Selects the input format, where format is one of sam, bam or
cram. Use this when reading via a pipe to avoid input bytes being
consumed when attempting to detect if the input is in SAM or BAM format.
Selects the output format, where format is one of sam, bam or cram.
|-1 to -9|
Sets the compression level from 1 (low compression, fast) to 9 (high
compression, slow) when writing in BAM or CRAM format. This is only
used during writing.
|-0 or -u|
Writes uncompressed data. In BAM this still uses BGZF containers, but
with no internal compression. In CRAM it stores blocks in RAW format
instead. The option has no effect on SAM output.
CRAM encoding only. Add bzip2 to the list of compression codes
potentially used during CRAM creation.
CRAM encoding only. Add lzma to the list of compression codes
potentially used during CRAM creation. Given the slow compression
speed of lzma, this may only be used where it gives a significant
advantage over zlib or bzip2, but with higher compression levels (-7)
this weighting is ignored as LZMA decompression speed is acceptable,
albeit still slower than zlib.
CRAM decoding only. Generate MD:Z: and NM:I: auxiliary fields based on
the reference-based compression.
CRAM encoding only. Forcibly pack sequences from multiple references
into the same slice. Normally CRAM will start a new slice when
changing from one reference to another, but will still automatically
switch to multi-reference slices if the number of sequences per slice
becomes too small.
Currently for CRAM input only, but SAM/BAM support is pending. This
indicates a reference sequence name and optionally a start and end
location within that reference, using the syntax ref_name or
ref_name:start-end. For efficient operation the CRAM
file needs a .crai format index (built using the cram_index
CRAM encoding only. Use this to specify the reference fasta file.
Note that if the input SAM or BAM file a file: or local file
system based URI specified in the @SQ headers then this option may
not be necessary.
CRAM encoding only. Specifies the number of sequecnes per slice.
Defaults to 10000.
CRAM encoding only. Specifies the number of slices per container.
Defaults to 1.
BAM and CRAM only. Specifies the number of compression or
decompression threads, adaptively shared between both encoding and
decoding. Defaults to 1 (no threading).
CRAM encoding only. Sets the CRAM file format version. Supported values are
"2.0", "2.1" and "3.0".
CRAM encoding only. Embed snippets of the reference sequence in every slice.
This means the files can be decoded without needing to specify the
reference fasta file.
CRAM encoding only. Omit reference based compression and instead
store details of every base verbatim.
Experimental, encoding only. When storing quality values, bin into 8
discrete values (plus 0), as typically used by modern Illumina
instruments. (Note that the bins may not be precisely the same ranges.)
CRAM v3.0 and above decoding only. Do not check CRCs. This option
should only be used when attempting to recover from a data corruption.
To convert a BAM file from stdin to CRAM on stdout, using reference MT.fa.
some_command | scramble -I bam -O cram -r MT.fa | some_command
The default CRAM output format is version 3.0, so no version needs to be specified when converting from 2.1 to 3.0. To perform the reverse use:
scramble -V 2.1 in.cram out.cram
James Bonfield, Wellcome Trust Sanger Institute
|SCRAMBLE (1)||March 19 2013|