jvarkit

FindHtsFileDictionary

Scan a set of HTS files (VCF, BAM, CRAM, BCF, etc…), return a tab delimited file (path-of-file,path-to-fasta)

Usage

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

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

Usage: findhtsfiledict [options] Files
  Options:
  * -D, -R, --repository, --dictionaries
      A tab delimited file with a required header, and required columns: 
      'name' (name of the reference) and 'fasta' (path to the indexed fasta 
      ref). 
    -e, --errors
      What shall we do on error
      Default: fatal
      Possible Values: [ignore, fatal, empty]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --no-header
      Do not print header
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• sam
• bam
• cram
• vcf
• dict

Creation Date

20190912

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/FindHtsFileDictionary.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 findhtsfiledict ? 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 references.txt
name	fasta
rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
toy	/home/lindenb/src/jvarkit-git/src/test/resources/toy.fa


$ find . -name "*.bam" -o -name "*.vcf" -o -name "*.vcf.gz" -o -name "*.cram" |\
	java -jar dist/jvarkit.jar findhtsfiledict  -R references.txt

[SEVERE][FindHtsFileDictionary]No Reference found for ./e90235dca2ff2d151ef796ad0be98915/test01.vcf
java.io.IOException: No Reference found for ./e90235dca2ff2d151ef796ad0be98915/test01.vcf
	at com.github.lindenb.jvarkit.tools.misc.FindHtsFileDictionary.scan(FindHtsFileDictionary.java:193)
	at com.github.lindenb.jvarkit.tools.misc.FindHtsFileDictionary.doWork(FindHtsFileDictionary.java:213)
	at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:756)
	at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:919)
	at com.github.lindenb.jvarkit.tools.misc.FindHtsFileDictionary.main(FindHtsFileDictionary.java:241)
#hts-file	dict.name	fasta
/home/lindenb/src/jvarkit-git/./b7/83f96c410c7cd75bc732d44a1522a7/Gene_32_1507.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
[INFO][Launcher]findhtsfiledict Exited with failure (-1)


$ find ${PWD}/ -name "*.bam" -o -name "*.vcf" -o -name "*.vcf.gz" -o -name "*.cram" |\
	java -jar dist/jvarkit.jar findhtsfiledict  -R references.txt -e ignore

#hts-file	dict.name	fasta
/home/lindenb/src/jvarkit-git/b7/83f96c410c7cd75bc732d44a1522a7/Gene_32_1507.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/db/aee9cc8f5c9c3d39c7af4cec63b7a5/Gene_0_1061.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/jeter.cram	toy	/home/lindenb/src/jvarkit-git/src/test/resources/toy.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S5.bam	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/toy.vcf.gz	toy	/home/lindenb/src/jvarkit-git/src/test/resources/toy.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S1.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S2.bam	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S5.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S4.bam	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S3.bam	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/toy.cram	toy	/home/lindenb/src/jvarkit-git/src/test/resources/toy.fa
/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S2.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S4.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S1.bam	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/toy.bam	toy	/home/lindenb/src/jvarkit-git/src/test/resources/toy.fa
/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.ann.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/S3.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa
/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.freebayes.vcf.gz	rf	/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa

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