Filtering a BAM with javascript.

The following was created to answer that question on biostar: "Exclude reads with XA tag". SamJs is a java program filtering the reads of a BAM file using the javascript engine for java (rhino).

Usage

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

for each SamRecord in the BAM, the program injects the following variables in the javascript context:

• 'record' a SamRecord ( http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMRecord.html ).
• 'header' a SAMFileHeader ( http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMFileHeader.html)

Options

• -S : SAM output.
• -e (script).
• -f (script-file).
• -L (int) limit to 'L' records.

Example

$ java -jar dist/samjs.jar -L 4  -S \
  -e '(record.inferredInsertSize > 60 || record.alignmentStart  < 50000000) && !record.readUnmappedFlag && record.getAttribute("MD")!=null ' \
 my.bam
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:247249719
IL31_4368:1:1:997:15684 163 chr1 241356442 60 54M = 241356612 224 CAGCCTCAGATTCAGCATTCTCAAATTCAGCTGCGGCTGAAACAGCAGCAGGAC EEEEDEEE9EAEEDEEEEEEEEEECEEAAEEDEE<CD=D=*BCAC?;CB,<D@, X0:i:1 X1:i:0 MD:Z:53T0 XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 XT:A:U
IL31_4368:1:1:997:1657 163 chr1 143630066 60 54M = 143630364 352 CCCACCTCTCTCAATGTTTTCCATATGGCAGGGACTCAGCACAGGTGGATTAAT A;0A?AA+@A<7A7019/<65,3A;'''07<A=<=>?7=?6&)'9('*%,>/(< X0:i:1 X1:i:0 MD:Z:54 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U
IL31_4368:1:1:999:9391 163 chr1 195364100 29 54M = 195364272 226 AAAAAAAAAAACCCTCATTTTTTTTAAGTACTAAATTTTTTTTCCCATTTGAAA 1>??E?>@BB>0A/43;,=9A98A(',0/<*4>>/@=90A51&(**3;>'*;=; MD:Z:11A5A7C12A2G1A1T1C6 XG:i:0 AM:i:29 NM:i:8 SM:i:29 XM:i:8 XO:i:0 XT:A:M
IL31_4368:1:1:1002:11012 99 chr1 147142473 60 54M = 147142575 156 NGATTAGTACATAGTAAGTACTCAATAGATGTTAGCTATTATTGTAATCACCGC (1*4+236332679?1..87><-6<@<7>>@><7;@@@>962$-6075584093 X0:i:1 X1:i:0 MD:Z:0A40C12 XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 XT:A:U

That's it,
Pierre