Equivalent of unix ‘comm’ for bams sorted on queryname
Usage: commbams [options] Files
Options:
-delim, --delimiter
Output delimiter
Default:
-empty, --empty
Empty content symbol
Default: .
-f, --format
What should I print ? (only the read name ? etc...)
Default: name
Possible Values: [name, but_metadata, all]
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-1, --hide1
suppress read unique to file 1
Default: false
-2, --hide2
suppress read unique to file 2
Default: false
-3, --hide3
suppress reads present in both files
Default: false
-o, --out
Output file. Optional . Default: stdout
-sortmethod, --sortmethod
[20171110]Method used to sort the read on query name. (samtools !=
picard) see https://github.com/samtools/hts-specs/issues/5
Default: picard
Possible Values: [samtools, picard]
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew commbams
The java jar file will be installed in the dist
directory.
20170420
The project is licensed under the MIT license.
Should you cite commbams ? 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
$ java -jar dist/commbams.jar \
-f but_metadata -delim '\n' \
B00GWFP_std.hg19.qname.bam B00GWFP_S1.hg19.qname.bam
PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/1 83 chr5 21564864 40 151M = 21564540 -475 CTCCCAGAGAGAAGCATCAACAGCTTAGGGTGTAGTCTAAACAGAAATCTTGCACTCCTCCTGCAGTAGCGTCTCTATTTTTTATGCTGAACATTATTTGCTAATTCCAACTGGCTCTAAGCTAATGTGTTTCCCAGGTTTTCTCAATGAN AFAA<,,,<,,,,,,,,7,,,,7,,,,A7KKF<,F,,7,7,A,A7F7,K<A,,,,7,,,7KKKFAFA,7,A7F7,7,,,KFF,,AKKFFFF<<K<<KAFAKA,A,,A7,AAAFKFA,A,FKKAA,AKKKKFFFKF<KKKKKKKFFAAAA<#
PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/1 77 * 0 0 * * 0 0 NTCATTGAGAAAACCTGGGAAACACATTAGCTTAGAGCCAGTTGGAATTAGCAAATAATGTTCAGCATAAAAAATAGAGACGCTACTGCAGGAGGAGTGCAAGATTTCTGTTTAGACTACACCCTAAGCTGTTGATGCTTCTCTCTGGGA !<AAAAFFKKKKKKK<FKFFFKKKKA,AAKKF,A,AFKFAAA,7A,,A,AKAFAK<<K<<FFFFKKA,,FFK,,,7,7F7A,7,AFAFKKK7,,,7,,,,A<K,7F7A,A,7,7,,F,<FKK7A,,,,7,,,,7,,,,,,,,<,,,<AAF
PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/2 163 chr5 21564540 60 8S106M37S = 21564864 475 NTAAGAATATTTCACACTTAAAACAAAATCTGATTAGACAAACACTTTGATTGTTATTATTCGCGTATATCATCTACCAGAAGCAAATAGACATCTACTACATCTTTCAAGAAAGTTTACCTATCAATATTACTCAACTGGACCCAATAAT #<A,<,,A,,K<7FKFF,7,,AF,,7,7AAF,,7<<,,7,AF,,7,7A<,7FA,,7,,7F,,A7FKK7,7,,,,,7,,,,,<,<,,,,7,<,,,,,,7FF7AF<7,,<,,,,7,7,,,,,,,<,,,,,,,,,,,,,,,,,,<,,,,,,,,,
PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/2 141 * 0 0 * * 0 0 NTAAGAATATTTCACACTTAAAACAAAATCTGATTAGACAAACACTTTGATTGTTATTATTCGCGTATATCATCTACCAGAAGCAAATAGACATCTACTACATCTTTCAAGAAAGTTTACCTATCAATATTACTCAACTGGACCCAATAA !<A,<,,A,,K<7FKFF,7,,AF,,7,7AAF,,7<<,,7,AF,,7,7A<,7FA,,7,,7F,,A7FKK7,7,,,,,7,,,,,<,<,,,,7,<,,,,,,7FF7AF<7,,<,,,,7,7,,,,,,,<,,,,,,,,,,,,,,,,,,<,,,,,,,,
$ java -jar dist/commbams.jar --samtools \
B00GWFP_std.hg19.qname.bam B00GWFP_S1.hg19.qname.bam
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/1
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:5388/2
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:6513/1
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:6513/2
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:7181/1
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:7181/2
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:10205/1
. . PANORAMIX:1:HJY2CCCXX:7:1101:1133:10205/2
. PANORAMIX:1:HJY2CCCXX:7:1101:1133:10380/1 .
. PANORAMIX:1:HJY2CCCXX:7:1101:1133:10380/2 .