jvarkit

IndexCovJfx

Last commit

display indexcov data in a jfx client

Usage

Usage: indexcovjfx [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help
      Possible Values: [usage, markdown, xml]
    --version
      print version and exit

Keywords

cnv
jfx
duplication
deletion
sv

Compilation

Requirements / Dependencies

java compiler SDK 1.8 (NOT the old java 1.7 or 1.6, not the new 1.9) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make >= 3.81
curl/wget
git

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make indexcovjfx

The *.jar libraries are not included in the main jar file, so you shouldn’t move them. The required libraries will be downloaded and installed in the dist directory.

Experimental: you can also create a fat jar which contains classes from all the libraries, on which your project depends (it’s bigger). Those fat-jar are generated by adding standalone=yes to the gnu make command, for example ` make indexcovjfx standalone=yes`.

edit ‘local.mk’ (optional)

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/IndexCovJfx.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/IndexCovJfxTest.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 indexcovjfx ? 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

Input

input is a tab-delimited file created by e.g: indexcov (https://github.com/brentp/goleft/tree/master/indexcov)

#chrom  start  end     SampleBB  SampleBC  SampleBD  SampleBE  SampleBF  SampleBG  SampleBH
chr1    23778  40778   1.59      1.31      1.67      1.61      1.83      1.52      1.48
chr1    29106  46106   1.9       1.54      1.72      1.97      1.88      1.53      1.95
chr1    84581  101581  0.764     0.841     1.2       1.16      1.18      1.13      1.23
chr1    15220  32220   0.355     0.704     1.09      0.784     0.81      1.37      0.954
chr1    58553  75553   0.353     0.436     0.912     0.836     1.16      1.09      0.611
chr1    19347  36347   0.381     0.411     0.811     0.795     1.16      1.22      0.495
chr1    81062  98062   1.09      0.972     1.35      1.22      1.66      1.76      1.1
chr1    17353  34353   1.06      1.06      1.23      1.26      1.44      1.43      1.03
chr1    48498  65498   1.08      0.996     1.28      1.44      1.52      1.57      1.05