Biostar90204

##Motivation

linux split equivalent for BAM file . See also http://www.biostars.org/p/90204

##Compilation

See also Compilation.

$ make biostar90204

##Synopsis

$ java -jar dist/biostar90204.jar (stdin|file) 

##Options

Option	Description
-n (int)	put NUMBER of SAM RECORD per output file. REQUIRED.
-p (prefix)	output file prefix. default:_splitbam
-a (int)	suffix length. default:.2
-M (fileout)	manifest file. Optional
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar90204.java

##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	??????????????????????????

##See also

• SplitBam

##History

• 2014: Creation