jvarkit

FindCorruptedFiles

Reads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ/BED/TBI/BAI)

Usage

Usage: findcorruptedfiles [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -E, --noempty
      empty file is an error.
      Default: false
    -V, --stringency
      BAM ValidationStringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit
    -N
      number of features (samrecord, variant) to read. -1= read everything.
      Default: 100

Keywords

• vcf
• bam
• fastq
• bed

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 findcorruptedfiles

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/FindCorruptedFiles.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 findcorruptedfiles ? 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

$ find  DIR1 DIR2 -type f |\
java -jar dist/findcorruptedfiles.jar \
	-V SILENT 2> /dev/null > redo.txt

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