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Biostar105754
##Motivation
bigwig : peak distance from specific genomic region
##Compilation
- java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . 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
- xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar105754
by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by adding standalone=yes
on the command line:
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make biostar105754 standalone=yes
The required libraries will be downloaded and installed in the dist
directory.
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
##Synopsis
$ java -jar dist/biostar105754.jar [options] (stdin|file)
- -o|--output (OUTPUT-FILE) Output file. Default:stdout.
- -B|--bigwig (FILE.bw) Big Wig file
- -h|--help print help
- -version|--version show version and exit
##Source Code
Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar105754.java
$ echo -e "1\t1000\t20000\n3\t100\t200\nUn\t10\t11" |\
java -jar dist/biostar105754.jar -B path/to//All_hg19_RS_noprefix.b
#no data found for Un 10 11
1 1000 1001 0.0 1 1000 20000
3 100 101 0.0 3 100 200
https://www.biostars.org/p/105754/
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
The project is licensed under the MIT license.
Should you cite biostar105754 ? 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