SamJS

Filtering a SAM/BAM file with javascript

Motivation

Filters a BAM using javascript ( java rhino engine http://en.wikipedia.org/wiki/Rhino_%28JavaScript_engine%29 ).

Synopsis

$  java -jar dist/samjs.jar [options] (-e script | -f file ) (f.bam|f.sam|stdin)

Compilation

See also Compilation

$ make samjs

Scripting

The script puts the following variables in the script context:

• 'record' a SamRecord ( https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/SAMRecord.java )
• 'header' ( https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/SAMFileHeader.java )

Options

Option	Description
-f (File)	javascript file
-e (script)	javascript expression.
-N (long)	limit to 'N' records. Optional.
-c (int)	max records in RAM. Optional.
-X (fail.bam) Save dicarded reads in that file. Optional. Default: no file.	max records in RAM. Optional.

Example

get a SAM where the read OR the mate is unmapped

java -jar dist/samjs.jar  \
	-e "record.readUnmappedFlag || record.mateUnmappedFlag;" \
	ex1.bam

@HD	VN:1.4	SO:unsorted
@SQ	SN:seq1	LN:1575
@SQ	SN:seq2	LN:1584
B7_591:4:96:693:509	73	seq1	1	99	36M	*	0	0	CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG	<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
EAS54_65:7:152:368:113	73	seq1	3	99	35M	*	0	0	CTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGT	<<<<<<<<<<0<<<<655<<7<<<:9<<3/:<6):	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
EAS51_64:8:5:734:57	137	seq1	5	99	35M	*	0	0	AGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCC	<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:66
B7_591:1:289:587:906	137	seq1	6	63	36M	*	0	0	GTGGCTCATTGTAATTTTTTGTTTTAACTCTTCTCT	(-&----,----)-)-),'--)---',+-,),''*,	H0:i:0	H1:i:0	MF:i:130	NM:i:5	UQ:i:38	Aq:i:63
EAS56_59:8:38:671:758	137	seq1	9	99	35M	*	0	0	GCTCATTGTAAATGTGTGGTTTAACTCGTCCATGG	<<<<<<<<<<<<<<<;<;7<<<<<<<<7<<;:<5%	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:72
EAS56_61:6:18:467:281	73	seq1	13	99	35M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCCTGGCCCA	<<<<<<<<;<<<8<<<<<;8:;6/686&;(16666	H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:5	Aq:i:39
EAS114_28:5:296:340:699	137	seq1	13	99	36M	*	0	0	ATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAG	<<<<<;<<<;<;<<<<<<<<<<<8<8<3<8;<;<0;	H0:i:1	H1:i:0	MF:i:18	NM:i:0	UQ:i:0	Aq:i:73
B7_597:6:194:894:408	73	seq1	15	99	35M	*	0	0	TGTAAATGTGTGGTTTAACTCGTCCATTGCCCAGC	<<<<<<<<<7<<;<<<<;<<<7;;<<<*,;;572<	H0:i:0	H1:i:1	MF:i:18	NM:i:1	UQ:i:9	Aq:i:43
EAS188_4:8:12:628:973	89	seq1	18	75	35M	*	0	0	AAATGTGTGGTTTAACTCGTCCATGGCCCAGCATT	==;=:;:;;:====;=;===:=======;==;===	H0:i:1	H1:i:0	MF:i:64	NM:i:0	UQ:i:0	Aq:i:0
(...)

##History

• Dec 2013: moved to a standard argc/argv command line.
• Dec 2013-20: added option -X

See also:

• http://www.biostars.org/p/75168/#75187
• http://www.biostars.org/p/81750/#81759
• http://www.biostars.org/p/75354/#75363
• http://www.biostars.org/p/77802/#77966
• https://www.biostars.org/p/103052
• https://www.biostars.org/p/106900/#106912
• https://www.biostars.org/p/150530/
• VCFFilterJS.

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

##See also

##History

• 2013 : Creation

License

The project is licensed under the MIT license.