jvarkit

FastqSplitInterleaved

Split interleaved Fastq files.

Usage

Usage: fastqsplitinterleaved [options] Files
  Options:
    -async, --async
      use async I/O
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -md5, --md5
      write md5 file
      Default: false
    --version
      print version and exit
  * -a, -R1, -F
      R1 file
  * -b, -R2, -R
      R2 file

Keywords

• fastq

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

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

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/fastq/FastqSplitInterleaved.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 fastqsplitinterleaved ? 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

$ curl -sk "https://raw.githubusercontent.com/bigdatagenomics/adam/fff8ae259e8f6958eefd8de9a3ec39d33392fb21/adam-core/src/test/resources/interleaved_fastq_sample1.fq" |\
	java -jar dist/fastqsplitinterleaved.jar  -R1 R1.fastq.gz -R2 R1.fastq.gz 

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