jvarkit

CommBams

Last commit

Equivalent of unix ‘comm’ for bams sorted on queryname

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar commbams  [options] Files

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