode
- BRECV(3) - receives data from a bytestream socket
- BRECVL(3) - receives data from a bytestream socket
- breduce(1) - read a portable bitmap and reduce it to 1/N
- BREGEX(1) - Bareos's 'regex' engine
- BREGEX(8) - Bacula's 'regex' engine
- BRISTOL(1) - a synthesiser emulation package.
- BRISTOLJACKSTATS(1) - ancillary program for bristol
- BRK(2) - change data segment size
- broadcast_dialog_message(3) - Broadcasts a message to all the objects in the active dialog. Allegro game programming library.
- BROADWAYD(1) - Broadway display server
- broot(1) - Tree view, file manager, configurable launcher
- brotli(1) - brotli, brcat, unbrotli - compress or decompress files
- BROWNFREQ(1) - Compute Information Content from the Brown Corpus
- BROWSER(1) - File manager and image viewer
- Browser::Open(3) - open a browser in a given URL
- BRRRIP(1) - rip SNES BRR sound samples
- bruteblock(8) - utility to block bruteforce attacks
- brz(1) - Breezy next-generation distributed version control
- BS(6) - battleships game
- BS::Event(3) - A class that provides an event callback interface
- BSb_back_solve(3) - Backward triangular matrix solution on a block of right hand sides
- BSb_backward(3) - Backward triangular matrix multiplication on a block of vectors
- BSb_for_solve(3) - Forward triangular matrix solution on a block of vectors
- BSb_forward(3) - Forward triangular matrix multiplication on a block of vectors
- BSback_solve(3) - Backward triangular matrix solution on a single vector
- BSback_solve1(3) - Backward triangular matrix solution on a single vector
- BSbackward(3) - Backward triangular matrix multiplication on a single vector
- BSbackward1(3) - Backward triangular matrix multiplication on a single vector
- BSbjacobi(3) - Apply the block Jacobi preconditioner
- BSCAN(8) - Bareos's 'Scan volumes'
- BScopy_nz(3) - Copy the nonzero values from one matrix to another
- BScopy_par_mat(3) - Create of copy of a matrix
- BScreate_ctx(3) - Create the execution time context for the package
- BSCRYPTO(8) - Bareos's 'SCSI Crypto'
- BSctx_print(3) - Print out the current state of the context.
- BSctx_set_cs(3) - Set the maximum clique size allowed
- BSctx_set_ct(3) - Set the type of coloring
- BSctx_set_err(3) - Set the type of error checking
- BSctx_set_guess(3) - Set whether to use zero as the initial vector for the iterative method or use the values given in the vector passed to the iterative method.
- BSctx_set_id(3) - Set the processor id
- BSctx_set_is(3) - Set the maximum i-node size allowed
- BSctx_set_max_it(3) - Set the maximum number of iterations to be allowed by the iterative solver.
- BSctx_set_method(3) - Set the iterative method to be used.
- BSctx_set_np(3) - Set the number of processors
- BSctx_set_num_rhs(3) - Set the number of RHSs to be solved for.
- BSctx_set_pr(3) - Set whether information on reordering should be printed
- BSctx_set_pre(3) - The preconditioner to be used by the iterative solver.
- BSctx_set_print_log(3) - Set whether logging information is printed
- BSctx_set_ps(3) - Set the processor set
- BSctx_set_restart(3) - Set the number of vectors stored by GMRES
- BSctx_set_rt(3) - Set whether information for fast future permutations
- BSctx_set_scaling(3) - Set whether or not the linear system should solved or not.
- BSctx_set_si(3) - Set whether or not inodes and cliques will be found
- BSctx_set_tol(3) - Set the relative residual tolerance for the iterative method.
- BSD(n) - Tcl interface to various BSD UNIX functions
- BSD.ARDUINO.MK(7) - build Arduino sketches with make(1)
- BSD.SNMPMOD.MK(7) - building modules for bsnmpd(1)
- BSD::devstat(3) - interface to devstat(3) API
- BSD::getloadavg(3) - Perl Interface to getloadavg (3)
- Process(3) - Information about running processes on BSD platforms
- Resource(3) - BSD process resource limit and priority functions
- stat(3) - stat() with BSD 4.4 extentions
- Sysctl(3) - Manipulate kernel sysctl variables on BSD-like systems
- BSDCAT(1) - expand files to standard output
- BSDCONFIG(8) - system configuration utility
- bsdconv(3) - Perl extension for bsdconv library
- BSDCRASHTAR(8) - archive kernel crash files
- BSDDIALOG(1) - TUI dialogs
- BSDDIALOG(3) - TUI dialogs
- BSDE_GET_RULE(3) - file system firewall rules list management
- BSDE_GET_RULE_COUNT(3) - file system firewall statistics
- BSDE_PARSE_RULE(3) - parse file system firewall rules
- BSDE_RULE_TO_STRING(3) - convert a ugidfw rule into its text representation
- BSDEBFETCH(1) - Prints short info about *BSD.
- BSDFAN(1) - a simple utility to manage thinkpads fan on FreeBSD
- BSDHWMON(8) - hardware sensor monitoring utility
- BSDIFF(1) - generate a patch between two binary files
- BSDINSTALL(8) - system installer
- BSDISKS(8) - daemon implementing the UDisks2 service
- BSDISKS.CONF(5) - configuration file for the bsdisks utility
- bsdl2jtag(1) - UrJTAG declaration file conversion
- BSDLABEL(8) - read and write BSD label
- BSDUNZIP(1) - extract files from a ZIP archive
- BSEARCH(1) - manages one-time passwords
- BSEARCH(3) - binary search of a sorted table
- BSeasy_A(3) - Given A in a standard numerical format, construct the sparse A that we need for BlockSolve. This routine is particularly useful for matrices created in Fortran. The rows on a processor must be...
- BSEND(3) - sends data to a socket
- BSENDL(3) - sends data to a socket
- bsetbg(1) - utility to manipulate the appearance of the X11 desktop's root window.
- bsetroot(1) - blackbox utility to change root window appearance
- BSfactor(3) - Compute the incomplete factor of a matrix
- BSfinalize(3) - Finalizes BlockSolve and MPI. Prints the log stuff if MLOG was defined.
- BSfor_solve(3) - Forward triangular matrix solution on a single vector
- BSfor_solve1(3) - Forward triangular matrix solution on a single vector
- BSforward(3) - Forward triangular matrix multiplication on a single vector
- BSforward1(3) - Forward triangular matrix multiplication on a single vector
- BSfree_comm(3) - Free the compiled communication pattern
- BSfree_copy_par_mat(3) - Free a copy of a sparse matrix (parallel format)
- BSfree_ctx(3) - Free the context
- BSfree_easymat(3) - Free a sparse matrix allocated in BSeasy_mat
- BSfree_off_map(3) - Free an offset mapping
- BSfree_par_mat(3) - Free a sparse matrix (parallel format)
- BSfree_reperm(3) - Free the reperm data structure
- BSfree_spmat(3) - Free a sparse matrix (original format)
- BSfreeg2l(3) - Free a global to local mapping
- BSfreel2g(3) - Free a local to global mapping
- BSget_diag(3) - Retrieve the diagonal of the matrix
- BSglob2loc(3) - Map global row numbers to local row numbers
- BSglob2proc(3) - Map global row numbers to processor id's
- BSglobal_flops(3) - Returns the global number of flops accumulated by BlockSolve
- BSglobal_nnz(3) - Returns the global number of nonzeros
- BSglobal_num_cliques(3) - Returns the global number of cliques
- BSglobal_num_inodes(3) - Returns the global number of i-nodes
- BSinit(3) - Initializes BlockSolve and MPI. BSinit() calls MPI_Init() if it has not already been called.
- BSinv_diag_block(3) - Invert the dense diagonal blocks of the matrix
- BSloc2glob(3) - Map local row numbers to global row numbers
- BSlocal_flops(3) - Returns the number of flops accumulated by BlockSolve
- BSlocal_nnz(3) - Returns the local number of nonzeros
- BSlocal_num_cliques(3) - Returns the local number of cliques
- BSlocal_num_inodes(3) - Returns the local number of i-nodes
- BSmain_perm(3) - Permute the matrix for efficient parallel execution
- BSmain_reperm(3) - Permute the sparse matrix using data structures generated by BSmain_perm on the same matrix structure
- BSmake_off_map(3) - Generate a mapping from global rows to processor id
- BSmat_subtract(3) - Subtract shift*B from A
- BSMTP(1) - Bareos's SMTP client (mail submission program)
- BSMTRACE(1) - host-based IDS based on OpenBSM
- BSMTRACE.CONF(5) - configuration file for bsmtrace
- bsnmp-regex(8) - an SNMP module which produces counters from logs or other text
- bsnmp-regex.conf(5) - the configuration file for the bsnmp-regex(8) module.
- bsnmp-ucd(8) - an SNMP module which implements parts of UCD-SNMP-MIB.
- BSNMPAGENT(3) - SNMP agent library
- BSNMPCLIENT(3) - SNMP client library
- BSNMPD(1) - simple and extensible SNMP daemon
- BSNMPGET(1) - simple tools for querying SNMP agents
- BSNMPLIB(3) - SNMP decoding and encoding library
- BSnum_colors(3) - Returns the number of colors
- bsod(6) - Blue Screen of Death emulator
- BSoffset(3) - Find a consistent global numbering
- BSON(3) - BSON serialization and deserialization (EOL)
- BSON::Array(3) - BSON type wrapper for a list of elements
- BSON::Binary(3) - Legacy BSON type wrapper for binary data (DEPRECATED)
- BSON::Bool(3) - Legacy BSON type wrapper for Booleans (DEPRECATED)
- BSON::Bytes(3) - BSON type wrapper for binary byte strings
- BSON::Code(3) - BSON type wrapper for Javascript code
- BSON::DBPointer(3) - Legacy BSON type wrapper for DBPointer data (DEPRECATED)
- BSON::DBRef(3) - BSON type wrapper for MongoDB DBRefs
- BSON::Decimal128(3) - BSON type wrapper for Decimal128
- BSON::Doc(3) - BSON type wrapper for ordered documents
- BSON::Double(3) - BSON type wrapper for Double
- BSON::Int32(3) - BSON type wrapper for Int32
- BSON::Int64(3) - BSON type wrapper for Int64
- BSON::MaxKey(3) - BSON type wrapper for MaxKey
- BSON::MinKey(3) - BSON type wrapper for MinKey
- BSON::ObjectId(3) - Legacy BSON type wrapper for Object IDs (DEPRECATED)
- BSON::OID(3) - BSON type wrapper for Object IDs
- BSON::PP(3) - Pure Perl BSON implementation
- BSON::Raw(3) - BSON type wrapper for pre-encoded BSON documents
- BSON::Regex(3) - BSON type wrapper for regular expressions
- BSON::String(3) - BSON type wrapper for strings
- BSON::Symbol(3) - BSON type wrapper for symbol data (DEPRECATED)
- BSON::Time(3) - BSON type wrapper for date and time
- BSON::Timestamp(3) - BSON type wrapper for timestamps
- BSON::Types(3) - Helper functions to wrap BSON type classes
- BSON::XS(3) - XS implementation of MongoDB's BSON serialization (EOL)
- BSON_ALIGNED_ALLOC(3) - This is a portable aligned_alloc() wrapper.
- BSON_ALIGNED_ALLOC0(3) - This is a portable aligned_alloc() wrapper that also sets the memory to zero.
- BSON_APPEND_ARRAY(3) - The bson_append_array() function shall append array to bson using the specified key. The type of the field will be an array, but it is the responsibility of the caller to ensure that the keys of...
- BSON_APPEND_ARRAY_BEGIN(3) - The bson_append_array_begin() function shall begin appending an array field to bson. This allows for incrementally building a sub-array. Doing so will generally yield better performance as you will...
- BSON_APPEND_ARRAY_END(3) - The bson_append_array_end() function shall complete the appending of an array field started with bson_append_array_begin(). child is invalid after calling this function.
- BSON_APPEND_BINARY(3) - The bson_append_binary() function shall append a new element to bson containing the binary data provided.
- BSON_APPEND_BOOL(3) - The bson_append_bool() function shall append a new element to bson containing the boolean provided.
- BSON_APPEND_CODE(3) - The bson_append_code() function shall append a new element to bson using the UTF-8 encoded javascript provided. javascript must be a NULL terminated C string.
- BSON_APPEND_CODE_WITH_SCOPE(3) - The bson_append_code_with_scope() function shall perform like bson_append_code() except it allows providing a scope to the javascript function in the form of a bson document.
- BSON_APPEND_DATE_TIME(3) - The bson_append_date_time() function shall append a new element to a bson document containing a date and time with no timezone information. value is assumed to be in UTC format of milliseconds since...
- BSON_APPEND_DBPOINTER(3) - WARNING:
- BSON_APPEND_DECIMAL128(3) - The bson_append_decimal128() function shall append a new element to bson containing a Decimal 128.
- BSON_APPEND_DOCUMENT(3) - The bson_append_document() function shall append child to bson using the specified key. The type of the field will be a document.
- BSON_APPEND_DOCUMENT_BEGIN(3) - The bson_append_document_begin() function shall begin appending a sub-document to bson. Use child to add fields to the sub-document. When completed, call bson_append_document_end() to complete the...
- BSON_APPEND_DOCUMENT_END(3) - The bson_append_document_end() function shall complete the appending of a document with bson_append_document_begin(). child is invalid after calling this function.
- BSON_APPEND_DOUBLE(3) - The bson_append_double() function shall append a new element to a bson document of type double.
- BSON_APPEND_INT32(3) - The bson_append_int32() function shall append a new element to bson containing a 32-bit signed integer.
- BSON_APPEND_INT64(3) - The bson_append_int64() function shall append a new element to bson containing a 64-bit signed integer.
- BSON_APPEND_ITER(3) - Appends the value at the current position of iter to the document.
- BSON_APPEND_MAXKEY(3) - The bson_append_maxkey() function shall append an element of type BSON_TYPE_MAXKEY to a bson document. This is primarily used in queries and unlikely to be used when storing a document to MongoDB.
- BSON_APPEND_MINKEY(3) - The bson_append_minkey() function shall append an element of type BSON_TYPE_MINKEY to a bson document. This is primarily used in queries and unlikely to be used when storing a document to MongoDB.
- BSON_APPEND_NOW_UTC(3) - The bson_append_now_utc() function is a helper to get the current date and time in UTC and append it to bson as a BSON_TYPE_DATE_TIME element.
- BSON_APPEND_NULL(3) - The bson_append_null() function shall append a new element to bson of type BSON_TYPE_NULL.
- BSON_APPEND_OID(3) - The bson_append_oid() function shall append a new element to bson of type BSON_TYPE_OID. oid MUST be a pointer to a bson_oid_t.
- BSON_APPEND_REGEX(3) - Appends a new field to bson of type BSON_TYPE_REGEX. regex should be the regex string. options should contain the options for the regex.
- BSON_APPEND_REGEX_W_LEN(3) - Appends a new field to bson of type BSON_TYPE_REGEX. regex should be the regex string. options should contain the options for the regex.
- BSON_APPEND_SYMBOL(3) - Appends a new field to bson of type BSON_TYPE_SYMBOL. This BSON type is deprecated and should not be used in new code.
- BSON_APPEND_TIME_T(3) - The bson_append_time_t() function is a helper that takes a time_t instead of milliseconds since the UNIX epoch.
- BSON_APPEND_TIMESTAMP(3) - This function is not similar in functionality to bson_append_date_time(). Timestamp elements are different in that they include only second precision and an increment field.
- BSON_APPEND_TIMEVAL(3) - The bson_append_timeval() function is a helper that takes a struct timeval instead of milliseconds since the UNIX epoch.
- BSON_APPEND_UNDEFINED(3) - The bson_append_undefined() function shall append a new element to bson of type BSON_TYPE_UNDEFINED. Undefined is common in Javascript. However, this element type is deprecated and should not be used...
- BSON_APPEND_UTF8(3) - The bson_append_utf8() function shall append a UTF-8 encoded string to bson.
- BSON_APPEND_VALUE(3) - Appends a new field to bson by determining the boxed type in value. This is useful if you want to copy fields between documents but do not know the field type until runtime.
- BSON_ARRAY_AS_CANONICAL_EXTENDED_JSON(3) - bson_array_as_canonical_extended_json() encodes bson as a UTF-8 string in Canonical Extended JSON. The outermost element is encoded as a JSON array ([ ... ]), rather than a JSON document ({ ... })....
- BSON_ARRAY_AS_JSON(3) - bson_array_as_json() encodes bson as a UTF-8 string using libbson's Legacy Extended JSON. The outermost element is encoded as a JSON array ([ ... ]), rather than a JSON document ({ ... }).
- BSON_ARRAY_AS_LEGACY_EXTENDED_JSON(3) - bson_array_as_legacy_extended_json() encodes bson as a UTF-8 string using libbson's Legacy Extended JSON. The outermost element is encoded as a JSON array ([ ... ]), rather than a JSON document ({...
- BSON_ARRAY_AS_RELAXED_EXTENDED_JSON(3) - bson_as_relaxed_extended_json() encodes bson as a UTF-8 string in the Relaxed Extended JSON. The outermost element is encoded as a JSON array ([ ... ]), rather than a JSON document ({ ... }). See...
- BSON_ARRAY_BUILDER_T(3)
- BSON_AS_CANONICAL_EXTENDED_JSON(3) - bson_as_canonical_extended_json() encodes bson as a UTF-8 string in the Canonical Extended JSON. See MongoDB Extended JSON format for a description of Extended JSON formats.
- BSON_AS_JSON(3) - bson_as_json() encodes bson as a UTF-8 string using libbson's Legacy Extended JSON.
- BSON_AS_JSON_WITH_OPTS(3) - bson_as_json_with_opts() encodes bson as a UTF-8 string in the MongoDB Extended JSON format or libbson's Legacy Extended JSON.
- BSON_AS_LEGACY_EXTENDED_JSON(3) - bson_as_legacy_extended_json() encodes bson as a UTF-8 string using libbson's Legacy Extended JSON. This function is superseded by bson_as_canonical_extended_json() and...
- BSON_AS_RELAXED_EXTENDED_JSON(3) - bson_as_relaxed_extended_json() encodes bson as a UTF-8 string in Relaxed Extended JSON. See MongoDB Extended JSON format for a description of Extended JSON formats.
- BSON_ASCII_STRTOLL(3) - A portable version of strtoll().
- BSON_CHARACTER_AND_STRING_ROUTINES(3)
- BSON_CHECK_VERSION(3) - Check at runtime if this release of libbson meets a required version.
- BSON_COMPARE(3) - The bson_compare() function shall compare two bson documents for equality.
- BSON_CONCAT(3) - The bson_concat() function shall append the contents of src to dst.
- BSON_CONTEXT_DESTROY(3) - The bson_context_destroy() function shall release all resources associated with context. Does nothing if context is NULL.
- BSON_CONTEXT_GET_DEFAULT(3)
- BSON_CONTEXT_NEW(3) - Creates a new bson_context_t. This is rarely needed as bson_context_get_default() serves most use-cases.
- BSON_CONTEXT_T(3) - The bson_context_t structure is context for generation of BSON Object IDs. This context allows overriding behavior of generating ObjectIDs. The flags BSON_CONTEXT_NONE, BSON_CONTEXT_THREAD_SAFE, and...
- BSON_COPY(3) - The bson_copy() function shall copy the contents of a bson document into a new bson_t.
- BSON_COPY_TO(3) - The bson_copy_to() function shall initialize dst with a copy of the contents of src.
- BSON_COPY_TO_EXCLUDING(3) - The bson_copy_to_excluding() function shall copy all fields from src to dst except those specified by the variadic, NULL terminated list of keys starting from first_exclude.
- BSON_COPY_TO_EXCLUDING_NOINIT(3) - The bson_copy_to_excluding_noinit() function shall copy all fields from src to dst except those specified by the variadic, NULL terminated list of keys starting from first_exclude. Works the same way...
- BSON_COPY_TO_EXCLUDING_NOINIT_VA(3) - The bson_copy_to_excluding_noinit_va() function shall copy all fields from src to dst except those specified by first_exclude and args.
- BSON_COUNT_KEYS(3) - The bson_count_keys() function shall count the number of elements within bson.
- BSON_DECIMAL128_FROM_STRING(3) - Parses the string containing ascii encoded Decimal128 and initialize the bytes in dec. See the Decimal128 specification for the exact string format.
- BSON_DECIMAL128_FROM_STRING_W_LEN(3) - Parses the string containing ascii encoded Decimal128 and initialize the bytes in dec. See the Decimal128 specification for the exact string format.
- BSON_DECIMAL128_T(3) - The bson_decimal128_t structure represents the IEEE-754 Decimal128 data type. The type bson_decimal128_t is an aggregate that contains two uint64_ts, named high and low. The declaration and layout...
- BSON_DECIMAL128_TO_STRING(3) - Converts dec into a printable string.
- BSON_DESTROY(3) - The bson_destroy() function shall free an allocated bson_t structure. Does nothing if bson is NULL.
- BSON_DESTROY_WITH_STEAL(3) - The bson_destroy_with_steal() function shall destroy a bson_t structure but return the underlying buffer instead of freeing it. If steal is false, this is equivalent to calling bson_destroy(). It is...
- BSON_EQUAL(3) - The bson_equal() function shall return true if both documents are equal.
- BSON_ERROR_T(3) - The bson_error_t structure is used as an out-parameter to pass error information to the caller. It should be stack-allocated and does not requiring freeing.
- BSON_FREE(3) - This function shall free the memory supplied by mem. This should be used by functions that require you free the result with bson_free().
- BSON_GET_DATA(3) - The bson_get_data() function shall return the raw buffer of a bson document. This can be used in conjunction with the len property of a bson_t if you want to copy the raw buffer around.
- BSON_GET_MAJOR_VERSION(3) - Get the first number in libbson's MAJOR.MINOR.MICRO release version.
- BSON_GET_MICRO_VERSION(3) - Get the third number in libbson's MAJOR.MINOR.MICRO release version.
- BSON_GET_MINOR_VERSION(3) - Get the middle number in libbson's MAJOR.MINOR.MICRO release version.
- BSON_GET_MONOTONIC_TIME(3) - The clock abstraction in Libbson provides a cross-platform way to handle timeouts within the BSON library. It abstracts the differences in implementations of gettimeofday() as well as providing a...
- BSON_GET_VERSION(3) - A string representation of Libbson's version, formatted something like "1.2.3" or "1.2.3-pre".
- BSON_HAS_FIELD(3) - Checks to see if key contains an element named key. This also accepts "dotkey" notation such as "a.b.c.d".
- BSON_INIT(3) - The bson_init() function shall initialize a bson_t that is placed on the stack. This is equivalent to initializing a bson_t to BSON_INITIALIZER.
- BSON_INIT_FROM_JSON(3) - The bson_init_from_json() function will initialize a new bson_t by parsing the JSON found in data. Only a single JSON object may exist in data or an error will be set and false returned.
- BSON_INIT_STATIC(3) - The bson_init_static() function shall initialize a read-only bson_t on the stack using the data provided. No copies of the data will be made and therefore must remain valid for the lifetime of the...
- BSON_ISSPACE(3) - A safer alternative to isspace with additional bounds checking.
- BSON_ITER_ARRAY(3) - The bson_iter_array() function shall retrieve the raw buffer of a sub-array from iter. iter MUST be on an element that is of type BSON_TYPE_ARRAY. This can be verified with bson_iter_type() or the...
- BSON_ITER_AS_BOOL(3) - Fetches the current field as if it were a boolean.
- BSON_ITER_AS_DOUBLE(3) - Fetches the current field as if it were a double.
- BSON_ITER_AS_INT64(3) - The bson_iter_as_int64() function shall return the contents of the current element as if it were a BSON_TYPE_INT64 element. The currently supported casts include:
- BSON_ITER_BINARY(3) - This function shall return the binary data of a BSON_TYPE_BINARY element. It is a programming error to call this function on a field that is not of type BSON_TYPE_BINARY. You can check this with the...
- BSON_ITER_BOOL(3) - The bson_iter_bool() function shall return the boolean value of a BSON_TYPE_BOOL element. It is a programming error to call this function on an element other than BSON_TYPE_BOOL. You can check this...
- BSON_ITER_CODE(3) - This function returns the contents of a BSON_TYPE_CODE field. The length of the string is stored in length if non-NULL.
- BSON_ITER_CODEWSCOPE(3) - The bson_iter_codewscope() function acts similar to bson_iter_code() except for BSON_TYPE_CODEWSCOPE elements. It also will provide a pointer to the buffer for scope, which can be loaded into a...
- BSON_ITER_DATE_TIME(3) - The bson_iter_date_time() function shall return the number of milliseconds since the UNIX epoch, as contained in the BSON_TYPE_DATE_TIME element.
- BSON_ITER_DBPOINTER(3) - Fetches the contents of a BSON_TYPE_DBPOINTER element.
- BSON_ITER_DECIMAL128(3) - Fetches the value from a BSON_TYPE_DECIMAL128 field. You should verify that this is a BSON_TYPE_DECIMAL128 field before calling this function.
- BSON_ITER_DOCUMENT(3) - The bson_iter_document() function shall retrieve the raw buffer of a sub-document from iter. iter MUST be on an element that is of type BSON_TYPE_DOCUMENT. This can be verified with bson_iter_type()...
- BSON_ITER_DOUBLE(3) - Fetches the contents of a BSON_TYPE_DOUBLE field.
- BSON_ITER_DUP_UTF8(3) - This function is similar to bson_iter_utf8() except that it calls bson_strndup() on the result.
- BSON_ITER_FIND(3) - The bson_iter_find() function shall advance iter to the first element named key or exhaust all elements of iter. If iter is exhausted, false is returned and iter should be considered invalid.
- BSON_ITER_FIND_CASE(3) - Advances iter to the first element matching the name of key or exhausting all elements.
- BSON_ITER_FIND_DESCENDANT(3) - The bson_iter_find_descendant() function shall follow standard MongoDB dot notation to recurse into subdocuments. descendant will be initialized and advanced to the descendant. If false is returned,...
- BSON_ITER_FIND_W_LEN(3) - The bson_iter_find_w_len() function shall advance iter to the first element named key or exhaust all elements of iter. If iter is exhausted, false is returned and iter should be considered invalid.
- BSON_ITER_INIT(3) - The bson_iter_init() function shall initialize iter to iterate upon the BSON document bson. Upon initialization, iter is placed before the first element. Callers must call bson_iter_next(),...
- BSON_ITER_INIT_FIND(3) - This function is identical to (bson_iter_init() && bson_iter_find()).
- BSON_ITER_INIT_FIND_CASE(3) - This function is identical to bson_iter_init() && bson_iter_find_case().
- BSON_ITER_INIT_FIND_W_LEN(3) - This function is identical to (bson_iter_init() && bson_iter_find_w_len()).
- BSON_ITER_INIT_FROM_DATA(3) - The bson_iter_init_from_data() function shall initialize iter to iterate upon the buffer data, which must contain a BSON document. Upon initialization, iter is placed before the first element....
- BSON_ITER_INIT_FROM_DATA_AT_OFFSET(3) - Creates a bson_iter_t and starts iteration on a field at the offset.
- BSON_ITER_INT32(3) - Fetches the value from a BSON_TYPE_INT32 element. You should verify that the field is a BSON_TYPE_INT32 field before calling this function.
- BSON_ITER_INT64(3) - Fetches the value from a BSON_TYPE_INT64 field. You should verify that this is a BSON_TYPE_INT64 field before calling this function.
- BSON_ITER_KEY(3) - Fetches the key for the current element observed by iter.
- BSON_ITER_KEY_LEN(3) - Fetches the length of the key for the current element observed by iter. This is a constant time computation, and therefore faster than calling strlen() on a key returned by bson_iter_key().
- BSON_ITER_NEXT(3) - Advances iter to the next element in the document.
- BSON_ITER_OFFSET(3) - Fetches the offset for the current element observed by iter.
- BSON_ITER_OID(3) - Fetches the bson_oid_t for a BSON_TYPE_OID element. You should verify it is an element of type BSON_TYPE_OID before calling this function.
- BSON_ITER_OVERWRITE_BOOL(3) - The bson_iter_overwrite_bool() function shall overwrite the contents of a BSON_TYPE_BOOL element in place.
- BSON_ITER_OVERWRITE_DATE_TIME(3) - The bson_iter_overwrite_date_time() function shall overwrite the contents of a BSON_TYPE_DATE_TIME element in place.
- BSON_ITER_OVERWRITE_DECIMAL128(3) - The bson_iter_overwrite_decimal128() function shall overwrite the contents of a BSON_TYPE_DECIMAL128 element in place.
- BSON_ITER_OVERWRITE_DOUBLE(3) - The bson_iter_overwrite_double() function shall overwrite the contents of a BSON_TYPE_DOUBLE element in place.
- BSON_ITER_OVERWRITE_INT32(3) - The bson_iter_overwrite_int32() function shall overwrite the contents of a BSON_TYPE_INT32 element in place.
- BSON_ITER_OVERWRITE_INT64(3) - The bson_iter_overwrite_int64() function shall overwrite the contents of a BSON_TYPE_INT64 element in place.
- BSON_ITER_OVERWRITE_OID(3) - The bson_iter_overwrite_oid() function shall overwrite the contents of a BSON_TYPE_OID element in place.
- BSON_ITER_OVERWRITE_TIMESTAMP(3) - The bson_iter_overwrite_timestamp() function shall overwrite the contents of a BSON_TYPE_TIMESTAMP element in place.
- BSON_ITER_RECURSE(3) - The bson_iter_recurse() function shall initialize child using the embedded document or array currently observed by iter.
- BSON_ITER_REGEX(3) - The bson_iter_regex() function shall retrieve the contents of a BSON_TYPE_REGEX element currently observed by iter.
- BSON_ITER_SYMBOL(3) - The symbol element type is DEPRECATED in the bson specification at http://bsonspec.org.
- BSON_ITER_T(3) - bson_iter_t is a structure used to iterate through the elements of a bson_t. It is meant to be used on the stack and can be discarded at any time as it contains no external allocation. The contents...
- BSON_ITER_TIME_T(3) - The bson_iter_time_t() function shall return the number of seconds since the UNIX epoch, as contained in the BSON_TYPE_DATE_TIME element.
- BSON_ITER_TIMESTAMP(3) - The BSON_TYPE_TIMESTAMP type is not a date/time and is typically used for intra-server communication.
- BSON_ITER_TIMEVAL(3) - The bson_iter_timeval() function shall return the number of seconds and microseconds since the UNIX epoch, as contained in the BSON_TYPE_DATE_TIME element into tv.
- BSON_ITER_TYPE(3) - The bson_iter_type() function shall return the type of the observed element in a bson document.
- BSON_ITER_UTF8(3) - The bson_iter_utf8() function shall retrieve the contents of a BSON_TYPE_UTF8 element currently observed by iter.
- BSON_ITER_VALUE(3) - Fetches the value for the currently observed type as a boxed type. This allows passing around the value without knowing the type at runtime.
- BSON_ITER_VISIT_ALL(3) - A convenience function to iterate all remaining fields of iter using the callback vtable provided by visitor.
- BSON_JSON_DATA_READER_INGEST(3) - Feed data to a memory based json reader.
- BSON_JSON_DATA_READER_NEW(3) - Creates a new streaming JSON reader that will convert JSON documents to BSON.
- BSON_JSON_MODE_T(3) - The bson_json_mode_t enumeration contains all available modes for encoding BSON into MongoDB Extended JSON.
- BSON_JSON_OPTS_DESTROY(3) - Destroys and releases all resources associated with opts. Does nothing if opts is NULL.
- BSON_JSON_OPTS_NEW(3) - The bson_json_opts_new() function shall create a new bson_json_opts_t using the mode and length supplied. The mode member is a bson_json_mode_t defining the encoding mode.
- BSON_JSON_OPTS_SET_OUTERMOST_ARRAY(3) - The bson_json_opts_set_outermost_array() function shall set the is_outermost_array variable on the bson_json_opts_t parameter using the boolean provided.
- BSON_JSON_OPTS_T(3) - The bson_json_opts_t structure contains options for encoding BSON into MongoDB Extended JSON.
- BSON_JSON_READER_DESTROY(3) - Frees a bson_json_reader_t. Does nothing if reader is NULL.
- BSON_JSON_READER_NEW(3) - Creates a new bson_json_reader_t that can read from an arbitrary data source in a streaming fashion.
- BSON_JSON_READER_NEW_FROM_FD(3) - Creates a new JSON to BSON converter that will be reading from the file-descriptor fd.
- BSON_JSON_READER_NEW_FROM_FILE(3) - Creates a new bson_json_reader_t using the underlying file found at filename.
- BSON_JSON_READER_READ(3) - Reads the next BSON document from the underlying JSON source.
- BSON_JSON_READER_T(3) - The bson_json_reader_t structure is used for reading a sequence of JSON documents and transforming them to bson_t documents.
- BSON_MALLOC(3) - This is a portable malloc() wrapper.
- BSON_MALLOC0(3) - This is a portable malloc() wrapper that also sets the memory to zero. Similar to calloc().
- BSON_MEM_RESTORE_VTABLE(3) - This function shall restore the default memory allocator to be used by Libbson.
- BSON_MEM_SET_VTABLE(3) - This function shall install a new memory allocator to be used by Libbson.
- BSON_MEMORY(3) - Libbson contains a lightweight memory abstraction to make portability to new platforms easier. Additionally, it helps us integrate with interesting higher-level languages. One caveat, however, is...
- BSON_NEW(3) - The bson_new() function shall create a new bson_t structure on the heap. It should be freed with bson_destroy() when it is no longer in use.
- BSON_NEW_FROM_BUFFER(3) - Creates a new bson_t using the data provided.
- BSON_NEW_FROM_DATA(3) - The bson_new_from_data() function shall create a new bson_t on the heap and copy the contents of data. This may be helpful when working with language bindings but is generally expected to be slower.
- BSON_NEW_FROM_JSON(3) - The bson_new_from_json() function allocates and initializes a new bson_t by parsing the JSON found in data. Only a single JSON object may exist in data or an error will be set and NULL returned.
- BSON_OID_COMPARE(3) - The bson_oid_compare() function shall return a qsort() style value of a lexicographical sort of oid1 and oid2.
- BSON_OID_COMPARE_UNSAFE(3) - Identical to bson_oid_compare(), but performs no integrity checking.
- BSON_OID_COPY(3) - Copies the contents of src into dst.
- BSON_OID_COPY_UNSAFE(3) - Identical to bson_oid_copy(), but performs no integrity checking.
- BSON_OID_EQUAL(3) - Checks if two bson_oid_t contain the same bytes.
- BSON_OID_EQUAL_UNSAFE(3) - Identical to bson_oid_equal(), but performs no integrity checking.
- BSON_OID_GET_TIME_T(3) - Fetches the generation time in seconds since the UNIX Epoch of oid.
- BSON_OID_GET_TIME_T_UNSAFE(3) - Identical to bson_oid_get_time_t(), but performs no integrity checking.
- BSON_OID_HASH(3) - Generates a hash code for oid suitable for a hashtable.
- BSON_OID_HASH_UNSAFE(3) - Identical to bson_oid_hash(), but performs no integrity checking.
- BSON_OID_INIT(3) - Generates a new bson_oid_t using either context or the default bson_context_t.
- BSON_OID_INIT_FROM_DATA(3) - Initializes a bson_oid_t using the raw buffer provided.
- BSON_OID_INIT_FROM_STRING(3) - Parses the string containing hex encoded oid and initialize the bytes in oid.
- BSON_OID_INIT_FROM_STRING_UNSAFE(3) - Identical to bson_oid_init_from_string(), but performs no integrity checking.
- BSON_OID_INIT_SEQUENCE(3) - Generates a new ObjectID with the next 64-bit sequence number in context. The first 4 bytes contain the current time and the following 8 contain the sequence number in big-endian format.
- BSON_OID_IS_VALID(3) - Checks if a string containing a hex encoded string is a valid BSON ObjectID.
- BSON_OID_T(3) - The bson_oid_t structure contains the 12-byte ObjectId notation defined by the BSON ObjectID specification.
- BSON_OID_TO_STRING(3) - Converts oid into a hex encoded string.
- BSON_READER_DESTROY(3) - Destroys and releases all resources associated with reader. Does nothing if reader is NULL.
- BSON_READER_DESTROY_FUNC_T(3) - An optional callback function that will be called when a bson_reader_t created with bson_reader_new_from_handle() is destroyed with bson_reader_destroy().
- BSON_READER_NEW_FROM_DATA(3) - The bson_reader_new_from_data() function shall create a new bson_reader_t using the buffer supplied. data is not copied and MUST be valid for the lifetime of the resulting bson_reader_t.
- BSON_READER_NEW_FROM_FD(3) - The bson_reader_new_from_fd() function shall create a new bson_reader_t that will read from the provided file-descriptor.
- BSON_READER_NEW_FROM_FILE(3) - Creates a new bson_reader_t using the file denoted by filename.
- BSON_READER_NEW_FROM_HANDLE(3) - This function allows for a pluggable data stream for the reader. This can be used to read from sockets, files, memory, or other arbitrary sources.
- BSON_READER_READ(3) - The bson_reader_read() function shall read the next document from the underlying file-descriptor or buffer.
- BSON_READER_READ_FUNC_T(3) - A callback function that will be called by bson_reader_t to read the next chunk of data from the underlying opaque file descriptor.
- BSON_READER_RESET(3) - Seeks to the beginning of the underlying buffer. Valid only for a reader created from a buffer with bson_reader_new_from_data(), not one created from a file, file descriptor, or handle.
- BSON_READER_SET_DESTROY_FUNC(3) - Allows for setting a callback to be executed when a reader is destroyed. This should only be used by implementations implementing their own read callbacks.
- BSON_READER_SET_READ_FUNC(3) - Sets the function to read more data from the underlying stream in a custom bson_reader_t.
- BSON_READER_T(3) - bson_reader_t is a structure used for reading a sequence of BSON documents. The sequence can come from a file-descriptor, memory region, or custom callbacks.
- BSON_READER_TELL(3) - Tells the current position within the underlying stream.
- BSON_REALLOC(3) - This is a portable realloc() wrapper.
- BSON_REALLOC_CTX(3) - This function is identical to bson_realloc() except it takes a context parameter. This is useful when working with pooled or specific memory allocators.
- BSON_REALLOC_FUNC(3) - This is a prototype for pluggable realloc functions used through the Libbson library. If you wish to use a custom allocator this is one way to do it. Additionally, bson_realloc_ctx() is a default...
- BSON_REFERENCE(3) - The bson_t structure represents a BSON document. This structure manages the underlying BSON encoded buffer. For mutable documents, it can append new data to the document.
- BSON_REINIT(3) - Reinitializes a bson_t.
- BSON_RESERVE_BUFFER(3) - Grow the internal buffer of bson to total_size and set the document length to total_size. Useful for eliminating copies when reading BSON bytes from a stream.
- BSON_SET_ERROR(3) - This is a helper function to set the parameters of a bson_error_t. It handles the case where error is NULL by doing nothing.
- BSON_SIZED_NEW(3) - The bson_sized_new() function shall create a new bson_t on the heap with a preallocated buffer. This is useful if you have a good idea of the size of the resulting document.
- BSON_SNPRINTF(3) - This is a portable wrapper around snprintf(). It also enforces a trailing \0 in the resulting string.
- BSON_STEAL(3) - Efficiently transfer the contents of src to dst and destroy src.
- BSON_STRCASECMP(3) - A portable version of strcasecmp().
- BSON_STRDUP(3) - Copies str into a new string. If str is NULL, then NULL is returned.
- BSON_STRDUP_PRINTF(3) - This function performs a printf style format but into a newly allocated string.
- BSON_STRDUPV_PRINTF(3) - This function is like bson_strdup_printf() except takes a va_list of parameters.
- BSON_STRERROR_R(3) - This is a portability wrapper around strerror().
- BSON_STRFREEV(3) - This will free each string in a NULL-terminated array of strings and then the array itself.
- BSON_STRING_APPEND(3) - Appends the ASCII or UTF-8 encoded string str to string. This is not suitable for embedding NULLs in strings.
- BSON_STRING_APPEND_C(3) - Appends c to the string builder string.
- BSON_STRING_APPEND_PRINTF(3) - Like bson_string_append() but formats a printf style string and then appends that to string.
- BSON_STRING_APPEND_UNICHAR(3) - Appends a unicode character to string. The character will be encoded into its multi-byte UTF-8 representation.
- BSON_STRING_FREE(3) - Frees the bson_string_t structure and optionally string->str.
- BSON_STRING_NEW(3) - Creates a new string builder, which uses power-of-two growth of buffers. Use the various bson_string_append*() functions to append to the string.
- BSON_STRING_T(3) - bson_string_t is an abstraction for building strings. As chunks are added to the string, allocations are performed in powers of two.
- BSON_STRING_TRUNCATE(3) - Truncates the string so that it is len bytes in length. This must be smaller or equal to the current length of the string.
- BSON_STRNCPY(3) - Copies up to size bytes from src into dst. dst must be at least size bytes in size. A trailing \0 is always set.
- BSON_STRNDUP(3) - Allocates a new string and copies up to n_bytes from str into it. A trailing \0 is always set.
- BSON_STRNLEN(3) - A portable version of strnlen().
- BSON_SUBTYPE_T(3) - This enumeration contains the various subtypes that may be used in a binary field. See http://bsonspec.org for more information.
- BSON_T(3) - The bson_t structure represents a BSON document. This structure manages the underlying BSON encoded buffer. For mutable documents, it can append new data to the document.
- BSON_TYPE_T(3) - The bson_type_t enumeration contains all of the types from the BSON Specification. It can be used to determine the type of a field at runtime.
- BSON_UINT32_TO_STRING(3) - Converts value to a string.
- BSON_UNICHAR_T(3) - bson_unichar_t provides an abstraction on a single unicode character. It is the 32-bit representation of a character. As UTF-8 can contain multi-byte characters, this should be used when iterating...
- BSON_UTF8_ESCAPE_FOR_JSON(3) - Allocates a new string matching utf8 except that special characters in JSON are escaped. The resulting string is also UTF-8 encoded.
- BSON_UTF8_FROM_UNICHAR(3) - Converts a single unicode character to a multi-byte UTF-8 sequence. The result is stored in utf8 and the number of bytes used in len.
- BSON_UTF8_GET_CHAR(3) - Converts the current character in a UTF-8 sequence to a bson_unichar_t, the 32-bit representation of the multi-byte character.
- BSON_UTF8_NEXT_CHAR(3) - Advances within utf8 to the next UTF-8 character, which may be multiple bytes offset from utf8. A pointer to the next character is returned.
- BSON_UTF8_VALIDATE(3) - Validates that the content within utf8 is valid UTF-8 (by the RFC 3629 standard). If allow_null is true, then embedded NULL bytes are allowed (\0).
- BSON_VALIDATE(3) - Validates a BSON document by walking through the document and inspecting the keys and values for valid content.
- BSON_VALIDATE_FLAGS_T(3) - bson_validate_flags_t is a set of binary flags which may be combined to specify a level of BSON document validation.
- BSON_VALIDATE_WITH_ERROR(3) - Validates a BSON document by walking through the document and inspecting the keys and values for valid content.
- BSON_VALIDATE_WITH_ERROR_AND_OFFSET(3) - Validates a BSON document by walking through the document and inspecting the keys and values for valid content.
- BSON_VALUE_COPY(3) - This function will copy the boxed content in src into dst. dst must be freed with bson_value_destroy() when no longer in use.
- BSON_VALUE_DESTROY(3) - Releases any resources associated with value. Does nothing if value is NULL.
- BSON_VALUE_T(3) - The bson_value_t structure is a boxed type for encapsulating a runtime determined type.
- BSON_VERSION(3)
- BSON_VISITOR_T(3) - The bson_visitor_t structure provides a series of callbacks that can be called while iterating a BSON document. This may simplify the conversion of a bson_t to a higher level language structure.
- BSON_VSNPRINTF(3) - Like bson_snprintf() but allows for variadic parameters.
- BSON_WRITER_BEGIN(3) - Begins writing a new document. The caller may use the bson structure to write out a new BSON document. When completed, the caller must call either bson_writer_end() or bson_writer_rollback().
- BSON_WRITER_DESTROY(3) - Cleanup after writer and release any allocated memory. Does nothing if writer is NULL. Note that the buffer supplied to bson_writer_new() is NOT freed from this method. The caller is responsible for...
- BSON_WRITER_END(3) - Complete writing of a bson_writer_t to the buffer supplied.
- BSON_WRITER_GET_LENGTH(3) - Fetches the current length of the content written by the buffer (including the initial offset). This includes a partly written document currently being written.
- BSON_WRITER_NEW(3) - Creates a new instance of bson_writer_t using the buffer, length, offset, and _realloc()_ function supplied.
- BSON_WRITER_ROLLBACK(3) - Abort the appending of the current bson_t to the memory region managed by writer. This is useful if you detected that you went past a particular memory limit. For example, MongoDB has 48MB message...
- BSON_WRITER_T(3) - The bson_writer_t API provides an abstraction for serializing many BSON documents to a single memory region. The memory region may be dynamically allocated and re-allocated as more memory is...
- BSON_ZERO_FREE(3) - This function behaves like bson_free() except that it zeroes the memory first. This can be useful if you are storing passwords or other similarly important data. Note that if it truly is important,...
- bsp(6) - node builder for WAD files
- BSpar_gmres(3) - Solve a nonsymmetric system of equations using gmres preconditioned by one of several preconditioners. The rhs can be a block of vectors.
- BSpar_isolve(3) - Solve a symmetric indefinite system of equations using symmlq preconditioned by one of several preconditioners.
- BSpar_solve(3) - General solver of a system of equations preconditioned by one of several preconditioners and using one of several possible methods. The rhs can be a block of vectors.
- BSpar_sym_solve(3) - Solve a symmetric positive definite system of equations using conjugate gradients preconditioned by one of several preconditioners. The rhs can be a block of vectors. The user should not call this...
- BSPATCH(1) - apply a patch built with bsdiff(1)
- BSPELL(1) - find spelling errors
- BSprint_log(3) - Print log stuff if MLOG is defined.
- BSPWM(1) - Binary space partitioning window manager
- BSQLDB(1) - batch SQL script processor using DB-Library
- BSQLODBC(FreeTDS) - batch SQL script processor using ODBC
- BSsave_diag(3) - Copy the diagonal of A into special storage in A
- BSscale_diag(3) - Symmetrically scale the matrix by a diagonal matrix
- BSset_diag(3) - Set the diagonal of A to a constant
- BSset_diagv(3) - Set the diagonal equal to a vector
- BSset_mat_icc_storage(3) - Set the matrix storage.
- BSset_mat_symmetric(3) - Set the matrix symmetry.
- BSsetup_block(3) - Change the setup for triangular matrix multiplication to allow for multiple vectors
- BSsetup_factor(3) - Set up the communication for factorization
- BSsetup_forward(3) - Set up the communication structure for triangular matrix solution
- BStri_mult(3) - Multiply the matrix (A - shift*B) by a block of vectors
- BStri_solve(3) - Multiply the matrix A(-1) by a block of vectors
- BSTRING(3) - byte string operations
- bsvplay(1) - convert BASICA music data to PCM
- BT_FORMAT_NAMES(1) - formatting BibTeX names for consistent output
- BT_INPUT(1) - input/parsing functions in btparse library
- BT_LANGUAGE(1) - the BibTeX data language, as recognized by btparse
- BT_MACROS(1) - accessing and manipulating the btparse macro table
- BT_MISC(1) - miscellaneous BibTeX-like string-processing utilities
- BT_POST_PROCESSING(1) - post-processing of BibTeX strings, values, and entries
- BT_POSTPROCESS(1) - post-processing of BibTeX strings, values, and entries
- BT_SPLIT_NAMES(1) - splitting up BibTeX names and lists of names
- BT_TRAVERSAL(1) - AST traversal/query functions in btparse library
- Battle Tanks(6) - fast 2D tank arcade game
- BTAPE(8) - Bareos's Tape interface test program
- BTAVCTPD(8) - Media control for Bluetooth devices
- BTCFLASH(1L) - Firmware flash utility for BTC DRW1008 DVD+/-RW recorder
- BTCHECK(1) - Bittorrent downloaded data checker
- btedit(1) - Direct editing of BTREE records
- BTHIDCONTROL(8) - Bluetooth HID control utility
- BTHIDD(8) - Bluetooth HID daemon
- BTHOST(1) - look up Bluetooth host names and Protocol Service Multiplexor values
- btm(1) - A customizable cross-platform graphical process/system monitor for the terminal. Supports Linux, macOS, and Windows.
- BTOA(1) - encode/decode binary to printable ASCII
- BTOOL_FAQ(1) - Frequently-Asked Questions about btparse and Text::BibTeX
- btop(1) - Resource monitor that shows usage and stats for processor, memory, disks, network, and processes.
- BTOWC(3) - convert between wide and single-byte characters
- BTPAND(8) - Bluetooth PAN daemon
- BTPARSE(1) - C library for parsing and processing BibTeX data files
- BTRACEBACK(8) - wrapper script around gdb and bsmtp
- BTREE(3) - btree database access method
- BTREE-DUMP(1) - unformatted dump of a B-Tree DB file
- BTSIXAD(8) - Driver for Sixaxis gamepad connected over Bluetooth
- BTSOCKSTAT(1) - show Bluetooth sockets information
- BTXLD(8) - link editor for BTX clients
- bu_check_files(1) - Verify the file integrity of backupuser(1) backups
- bubble3d(6) - 3d rising bubbles.
- bubblecolors(6) - screen saver.
- Bucardo(3) - Postgres multi-master replication system
- BUCARDO(1) - utility script for controlling the Bucardo program
- BUCKETIZE(1) - Move files into buckets
- BUDDY-NG(1) - a tool to work with easside-ng
- BUDGIE-DAEMON(1) - budgie process to interface with various budgie and GNOME dbus interfaces
- BUDGIE-DESKTOP(1) - central entry point from gnome-session to display the graphical interface
- BUDGIE-DESKTOP-SETTINGS(1) - Settings window for budgie-desktop
- BUDGIE-PANEL(1) - graphical component that display budgie widgets
- BUDGIE-RUN-DIALOG(1) - user invoked application to quickly search and execute applications
- budgie-screensaver(1) - screen saver and locker
- budgie-screensaver-command(1) - controls Budgie Desktop screensaver
- budgie-session(1) - Start the budgie desktop environment
- BUDGIE-SESSION-INH(1) - inhibit budgie-session functionality
- budgie-SESSION-QUIT(1) - End the current budgie session
- BUDGIE-WM(1) - wrapper around libmutter that forms the window management for budgie
- BUF(9) - kernel buffer I/O scheme used in FreeBSD VM system
- BUF_ISLOCKED(9) - returns the state of the lock linked to the buffer
- BUF_LOCK(9) - locks a buffer
- BUF_LOCKFREE(9) - destroys a buffer's lock
- BUF_LOCKINIT(9) - initializes a buffer lock
- BUF_MEM_NEW(3ossl) - simple character array structure
- BUF_RECURSED(9) - checks if the lock linked to the buffer is recursed
- BUF_RING(9) - multi-producer, {single, multi}-consumer lock-less ring buffer
- BUF_TIMELOCK(9) - locks a buffer
- BUF_UNLOCK(9) - unlocks a locked buffer
- BUFFCHAN(8) - Buffered file-writing backend for INN
- Buffer(3) - Extensible buffers.
- buffer(3) - simple character array structure
- BUFFINDEXED.CONF(5) - Configuration for the buffindexed overview method
- BUFR_REENCODE(1) - Encode BUFR messages from a file containing decoded BUFR messages from bufrread.pl (possibly edited). Prints to STDOUT unless option "--outfile" is used.
- BUFRALTER(1) - Will alter the BUFR messages in <bufr file> according to what is specified by the options provided. The modified file (text surrounding the BUFR messages will not be affected) will be printed...
- BUFRENCODE(1) - Encode a BUFR message, reading data and metadata from files. The resulting BUFR message will be printed to STDOUT unless option "--outfile" is set.
- BUFREXTRACT(1) - Extract all BUFR messages and/or corresponding AHLs from BUFR file(s), possibly filtering on AHL.
- BUFRREAD(1) - Extract BUFR messages from BUFR file(s) and print the decoded content to screen, including AHL (Abbreviated Header Line) if present.
- BUFRRESOLVE(1) - Utility program for fetching info from BUFR tables.
- BUGPOINT(1) - automatic test case reduction tool
- BUGSX(1) - display and evolve biomorphs
- bugz(1) - command line interface to bugzilla
- BUGZILLA(1) - command line tool for interacting with Bugzilla
- buici-clock(1) - attractive X11 clock
- BUILD(7) - general instructions on how to build the FreeBSD
- BUILD-ASTROMETRY-INDEX(1) - Create astrometry.net index files
- BUILD-BCD-FOR-FIREFOX(1) - build user agent data from the @mdn/browser-compat-data repo
- BUILD.COMMON.MK(5) - bsdbuild - common defines
- BUILD.DEP.MK(5) - bsdbuild - dependency generation
- BUILD.LIB.MK(5) - bsdbuild - compilation of libraries
- BUILD.MAN.MK(5) - bsdbuild - compilation of UNIX manual pages
- BUILD.PROG.MK(5) - bsdbuild - compilation of executables
- BUILD.PROJ.MK(5) - bsdbuild - compilation of IDE project files
- BUILD.WWW.MK(5) - bsdbuild - HTML document preprocessing
- build.xml(5) - configuration file used by Apache Ant to build projects
- build_3dbox(3) - Generate a 3D cube model
- build_3dplane(3) - Build a model comprised of a tesselated plane.
- build_cylinder(3) - Generate a full or half cylinder model
- Build_path_prefix_map(3) - Rewrite paths for reproducible builds
- build_pointcloud(3) - Create a 3D object that is comprised of a cloud of points.
- build_shader(3) - using
- build_sphere(3) - Generate a 3D sphere or hemisphere model
- buildah(1) - A command line tool that facilitates building OCI container images.
- buildah-add(1) - Add the contents of a file, URL, or a directory to a container.
- buildah-build(1) - Build an image using instructions from Containerfiles
- buildah-commit(1) - Create an image from a working container.
- buildah-config(1) - Update image configuration settings.
- buildah-containers(1) - List the working containers and their base images.
- buildah-copy(1) - Copies the contents of a file, URL, or directory into a container's working directory.
- buildah-from(1) - Creates a new working container, either from scratch or using a specified image as a starting point.
- buildah-images(1) - List images in local storage.
- buildah-info(1) - Display Buildah system information.
- buildah-inspect(1) - Display information about working containers or images or manifest lists.
- buildah-login(1) - Login to a container registry
- buildah-logout(1) - Logout of a container registry
- buildah-manifest(1) - Create and manipulate manifest lists and image indexes.
- buildah-manifest-add(1) - Add an image or artifact to a manifest list or image index.
- buildah-manifest-annotate(1) - Add and update information about an image or artifact to a manifest list or image index.
- buildah-manifest-create(1) - Create a manifest list or image index.
- buildah-manifest-exists(1)() - Check if the given manifest list exists in local storage
- buildah-manifest-inspect(1) - Display a manifest list or image index.
- buildah-manifest-push(1) - Push a manifest list or image index to a registry.
- buildah-manifest-remove(1) - Remove an image from a manifest list or image index.
- buildah-manifest-rm(1) - Removes one or more manifest lists.
- buildah-mkcw(1) - Convert a conventional container image into a confidential workload image.
- buildah-mount(1) - Mount a working container's root filesystem.
- buildah-pull(1) - Pull an image from a registry.
- buildah-push(1) - Push an image, manifest list or image index from local storage to elsewhere.
- buildah-rename(1) - Rename a local container.
- buildah-rm(1) - Removes one or more working containers.
- buildah-rmi(1) - Removes one or more images.
- buildah-run(1) - Run a command inside of the container.
- buildah-source(1) - Create, push, pull and manage source images and associated source artifacts
- buildah-source-add(1) - Add a source artifact to a source image
- buildah-source-create(1) - Create and initialize a source image
- buildah-source-pull(1) - Pull a source image from a registry to a specified path
- buildah-source-push(1) - Push a source image from a specified path to a registry.
- buildah-tag(1) - Add additional names to local images.
- buildah-umount(1) - Unmount the root file system on the specified working containers.
- buildah-unshare(1) - Run a command inside of a modified user namespace.
- buildah-version(1) - Display the Buildah Version Information.
- BUILDBOT-WORKER(1) - a tool for managing buildbot worker instances
- BUILDDBM(8) - build a DBM version of Radius users database
- BUILDFLAGS.AWK(1) - convert buildflags.conf(5) files into make syntax
- BUILDFLAGS.CONF(5) - set build options for ports(7), world and everything
- BUILDFLAGS.MK(1) - import buildflags.conf(5)
- BUILDINFO(5) - Makepkg package build information file
- build-info(n) - Build info
- BUILDIT(8) - time a command, log its output and mail notification when finished
- BUILDRDSWINDOW(3) - builds windowing of a figure
- BUILTIN(1) - index of FreeBSD shell built-in commands
- builtin(3) - Perl pragma to import built-in utility functions
- Builtin_attributes(3) - Support for some of the builtin attributes
- BUKU(1) - Bookmark manager like a text-based mini-web
- BULK(8) - Daemon for submitting messages to SMTP engine
- BULK_EXTRACTOR(1) - Scans a disk image for regular expressions and other content.
- BULK_MAILER(1) - assist in delivery of mail to large numbers of recipients
- bumps(6) - move distorting spotlight around desktop
- BUNDLE(3) - create an empty coroutine bundle
- Bundle::Apache2(3) - Install Apache mod_perl2 and related modules
- Bundle::Apache::ASP(3) - Install Apache::ASP and required
- Bundle::Apache::ASP::Extra(3) - Install modules that provide additional functionality to Apache::ASP
- Bundle::ApacheTest(3) - A bundle to install all Apache-Test related modules
- Bundle::CGI::Builder::Complete(3) - A bundle to install the complete CGI::Builder framework.
- Bundle::DBD::CSV(3) - A bundle to install the DBD::CSV driver
- Bundle::DBD::mysql(3) - This package only exists for legacy reasons. Please use the DBD::mysql package instead.
- Bundle::DBD::Pg(3) - A bundle to install all DBD::Pg related modules
- Bundle::DBI(3) - A bundle to install DBI and required modules.
- Bundle::HTTP::WebTest(3) - a bundle to install HTTP::WebTest
- Bundle::Image::Info::Everything(3) - complete support for Image::Info
- Bundle::Image::Info::PNG(3) - full PNG support for Image::Info
- Bundle::Image::Info::SVG(3) - SVG support for Image::Info
- Bundle::Image::Info::XBM(3) - XBM (X11 bitmap) support for Image::Info
- Bundle::Image::Info::XPM(3) - XPM (X11 pixmap) support for Image::Info
- Bundle::Net::LDAP(3) - A bundle for Net::LDAP
- Bundle::Object::InsideOut(3) - A bundle of modules for full Object::InsideOut support
- Bundle::ParallelUA(3) - CPAN Bundle for the LWP Parallel User Agent extension
- Bundle::Perl6(3) - A bundle to install Perl6-related modules
- Bundle::PerlPoint(3) - A bundle to install PerlPoint related modules
- Bundle::PlRPC(3) - A bundle to install PlRPC-Server, Client and prerequisites.
- Bundle::SNMP::MIB::Compiler(3) - A bundle to install all SNMP::MIB::Compiler related modules
- Bundle::Template::Magic(3) - A bundle to install MagicTemplate distribution plus all related extensions and prerequisites.
- Bundle::Text::Query::BuildSQL(3) - A bundle to install related modules
- BUNDLE_GO(3) - launches a coroutine within a bundle
- BUNDLE_GO_MEM(3) - launches a coroutine within a bundle
- BUNDLE_MEM(3) - create an empty coroutine bundle
- BUNDLE_WAIT(3) - wait while coroutines in the bundle finish
- bup(1) - Backup program using rolling checksums and git file formats
- bup-bloom(1) - generates, regenerates, updates bloom filters
- bup-cat-file(1) - extract archive content (low-level)
- bup-daemon(1) - listens for connections and runs bup server
- bup-damage(1) - randomly destroy blocks of a file
- bup-drecurse(1) - recursively list files in your filesystem
- bup-features(1) - report the current status and capabilities of bup itself
- bup-fsck(1) - verify or repair a bup repository
- bup-ftp(1) - ftp-like client for navigating bup repositories
- bup-fuse(1) - mount a bup repository as a filesystem
- bup-gc(1) - remove unreferenced, unneeded data
- bup-get(1) - copy repository items (CAUTION: EXPERIMENTAL)
- bup-help(1) - open the documentation for a given bup command
- bup-import-duplicity(1) - import duplicity backups
- bup-import-rdiff-backup(1) - import a rdiff-backup archive
- bup-import-rsnapshot(1) - import a rsnapshot archive
- bup-index(1) - print and/or update the bup filesystem index
- bup-init(1) - initialize a bup repository
- bup-join(1) - concatenate files from a bup repository
- bup-ls(1) - list the contents of a bup repository
- bup-margin(1) - figure out your deduplication safety margin
- bup-memtest(1) - test bup memory usage statistics
- bup-meta(1) - create or extract a metadata archive
- bup-midx(1) - create a multi-index (.midx) file from several .idx files
- bup-mux(1) - multiplexes data and error streams over a connection
- bup-on(1) - run a bup server locally and client remotely
- bup-prune-older(1) - remove older saves
- bup-random(1) - generate a stream of random output
- bup-restore(1) - extract files from a backup set
- bup-rm(1) - remove references to archive content
- bup-save(1) - create a new bup backup set
- bup-server(1) - the server side of the bup client-server relationship
- bup-split(1) - save individual files to bup backup sets
- bup-tag(1) - tag a commit in the bup repository
- bup-tick(1) - wait for up to one second
- BURGERSPACE(6) - A hamburger-smashing video game
- Burp(8) - BackUp and Restore Program
- burp_ca(8) - program for generating certificates for use with burp
- BURST(1) - explode digests into nmh messages
- burst_buffer.conf(5) - Slurm configuration file for burst buffer management.
- BUS_ACTIVATE_RESOURCE(9) - activate or deactivate a resource
- BUS_ADD_CHILD(9) - add a device node to the tree with a given priority
- BUS_ADJUST_RESOURCE(9) - adjust resource allocated from a parent bus
- BUS_ALLOC_RESOURCE(9) - allocate resources from a parent bus
- BUS_ATTACH_CHILDREN(9) - manage child devices of a bus device
- BUS_BIND_INTR(9) - bind an interrupt resource to a specific CPU
- BUS_CHILD_DELETED(9) - notify a bus device that a child is being deleted
- BUS_CHILD_DETACHED(9) - notify a bus device that a child was detached
- BUS_CHILD_LOCATION(9) - obtain the location of a child on the bus.
- BUS_CHILD_PNPINFO(9) - obtain the plug and play information from a device
- BUS_CHILD_PRESENT(9) - ask the bus driver to see if this device is still really present
- BUS_CONFIG_INTR(9) - configure interrupt polarity and trigger mode
- BUS_DESCRIBE_INTR(9) - associate a description with an active interrupt handler
- BUS_DMA(9) - Bus and Machine Independent DMA Mapping Interface
- BUS_GENERIC_DETACH(9) - generic implementation of DEVICE_DETACH for buses
- BUS_GENERIC_NEW_PASS(9) - generic implementation of BUS_NEW_PASS for bus devices
- BUS_GENERIC_PRINT_CHILD(9) - generic implementation of BUS_PRINT_CHILD(9)
- BUS_GENERIC_READ_IVAR(9) - generic implementation of BUS_READ_IVAR and BUS_WRITE_IVAR for buses
- BUS_GENERIC_SHUTDOWN(9) - generic implementation of DEVICE_SHUTDOWN for buses
- BUS_GET_CPUS(9) - request a set of device-specific CPUs
- BUS_GET_PROPERTY(9) - get child's specific property
- BUS_GET_RESOURCE(9) - read a resource range/value with a given resource ID
- BUS_HINTED_CHILD(9) - notify a bus device about a potential child device identified by hints
- BUS_MAP_RESOURCE(9) - map or unmap an active resource
- BUS_NEW_PASS(9) - notify a bus that the pass level has been changed
- BUS_PRINT_CHILD(9) - print information about a device
- BUS_READ_IVAR(9) - manipulate bus-specific device instance variables
- BUS_RELEASE_RESOURCE(9) - release resources on a bus
- BUS_RESCAN(9) - rescan a bus checking for devices that have been added or removed
- BUS_SET_PASS(9) - raise the bus pass level
- BUS_SET_RESOURCE(9) - associate a definite resource with a given resource ID
- BUS_SETUP_INTR(9) - create, attach and teardown an interrupt handler
- BUS_SPACE(9) - bus space manipulation functions
- CreditCard(3) - Validate/generate credit card checksums/names
- Business::EDI(3) - Top level class for generating U.N. EDI interchange objects and subobjects.
- Business::EDI::CodeList(3)
- Business::EDI::Composite(3)
- Business::EDI::Spec(3) - Object class for CSV-based U.N. EDI specifications
- FraudDetect(3) - A cohort to Business::OnlinePayment
- FraudDetect::preCharge(3) - backend for Business::FraudDetect (part of Business::OnlinePayment)
- Business::Hours(3) - Calculate business hours in a time period
- Business::IS::PIN(3) - Validate and process Icelandic PIN numbers (Icelandic: kennitölur)
- Business::ISBN(3) - work with International Standard Book Numbers
- Business::ISBN10(3) - work with 10 digit International Standard Book Numbers
- Business::ISBN13(3) - work with 13 digit International Standard Book Numbers
- Business::ISBN::Data(3) - data pack for Business::ISBN
- ISIN(3) - validate International Securities Identification Numbers
- Business::ISMN(3) - work with International Standard Music Numbers
- Business::ISMN::Data(3) - data pack for Business::ISMN
- Business::ISSN(3) - Perl extension for International Standard Serial Numbers
- Business::MaxMind(3) - API for MaxMind minFraud Services
- Business::MaxMind::CreditCardFraudDetection(3) - Access MaxMind minFraud services
- Business::MaxMind::HTTPBase(3) - Base class for accessing HTTP web services
- Business::MaxMind::TelephoneVerification(3) - Access MaxMind's Telephone Verification services
- OnlinePayment(3) - Perl extension for online payment processing
- 2CheckOut(3) - 2CheckOut backend for Business::OnlinePayment
- AuthorizeNet(3) - AuthorizeNet backend for Business::OnlinePayment
- AuthorizeNet::AIM(3) - AuthorizeNet AIM backend for Business::OnlinePayment
- AuthorizeNet::AIM::ErrorCodes(3) - Easy lookup of Authorize.Net's AIM result reason codes
- AuthorizeNet::ARB(3) - AuthorizeNet ARB backend for Business::OnlinePayment
- BankOfAmerica(3) - Bank of America backend for Business::OnlinePayment
- Beanstream(3) - Beanstream backend for Business::OnlinePayment
- Cardstream(3) - Cardstream Plugin for Business::OnlinePayment
- eSec(3) - eSec backend for Business::OnlinePayment
- OnlinePayment::HTTPS(3) - Base class for HTTPS payment APIs
- iAuthorizer(3) - iAuthorizer.net backend for Business::OnlinePayment
- Jettis(3) - Jettis backend for Business::OnlinePayment
- LinkPoint(3) - LinkPoint (Cardservice) backend for Business::OnlinePayment
- MerchantCommerce(3) - Merchant Commerce backend for Business::OnlinePayment. Please see Buisness::OnlinePayment for details.
- Network1Financial(3) - Network1 Financial backend for Business::OnlinePayment
- OCV(3) - OCV backend for Business::OnlinePayment
- PayConnect(3) - PaymentOne (formerly eBillit) PayConnect backend for Business::OnlinePayment
- Business::OnlinePayment::PaymenTech(3) - Chase Paymentech backend for Business::OnlinePayment
- PaymentsGateway(3) - PaymentsGateway.Net backend for Business::OnlinePayment
- SurePay(3) - SurePay backend for Business::OnlinePayment
- VirtualNet(3) - Vital VirtualNet backend for Business::OnlinePayment
- Business::PayPal(3) - Perl extension for automating PayPal transactions
- Business::PayPal::EWP(3) - Perl extension for PayPal's Encrypted Website Payments
- IPN(3) - Perl extension that implements PayPal IPN v1.5
- Stripe(3) - Interface for Stripe payment system.
- Business::TW::Invoice::U420(3) - Print Taiwan Unified Invoice with U420 printer
- Business::TW::TSIB::CStorePayment(3) - Module for Taishin Bank Convenient Store Payment Management
- Business::TW::TSIB::VirtualAccount(3) - Module for Taishin Bank Virtual Account Management
- Business::UPS(3) - A UPS Interface Module
- Junior(3) - Perl module to handle WorldPay Junior for payment services, including callback services.
- busy(n) - confine pointer events to a window sub-tree
- BUSYBOX(1) - The Swiss Army Knife of Embedded Linux
- button(n) - Create and manipulate 'button' action widgets
- BVI(1) - visual editor for binary files
- BVM(8) - Bhyve Virtual machines Management tool
- BW_FILE_RD(8) - time the reading and summing of a file
- BW_MEM(8) - time memory bandwidth
- BW_MEM_RD(8) - time memory read rate (with overhead)
- BW_MMAP_RD(8) - time the reading and summing of a file
- BW_PIPE(8) - time data movement through pipes
- BW_TCP(1) - time data movement through TCP/IP sockets
- BW_UNIX(8) - UNIX pipe bandwidth
- bwa(1) - Burrows-Wheeler Alignment Tool
- BWI(4) - Broadcom BCM43xx IEEE 802.11b/g wireless network driver
- BWILD(1) - Bareos's 'wildcard' engine
- BWILD(8) - Bacula's 'wildcard' engine
- bwm-ng(1) - Bandwidth Monitor NG (Next Generation), a live bandwidth monitor for network and disk io.
- BWN(4) - Broadcom BCM43xx SoftMAC IEEE 802.11 wireless network driver
- bwping(8) - bwping and bwping6 are tools to measure bandwidth and response times between two hosts using Internet Control Message Protocol (ICMP) echo request/echo reply mechanism.
- BXE(4) - QLogic NetXtreme II Ethernet 10Gb PCIe adapter driver
- bximage(1) - Interactive Disk Image Creation, Conversion, Resize and Redolog Commit Tool for Bochs
- bxl2txt(1) - decode a binary BXL file and dump the plain text content
- byobu(1) - wrapper script for seeding a user's byobu configuration and launching a text based window manager (either screen or tmux)
- byobu-config(1) - Configuration utility for byobu
- byobu-ctrl-a(1) - Configure Byobu's ctrl-a behavior
- byobu-enable(1) - wrapper script for enabling/disabling automatic startup of byobu after login into text console
- byobu-export(1) - DEPRECATED
- byobu-janitor(1) - script for cleaning and upgrading environment after upgrades
- byobu-keybindings(1) - toggle on/off Byobu's keybindings
- byobu-launcher(1) - Byobu Launcher
- byobu-launcher-install(1) - Byobu Launcher installation utility
- byobu-launcher-uninstall(1) - Byobu Launcher uninstallation utility
- byobu-layout(1) - Save and restore byobu-tmux layouts
- byobu-prompt(1) - add and remove a nice color prompt to your shell configuration
- byobu-quiet(1) - Silence all of Byobu's status indicators and eliminate the hardstatus line
- byobu-reconnect-sockets(1) - Sourcable script that updates GPG_AGENT_INFO and DBUS_SESSION_BUS_ADDRESS in the environment
- byobu-screen(1) - Launch byobu with screen as the backend
- byobu-select-backend(1) - select your default Byobu backend window manager
- byobu-select-profile(1) - select your Byobu foreground and background colors
- byobu-select-session(1) - select and connect to a byobu session
- byobu-shell(1) - Print the message of the day and launch a shell
- byobu-silent(1) - byobu-silent- Silence all of Byobu's status indicators, eliminate the hardstatus line, and the window list
- byobu-status(1) - displays status suitable for printing by the BYOBU_BACKEND
- byobu-status-detail(1) - Wrapper that uses a sensible pager
- byobu-tmux(1) - Launch byobu with tmux as the backend
- byobu-ugraph(1) - helper script for notification history graphs
- byobu-ulevel(1) - helper script for notification level indicators
- BYTE2UNI(1) - shows what some encoding's byte should be in Unicode
- ByteLoader(3) - load byte compiled perl code
- BYTEORDER(3) - convert values between host and network byte order
- BYTEORDER(9) - byte order operations
- Bytes(3) - Byte sequence operations.
- bytes(3) - Perl pragma to expose the individual bytes of characters
- Bytes::Random::Secure(3) - Perl extension to generate cryptographically-secure random bytes.
- Bytes::Random::Secure::Tiny(3) - A tiny Perl extension to generate cryptographically-secure random bytes.
- BYTESHUF(1) - Shuffle or unshuffle bytes in a file
- BytesLabels(3) - Byte sequence operations.
- BYTGPIO(4) - Intel Bay Trail SoC GPIO controller
- bz2(n) - Data compression "bz2"
- bz3grep(1) - print lines matching a pattern in bzip3-compressed files
- bz3less(1) - view bzip3-compressed files
- bz3more(1) - view bzip3-compressed files
- bz3most(1) - view bzip3-compressed files
- BZ::Client(3) - A client for the Bugzilla web services API.
- BZ::Client::API(3) - This is an abstract base class for classes like BZ::Client::Product, which are subclassing this one, in order to inherit common functionality.
- BZ::Client::Bug(3) - This class provides methods for accessing and managing bugs in Bugzilla.
- BZ::Client::Bugzilla(3) - This class provides methods for accessing information about the Bugzilla servers installation.
- BZ::Client::Exception(3) - BZ::Client does not return error codes or do similar stuff. Instead, it throws instances of BZ::Client::Exception.
- BZ::Client::Product(3) - This class provides methods for accessing and managing products in Bugzilla. Instances of this class are returned by BZ::Client::Product::get.
- BZ::Client::Test(3) - Module for writing integration tests
- BZ::Client::XMLRPC(3) - Performs XML-RPC calls on behalf of the client.
- BZADMIN(6) - a text based client for BZFlag
- BZDIFF(1) - compare bzip2 compressed files
- BZERO(3) - write zeroes to a byte string
- BZFLAG(6) - a tank battle game
- BZFS(6) - BZFlag game server
- BZIP(1) - a block-sorting file compressor, v0.21
- bzip2(1) - a block-sorting file compressor, v1.0.8 bzcat - decompresses files to stdout bzip2recover - recovers data from damaged bzip2 files
- bzip3(1) - an efficient statistical file compressor and spiritual successor to bzip2
- BZMORE(1) - file perusal filter for crt viewing of bzip2 compressed text
- BZW(5) - BZFlag world file format
- BZZ(1) - DjVu general purpose compression utility.