update manual

README.rst

@@ -20,7 +20,7 @@ See LICENSE for license information
 What is HiC-Pro ?
 =================
 
-| HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.6.1, HiC-Pro can analyse data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C.
+| HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro can analyse data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C.
 | The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler. HiC-Pro is sequential and each step of the workflow can be run independantly.
 | HiC-Pro includes a fast implementatation of the ICE normalization method (see the `iced <https://github.com/hiclib/iced>`_ python library for more information).
 | In addition, HiC-Pro can use phasing data to build :ref:`allele specific contact maps <AS>`.
@@ -119,7 +119,7 @@ How to use it ?
   usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
   Use option -h|--help for more information
 
-  HiC-Pro 2.6.1
+  HiC-Pro 2.7.0
   ---------------
   OPTIONS
 

doc/FAQ.rst

@@ -46,7 +46,7 @@ Another way to generate this file is, for instance, to use the R environment.
 
 * The restriction fragments file has to be generated according to the reference genome, and the restriction enzyme(s) used to generate the Hi-C data.
 
-| Since version 2.6.1, HiC-Pro proposes the utility *digest_genome.py* to generate this file using as input, the fasta file and the name(s) or sequence(s) of the restriction enzyme(s).
+| Since version 2.7.0, HiC-Pro proposes the utility *digest_genome.py* to generate this file using as input, the fasta file and the name(s) or sequence(s) of the restriction enzyme(s).
 | See the :ref:`HiC-Pro Utilities <UTILS>` section for more details.
 | Another way is to generate the list of restriction fragments is to use the `HiTC <http://bioconductor.org/packages/release/bioc/html/HiTC.html>`_ BioConductor package. 
 | Note that this method only works for the genomes which are already available in BioConductor and for one restriction enzyme. 

doc/MANUAL.rst

@@ -2,13 +2,13 @@
 
 .. Nicolas Servant
 .. HiC-Pro
-.. v2.6.1
+.. v2.7.0
 .. 15-09-02
 
 HiC-Pro Manual
 ******************
 Modified - 09th September 2015
-Reference version - HiC-Pro 2.6.1
+Reference version - HiC-Pro 2.7.0
 
 Setting the configuration file
 ==============================
@@ -153,7 +153,7 @@ Available steps are described in the help command.
   usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
   Use option -h|--help for more information
 
-  HiC-Pro 2.6.0
+  HiC-Pro 2.7.0
   ---------------
   OPTIONS