jvarkit

PadEmptyFastq

Pad empty fastq sequence/qual with N/#

DEPRECATED

use awk

Usage

Usage: pademptyfastq [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -N
      number of bases/qual to be added.  -1=length of the first read
      Default: -1

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 pademptyfastq

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/misc/PadEmptyFastq.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/PadEmptyFastqTest.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 pademptyfastq ? 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

AWK

compiled version of awk:

{if(NR%4==2 && length($0)==0) { printf("NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n");} else if(NR%4==0 && length($0)==0) { printf("##################################################\n");} else {print;}}

Example

$ cutadapt -a AGATCGGAAGAGCGTCGT  2> /dev/null in.fastq.gz |\
  java -jar dist/pademptyfastq.jar -o pad.fastq.gz

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