Changes

== Source Code Distribution ==

== Source Code Distribution ==

We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20120213.tar.gz qplot-source.20120213.tar.gz]. Optionally, you can download example file or data file:

We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20120213.tar.gz qplot-source.20120213.tar.gz]. Optionally, you can download example file and/or data file:

[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz  example]: example input file, and expected outputs if you following the [[#Built-in example direction | direction]].  

[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz  example]: example input file, and expected outputs if you following the [[#Built-in example direction | direction]].  

This step will then build qplot. Upon success, the executable qplot can be found under qplot/bin/.

This step will then build qplot. Upon success, the executable qplot can be found under qplot/bin/.

* 4. (Optional) unarchive example data

* 4. (Optional) unarchive example and/or data

  tar zvxf qplot-example-data.tar.gz

  tar zvxf qplot-example.tar.gz

Example data will be extracted to qplot/data/.

An example file, ''chrom20.9M.10M.bam'', will be extracted to qplot/example/. It contains ~1.1 million aligned Ilumina sequencing reads of NA12878 from 1000 Genome Project. Example command line, ''cmd.sh'', example outputs, ''qplot.pdf'', ''qplot.stats'', and ''qplot.R'' are also provided and will be extracted qplot/example/ as well.

 

tar zvxf qplot-data.tar.gz

 

Three files will be extracted to qplot/data/: ''human.g1k.v37-bs.umfa'' is binary NCBI reference genome build 37; ''dbSNP130.UCSC.coordinates.tbl'' is dbSNP version 130; and ''human.g1k.w100.gc'' is pre-calculated GC content with windows size 100.

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