Changes

== Binary Download ==

== Binary Download ==

We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]  

We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]  

The executable file is under qplot/bin/qplot.  

The executable file is under qplot/bin/qplot.  

== 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.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file:

We provide a source code only download in [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.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]].  

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

[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.

[http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.

You can put above file(s) in the same folder and follow these steps:

You can put above file(s) in the same folder and follow these steps:

* Input file options :

* Input file options :

BAM files are compress by BGZF algorithm and it should contain EOF by default. QPLOT will by default stop working when it does not found a valid EOF tag inside BAM files.  

BAM files are compressed using BGZF and should contain the EOF indicator by default. QPLOT will, by default, stop working if it does not find a valid EOF indicator inside the BAM files.  

However, you can force QPLOT to continue process using --noeof. But you should be aware the input files may be corrupted.

However, you can force QPLOT to continue processing BAM files without an EOF indicator using --noeof. But you should be aware the input files may be corrupted.