jvarkit

Biostar84452

Last commit

remove clipped bases from a BAM file

Usage

Usage: biostar84452 [options] Files
  Options:
    --bamcompression
      Compression Level.
      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
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    -t, --tag
      tag to flag samrecord as processed
    --version
      print version and exit

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar84452

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar84452.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar84452 ? 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

Cited In

Example

$  java -jar dist/biostar84452.jar samtools-0.1.18/examples/toy.sam > out.sam

@HD	VN:1.4	SO:unsorted
@SQ	SN:ref	LN:45
@SQ	SN:ref2	LN:40
@PG	ID:0	PN:com.github.lindenb.jvarkit.tools.biostar.Biostar84452	VN:b5ebf67dd2926d8a6afadb4d1e36a4959508057f	CL:samtools-0.1.18/examples/toy.sam
(...)
r002	0	ref	9	0	2I6M1P1I1P1I4M2I	*	0	0	AAAGATAAGGGATAAA	*
(...)


$ grep r002 samtools-0.1.18/examples/toy.sam
r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*

See also