jvarkit

Biostar90204

Last commit

Bam version of linux split.

Usage

Usage: biostar90204 [options] Files
  Options:
    --bamcompression
      Compression Level.
      Default: 5
    -n, --count
      Number of records per file.
      Default: -1
    --filter
      A JEXL Expression that will be used to filter out some sam-records (see 
      https://software.broadinstitute.org/gatk/documentation/article.php?id=1255). 
      An expression should return a boolean value (true=exclude, false=keep 
      the read). An empty expression keeps everything. The variable 'record' 
      is the current observed read, an instance of SAMRecord (https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html).
      Default: 'Accept all' (Empty expression)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -M, --manifest, -o
      Manifest file. Optional
    -a, --padding
      '0' padding length
      Default: 2
    -p, --prefix
      (prefix) output file prefix.
      Default: _splitbam
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar90204

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar90204.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar90204Test.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar90204 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

##Example

$ java -jar dist/biostar90204.jar -m bam.manifest -n 3 -a 5 samtools-0.1.18/examples/toy.sam

$ cat bam.manifest
_splitbam.00001.bam	1	3
_splitbam.00002.bam	4	6
_splitbam.00003.bam	7	9
_splitbam.00004.bam	10	12

$ samtools-0.1.18/samtools view -h _splitbam.00003.bam 
@HD	VN:1.4	SO:unsorted
@SQ	SN:ref	LN:45
@SQ	SN:ref2	LN:40
@PG	ID:0	PN:com.github.lindenb.jvarkit.tools.biostar.Biostar90204	VN:7e17f8bd273cf081d4415bc4f579cd34e2c681d1	CL:-m bam.manifest -n 3 -a 5 samtools-0.1.
18/examples/toy.sam
@CO	SPLIT:3
@CO	SPLIT:Starting from Read7
x1	0	ref2	1	30	20M	*	0	0	AGGTTTTATAAAACAAATAA	????????????????????
x2	0	ref2	2	30	21M	*	0	0	GGTTTTATAAAACAAATAATT	?????????????????????
x3	0	ref2	6	30	9M4I13M	*	0	0	TTATAAAACAAATAATTAAGTCTACA	??????????????????????????