jvarkit

Biostar234230

Sliding Window : discriminate partial and fully contained fragments (from a bam file)

Usage

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

Usage: java -jar dist/jvarkit.jar biostar234230  [options] Files

Usage: biostar234230 [options] Files
  Options:
    -filter, --filter
      A filter expression. Reads matching the expression will be filtered-out. 
      Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj 
      for a complete syntax. 'default' is 'mapqlt(1) || Duplicate() || 
      FailsVendorQuality() || NotPrimaryAlignment() || 
      SupplementaryAlignment()' 
      Default: mapqlt(1) || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment()
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -s, --winshift
      Shift each window by 's' bases.A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 50
    -w, --winsize
      Window size. A distance specified as a positive integer.Commas are 
      removed. The following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 100

Keywords

• sam
• bam

See also in Biostars

• https://www.biostars.org/p/234230

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar234230.java

Contribute

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

License

The project is licensed under the MIT license.

Citing

Should you cite biostar234230 ? 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

Example:

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110915_CEUtrio_b37_decoy_alignment/CEUTrio.HiSeq.WGS.b37_decoy.NA12892.clean.dedup.recal.bam" |  java -jar dist/biostar234230.jar 
#contig	start	end	pairs_in_window	pairs_over_window	pairs_partial_overlap
1	10000	10100	0	2	240
1	10050	10150	4	615	274
1	10100	10200	0	800	276
1	10150	10250	0	216	649
1	10200	10300	0	2982	809
1	10250	10350	0	2918	207
1	10300	10400	0	1923	2851
1	10350	10450	0	227	4498
1	10400	10500	0	31	1971
(...)

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