jvarkit

Biostar234081

convert extended CIGAR to regular CIGAR (‘X’,’=’ -> ‘M’)

Usage

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

Usage: java -jar dist/jvarkit.jar biostar234081  [options] Files

Usage: biostar234081 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      For reading/writing CRAM files. Indexed fasta Reference file. This file 
      must be indexed with samtools faidx and with picard/gatk 
      CreateSequenceDictionary or samtools dict
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

• sam
• bam
• cigar

See also in Biostars

• https://www.biostars.org/p/234081

Creation Date

20170130

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar234081.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar234081Test.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 biostar234081 ? 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

 $ cat toy.sam 
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  1M2X5=4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG*XX:B:S,12561,2,20,112

 $ java -jar dist/biostar234081.jar toy.sam 
@HD VN:1.5  SO:unsorted
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG*XX:B:S,12561,2,20,112

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