--- a/README.rst	Tue Mar 29 16:51:06 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-=======
-ezBAMQC
-=======
-
-*"ezBAMQC, a tool to check the quality of mapped next generation sequencing files."*
-
-:Codeology Icon:
-
-   .. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.gif
-     :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
-     :align: right
-     :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc
-
-:Description:
-
-   ezBAMQC is a tool to check the quality of either one or many mapped next-generation-sequencing datasets. It conducts comprehensive evaluations of aligned sequencing data from multiple aspects including: clipping profile, mapping quality distribution, mapped read length distribution, genomic/transcriptomic mapping distribution, inner distance distribution (for paired-end reads), ribosomal RNA contamination, transcript 5’ and 3’ end bias, transcription dropout rate, sample correlations, sample reproducibility, sample variations. It outputs a set of tables and plots and one HTML page that contains a summary of the results. Many metrics are designed for RNA-seq data specifically, but ezBAMQC can be applied to any mapped sequencing dataset such as RNA-seq, CLIP-seq, GRO-seq, ChIP-seq, DNA-seq and so on.
-
-:Links:
-
-    `Github Page <https://github.com/mhammell-laboratory/bamqc>`_
-
-    `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_
-
-    `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
-
-:Authors:
-    Ying Jin, David Molik, and Molly Hammell
-
-:Version: 0.6.7
-
-:Contact:
-    Ying Jin (yjin@cshl.edu)
-
-Installation guide for ezBAMQC for from source installs
-=======================================================
-
-When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you'll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you'll need Python, R and Corrplot for interfacing with the C code.
-
-:Intallation:
-   `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_
-
-   `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_
-
-:Prerequisites:
-    * `python2.7 <https://www.python.org/download/releases/2.7/>`_
-    * `R <https://www.r-project.org/>`_
-    * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
-    * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install 
-
-:Notes:
-    * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
-    * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
-    * `IUS <https://ius.io/>`_ for Python2.7
-    * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
-    * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
-
-Setup
-=====
-
-1) Make sure that the GCC comiler is in your PATH:
-
-::
-
-   export PATH=/path/to/gcc:$PATH
-
-2) Make sure that python2.7 is in your PYTHONPATH:
-
-::
-
-   export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
-
-3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. 
-
-From Source
-~~~~~~~~~~~
-
-1) Download source 
-
-2) Unpack tarball and go to the directory of the package: 
-
-::
-
-   tar xvfz bamqc-0.6.7.tar.gz
-
-   cd bamqc-0.6.7
-
-3) Run make:
-
-::
-
-   make
-
-From Setup.py
-~~~~~~~~~~~~~
-
-::
-
-   python2.7 setup.py install 
-
-From Pypi
-~~~~~~~~~
-
-::
-
-   pip2.7 install BAMqc
-
-Usage
-=====
-
-::
-
-   ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]
-   [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]
-   [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]
-
-optional arguments:
-
-::
-
-   -h, --help               show this help message and exit.
-   -i, --inputFile          alignment files. Could be multiple SAM/BAM files separated by space. Required.
-   -r, --refgene            gene annotation file in GTF format. Required
-   -f                       the read summation at which feature level in the GTF file. DEFAULT: gene_id.
-   --rRNA                   rRNA coordinates in BED format.
-   -o, --outputDir          output directory. Required.
-   --stranded               strandness of the library? 
-                            yes : sense stranded
-                            reverse : reverse stranded
-                            no : not stranded
-                            DEFAULT: yes.
-   -q, --mapq               Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30
-   -l, --label              Labels of input files. DEFAULT:smp1 smp2 ...
-   -t, --threads            Number of threads to use. DEFAULT:1
-
-Example: 
-
-::
-
-   ezBAMQC -i test-data/exp_data/treat1.bam test-data/exp_data/treat2.bam test-data/exp_data/treat3.bam -r test-data/exp_data/hg9_refGene.gtf -q 30 --rRNA test-data/exp_data/hg19_rRNA.bed -o exp_output2
-
-   Please find the example output from folder test-data.
-
-FAQ
-===
-Q: Why use ezBAMQC?
-
-A: ezBAMQC is efficient and easy to use. With one command line, it reports a comprehensive evaluation of the data with a set of plots and tables.The ability to assess multiple samples together with high efficiency make it especially useful in cases where there are a large number of samples from the same condition, genotype, or treatment. ezBAMQC was written in C++ and supports multithreading. A mouse RNA-seq sample with 120M alignments can be done in 8 minutes with 5 threads.
-
-Q: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?
-
-A: The difference is because of non-uniquely mapped reads or multiply aligned reads (multi-reads). Samtools flagstat counts each multiple aligment as a different reads, but ezBAMQC counts reads accoriding to the read ID, i.e., each individual read will be counted once no matter that it is a uniquely mapped read or multi-read. 
-
-Q: What is "Low Quality Reads" ?
-
-A: Reads marked as qc fail accoriding to SAM format or reads with mapping quality lower than the value set by the option -q will be considered as "Low Quality Reads".
-
-Q: How the setting of option -q alter the results? 
-
-A: Reads with low quality, i.e., did not pass -q cutoff, are only counted in Total Reads, Mapped Reads, and Mappability by mapping quality plot. The rest of the report does not include low quality reads. 
-
-Q: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?
-
-A: No. Only uniquely mapped reads were counted. 
-
-
-Acknowledgements
-================
-
-#) Samtools contributors
-#) Users' valuable feedback
-
-Copying & Distribution
-======================
-
-ezBAMQC is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but *WITHOUT ANY WARRANTY*; without even the implied warranty of
-*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with ezBAMQC.  If not, see `this website <http://www.gnu.org/licenses/>`_