NAME

BIOLIBC - Library of high-performance low-level functions for bioinformatics programming

SYNOPSIS

One of more of the following headers will be needed for each function used:

#include <biolibc/bed.h>
#include <biolibc/biolibc.h>
#include <biolibc/biostring.h>
#include <biolibc/gff.h>
#include <biolibc/overlap.h>
#include <biolibc/pos-list.h>
#include <biolibc/sam.h>
#include <biolibc/sam-buff.h>
#include <biolibc/vcf.h>
cc -I<prefix>/include program.c -L<prefix>/lib -lbiolibc -lxtend

PURPOSE

Biolibc is a library of fast, memory-efficient, low-level functions for processing biological data.

Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications.

These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc.

Documentation on individual functions should be available soon.

FUNCTIONS

bl_align_map_seq_exact(3) - Locate little sequence within big sequence
bl_align_map_seq_sub(3) - Locate little sequence within big sequence
bl_bed_check_order(3) - Compare positions of two bed records
bl_bed_gff3_cmp(3) - Compare positions of BED and GFF3 objects
bl_bed_read(3) - Read a BED record
bl_bed_skip_header(3) - Read past BED header
bl_bed_write(3) - Write a BED record
bl_chrom_name_cmp(3) - Compare chromosome names numerically or lexically
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_write(3) - Write a FASTA object
bl_fastq_3p_trim(3) - Trim 3' end of a FASTQ object
bl_fastq_find_3p_low_qual(3) - Find start of low-quality 3' 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_read(3) - Read a FASTQ record
bl_fastq_write(3) - Write a FASTQ record
bl_fastx_desc(3) - Return  description of a FASTX (FASTA or FASTQ) object
bl_fastx_desc_len(3) - Return length of a FASTX (FASTA or FASTQ)
bl_fastx_free(3) - Free memory for a FASTX (FASTA or FASTQ) object
bl_fastx_init(3) - Initialize a FASTX (FASTA or FASTQ) 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 FASTA or FASTQ record
bl_fastx_seq(3) - Return sequence of a FASTX (FASTA or FASTQ) object
bl_fastx_seq_len(3) - Return sequence length of a FASTX (FASTA or FASTQ)
bl_fastx_write(3) - Write FASTA or FASTQ 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_init(3) - Initialize all fields in a GFF3 object
bl_gff3_read(3) - Read a GFF3 feature
bl_gff3_sam_cmp(3) - Compare positions of a SAM alignment and GFF3
bl_gff3_sam_overlap(3) - Compute overlap between a SAM alignment
and a GFF3 feature
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_next_start_codon(3) - Find next start codon
bl_next_stop_codon(3) - Find next stop codon
bl_overlap_print(3) - Print overlap summary for two features
bl_overlap_set_all(3) - Set overlap fields for two features
bl_pos_list_add_position(3) - Add a position to a list
bl_pos_list_allocate(3) - Initialize position list object
bl_pos_list_free(3) - Free a position list object
bl_pos_list_from_csv(3) - Convert from comma-separated data to
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_check_order(3) - Check sort order of SAM records
bl_sam_buff_free_alignment(3) - Free an alignment in a SAM buffer
bl_sam_buff_init(3) - Initialize a SAM buffer object
bl_sam_buff_out_of_order(3) - Print sort order message and exit
bl_sam_buff_shift(3) - Close gap after removing a SAM alignment
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_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) - Return the amount of overlap between a
SAM alignment and a GFF3 feature
bl_sam_init(3) - Initialize all fields of a SAM object
bl_sam_read(3) - Read one SAM record
bl_sam_skip_header(3) - Read past SAM header
bl_sam_write(3) - Write a SAM object to a file stream
bl_vcf_call_downstream_of_alignment(3) - Return true if the location
of a VCF call is downstream of an alignment
bl_vcf_call_in_alignment(3) - Return true if location of VCF call is
bl_vcf_call_out_of_order(3) - Terminate with VCF sort error message
bl_vcf_free(3) - Destroy a VCF object
bl_vcf_get_sample_ids(3) - Extract sample IDs from a VCF header
bl_vcf_init(3) - Initialize fields in a VCF object
bl_vcf_parse_field_spec(3) - Convert comma-separated fields to bitmask
bl_vcf_read_ss_call(3) - Read a single-sample VCF call
bl_vcf_read_static_fields(3) - Read static VCF fields
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

SEE ALSO

vcf-split, ad2vcf, vcf2hap, peak-classifier

BUGS

Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR

J. Bacon