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/gatk
CreateSequenceDictionary or samtools dict
--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
- https://www.biostars.org/p/9567318
- https://www.biostars.org/p/9586160
- https://www.biostars.org/p/9586764
Creation Date
20170807
Source code
Unit Tests
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.