jvarkit

FastqRecordTreePack

Create a TreeMap from one or more Fastq file. Ouput is a SVG file

Usage

Usage: fastqrecordtreepack [options] Files
  Options:
    -c, --config
      XML config file
    -x, --dimension
      dimension of the output rectangle
      Default: 1000x1000
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

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 fastqrecordtreepack

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/treepack/FastqRecordTreePack.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 fastqrecordtreepack ? 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

Synopsis

$ java -jar dist/fastqrecordtreepack.jar -c config.xml (stdin|fq1.gz fq2.gz ...) gt; out.svg

XML config

XML root is . children is '' . A '' has an attribute 'name'. The text content of the will be evaluated as a javascript expression with the embedded javascript engine. The javascript engine injects record a https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/fastq/FastqRecord.html and header a https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html.

Example

$ cat config.xml

<?xml version="1.0"?>
<treepack>
	<node name="length">record.length()</node>
	<node name="firstBase">(record.length()&gt;0?record.getReadString().charAt(0):null)</node>
</treepack>

s

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA21144/sequence_read/ERR047877.filt.fastq.gz" |\
   gunzip -c | java -jar dist/fastqrecordtreepack.jar -c) config.xml  > out.svg

See also

• VcfTreePack
• http://www.cs.umd.edu/hcil/treemap-history/

XML config

XML root is . children is '' . A '' has an attribute 'name'. The text content of the will be evaluated as a javascript expression with the embedded javascript engine. The javascript engine injects **record** a [https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/fastq/FastqRecord.html](https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/fastq/FastqRecord.html) and **header** a [https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html](https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html).

Example

$ cat config.xml

<?xml version="1.0"?>
<treepack>
	<node name="length">record.length()</node>
	<node name="firstBase">(record.length()&gt;0?record.getReadString().charAt(0):null)</node>
</treepack>

s

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA21144/sequence_read/ERR047877.filt.fastq.gz" |\
   gunzip -c | java -jar dist/fastqrecordtreepack.jar -c) config.xml  > out.svg

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