Merge tag '1.13.0' into dev

* Overlapping reads now handled #78
* Fixes for #64, #65, #61

CHANGES.md

@@ -1,74 +1,97 @@
 # CHANGES
 
-## NEXT - major release
-* Overlapping reads now handled
+## 1.13.0
+
+* Overlapping reads now handled #78
+* Fixes for #64, #65, #61
 
 ## 1.12.1
+
 * Resolves #74
 
 ## 1.12.0
+
 * Now outputs snp and mut vcf files as gzipped.
 * Requires [zlib](https://zlib.net/) >= 1.2.3.5
 
 ## 1.11.3
+
 * Makefile update to cope with central/prefix install of htslib
 
 ## 1.11.2
+
 * Update htslib version (1.11.1 updated an unused reference to this archive)
 
 ## 1.11.0
+
 * Rearrangement to htslib pileup code gives large speed increases
 
 ## 1.10.1
+
 * Correction to fclose checking in estep.c
 
 ## 1.10.0
+
 * Added checks to all fflush and fclose calls
 
 ## 1.9.5
+
 * Removed dependency on ENA during compilation
 
 ## 1.9.4
+
 * Correct main method to ensure failure is passed through from running the by section main methods.
 
 ## 1.9.3
+
 * Fix bug in ignore regions file reading where bed file resulted in incorrect coords
 
 ## 1.9.2
+
 * Resolves #45 - New [samtools/htslib 1.3](https://github.com/samtools/htslib/releases/tag/1.3) to remove need for patch.
 
 ## 1.9.1
+
 * Removed unnecessary dependancy on `rsync` when `cp` will do.
 
 ## 1.9.0
+
 * Corrections to install methods to ensure all relevant files were installed.
 
 ## 1.8.0
+
 * Commmandline params checked
 * Readlength taken into account in split sections
 * setup.sh installs perl scripts
 
 ## 1.7.3
+
 * Fixed generateCavemanUMNormVCF - command line help has errors #28
 * Fixed check BAM headers in setup for readgroups #34
 
 ## 1.7.2
+
 * RG lane id search no longer requires ID to be at the beginning of the RG line.
 
 ## 1.7.1
+
 * Added header read to bam_access_get_by_position_counts method. Fixes #41
 
 ## 1.7.0
+
 * Updated merge script to check number of files against splitList.
 
 ## 1.6.4
+
 * Fixed #37, Fixed bug where error thrown when no CN file, and should be using default.
 * Fixed #38, removed need for stack memory usage in array reading and writing.
 
 ## 1.6.2
+
 * Fixed bug in generateCavemanVCFUnatchedNormalPanel.c where q was not read at commandline.
 
 ## 1.6.0
+
 * Cram support added using htslib
 * Added setup script to download and compile htslib with patch (required for CRAM support).
 * Added 2015 and date additional info to licenses in all files

Makefile

@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.12.1
+CAVEMAN_VERSION=1.13.0
 TEST_REF?=""
 #Compiler
 CC?=gcc

README.md

@@ -8,9 +8,9 @@ use of an index parameter. The split step is designed to divide the genome into
 chunks of adjustable size to optimise for runtime/memory usage requirements.
 For simple execution of CaVEMan please see [cgpCaVEManWrapper](https://github.com/cancerit/cgpCaVEManWrapper)
 
-| Master | Dev |
-|---|---|
-|  [![Build Status](https://travis-ci.org/cancerit/CaVEMan.svg?branch=master)](https://travis-ci.org/cancerit/CaVEMan) | [![Build Status](https://travis-ci.org/cancerit/CaVEMan.svg?branch=dev)](https://travis-ci.org/cancerit/CaVEMan) |
+| Master                                                                                                              | Dev                                                                                                              |
+| ------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------- |
+| [![Build Status](https://travis-ci.org/cancerit/CaVEMan.svg?branch=master)](https://travis-ci.org/cancerit/CaVEMan) | [![Build Status](https://travis-ci.org/cancerit/CaVEMan.svg?branch=dev)](https://travis-ci.org/cancerit/CaVEMan) |
 
 Installation
 ============