jvarkit

SamJdk

Filters a BAM using a java expression compiled in memory.

Usage

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

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

Usage: samjdk [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --body
      user's code is the whole body of the filter class, not just the 'apply' 
      method. 
      Default: false
    -e, --expression
      java expression
    -X, --fail
      Save dicarded reads in that file
    -f, --file
      java file. Either option -e or -f is required.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -N, --limit
      limit to 'N' records (for debugging).
      Default: -1
    --nocode
       Don't show the generated code
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --pair
      [20171110] PAIR-MODE .The signature of java function is `public Object 
      apply(final List<SAMRecord> records)`. This function must return `true` 
      to accept the whole list, `false` to reject eveything, or another 
      `List<SAMRecord>`.Input MUST be sorted on query name using picard 
      SortSam (not `samtools sort` 
      https://github.com/samtools/hts-specs/issues/5 ).
      Default: false
    -R, --reference
      For reading CRAM. Indexed fasta Reference file. This file must be 
      indexed with samtools faidx and with picard CreateSequenceDictionary
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --saveCodeInDir
      Save the generated java code in the following directory
    --version
      print version and exit

Keywords

• sam
• bam
• java
• jdk
• filter

See also in Biostars

• https://www.biostars.org/p/270879
• https://www.biostars.org/p/274183
• https://www.biostars.org/p/278902
• https://www.biostars.org/p/279535
• https://www.biostars.org/p/283969
• https://www.biostars.org/p/286284
• https://www.biostars.org/p/286585
• https://www.biostars.org/p/286851
• https://www.biostars.org/p/286819
• https://www.biostars.org/p/287057
• https://www.biostars.org/p/299673
• https://www.biostars.org/p/301080
• https://www.biostars.org/p/305526
• https://www.biostars.org/p/306034
• https://www.biostars.org/p/309143
• https://www.biostars.org/p/327317
• https://www.biostars.org/p/335998
• https://www.biostars.org/p/336965
• https://www.biostars.org/p/340479
• https://www.biostars.org/p/342675
• https://www.biostars.org/p/345679
• https://www.biostars.org/p/362298
• https://www.biostars.org/p/368754
• https://www.biostars.org/p/378205
• https://www.biostars.org/p/408279
• https://www.biostars.org/p/417123
• https://www.biostars.org/p/427976
• https://www.biostars.org/p/424431
• https://www.biostars.org/p/450160
• https://www.biostars.org/p/9464312
• https://www.biostars.org/p/9489815
• https://www.biostars.org/p/9493510
• https://www.biostars.org/p/9498170
• https://www.biostars.org/p/9511167
• https://www.biostars.org/p/9524098
• https://www.biostars.org/p/9532167
• https://www.biostars.org/p/9537698

Creation Date

20170807

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/samjs/SamJdk.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/samjs/SamJdkTest.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 samjdk ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

• “bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files” . Bioinformatics, 2017. Pierre Lindenbaum & Richard Redon https://doi.org/10.1093/bioinformatics/btx734.

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