Biostar173114

Last commit

make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114/

Usage

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

Usage: java -jar dist/jvarkit.jar biostar173114  [options] Files

Usage: biostar173114 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 9
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -keepAtt, --keepAttributes
      keep Attributes
      Default: false
    -keepCigar, --keepCigar
      keep cigar : don't remove hard clip
      Default: false
    -keepName, --keepName, --name
      keep Read Name, do not try to create a shorter name
      Default: false
    -keepQuals, --keepQualities
      keep base qualities
      Default: false
    -keepRG, --keepReadGroup
      if attributes are removed, keep the RG
      Default: false
    -keepSeq, --keepSequence
      keep read sequence
      Default: false
    -mate, --mate
      keep Mate/Paired Information
      Default: false
    -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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar173114.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar173114Test.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 biostar173114 ? 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

 $ java -jar dist/biostar173114.jar --keepSequence    my.bam  

@HD VN:1.5  GO:none SO:coordinate
@SQ SN:rotavirus    LN:1074
R0  0   rotavirus   1   60  70M *   0   0   GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAATATGGCGTCAACTCAGCAGATGGTCAGCTCTAATATT  *
R1  0   rotavirus   1   60  70M *   0   0   GGCTTTTACTGCTTTTCAGTGGTTGCTTCTCAAGATGGAGTGTACTCATCAGATGGTAAGCTCTATTATT  *
R2  0   rotavirus   1   60  70M *   0   0   GGCTTTTAATGCTTTTCATTTGATGCTGCTCAAGATGGAGTCTACACAGCAGATGGTCAGCTCTATTATT  *
R3  0   rotavirus   1   60  70M *   0   0   GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTCCTGAGCAGCTGGTAAGCTCTATTATT  *
R4  0   rotavirus   1   60  70M *   0   0   GGCATTTAATGCTTAACAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTCTTATT  *
R5  0   rotavirus   2   60  70M *   0   0   GCTTTTAAAGCTTTTCAGTTGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGTTACGCTCTATTATTA  *
R6  0   rotavirus   2   60  51M19S  *   0   0   GCTTTTAATGCTTTTCAGTTGTTGCTGCACAAGATGGAGTCTACACAGCAGCTGTTCATCTCTCTTCATC  *
R7  0   rotavirus   2   60  70M *   0   0   GCTTTTAATGCTTTTCAGTGGTTTCTTCTCACGATGGAGTCTACTCAGCAGAAGGTAAGCACTATTATTA  *
R8  0   rotavirus   2   60  70M *   0   0   GCTTTTAAAGCATTACAGTTGTTGCAGCTCAAGAAGGAGACTACTCAGCAGATGGTAAGCTCTATAATTA  *
R9  0   rotavirus   2   60  70M *   0   0   GCTTTTAATTCTATTCAGTGGTTGCTGCTCCAGAAGGAGTCTACTCAGGAGATGGTACGCTCTCTTATTA  *
Ra  0   rotavirus   2   60  70M *   0   0   GCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCAATTATTA  *
Rb  0   rotavirus   2   60  70M *   0   0   GCTTTTAATGCTTTTCAGTTGTAGCTGCTCAAGATGGAGTCTACTCATCAGATGGTAAGCTCTCTTCTTA  *
Rc  0   rotavirus   2   60  63M7S   *   0   0   TCTTTAAATGCTTTTCAGTGTTTGCTGCTCAAGATGGAGTCTACTCAGCAGAAGGTAAGCTCTCTTAAAC  *
Rd  0   rotavirus   2   60  66M4S   *   0   0   GCATTTAATGCTTTTCAGTGGTTGCTGCACAAGATGGAGTCTACTCAGCAGATTGTAAGCTCTATTCTAA  *
Re  0   rotavirus   3   60  70M *   0   0   CTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGAAGGCGTCTCCTGATGAGATGGTAAGCTCTATTATTAA  *
Rf  0   rotavirus   3   60  70M *   0   0   CTTTTAATGGTTATGAGTGGTTGGTGCACAAGATGGAGTCTACTCAGCAGATGGTACTCTCTATAATTAA  *
R10 0   rotavirus   3   60  70M *   0   0   CTTTTAAAGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTACTCTCTATTCTTAA  *
R11 0   rotavirus   3   60  70M *   0   0   CTTTTAAAGCTTTTCAGAGGTTGCTGCTCAAGATGTAGTCTACTCAGGAGATTGTAAGCTCTATTATTAA