Rolling 1.0.0

Author: keiranmraine

Changes

@@ -1,3 +1,8 @@
+1.0.0
+  bam_stats.pl actually installed now.
+  Basic *.bas perl access module.
+  Upgraded libmaus/biobambam to resolve patch and CentOS install issue.
+  Reference implementations ensure unique RG:ID between files.
 0.3.0
   Changes for the re-worked PanCancer submission SOP.
   Patch for libmaus issue as not going to be a release in time.

INSTALL

@@ -14,14 +14,25 @@ OS:
 Other Software
   For installation to proceed you require the following packages:
 
-    zlib1g-dev
-    g++
-    dh-autoreconf
-    libncurses-dev
-    pkg-config
-    libgd2-xpm-dev
-
-    This listing is based on Ubuntu 12.04
+    For Ubuntu (tested with 12.04)
+      apt-get
+        zlib1g-dev
+        g++
+        dh-autoreconf
+        libncurses-dev
+        pkg-config
+        libgd2-xpm-dev
+
+    For CentOS (tested with 6.4)
+      yum install
+        zlib-devel
+        gcc-c++
+        autoconf
+        automake
+        libtool
+        boost-devel.x86_64
+        ncurses-devel.x86_64
+        gd-devel
 
   setup.sh will install
     biobambam

MANIFEST

@@ -21,7 +21,6 @@ LICENSE
 Makefile.PL
 MANIFEST			This list of files
 MANIFEST.SKIP
-patches/fileModeFix.diff
 prerelease.sh
 README.md
 setup.sh

MYMETA.json

@@ -53,5 +53,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v0.3.0"
+   "version" : "v1.0.0"
 }

MYMETA.yml

@@ -35,4 +35,4 @@ requires:
   Term::UI: 0.42
   Test::Fatal: 0.013
   Try::Tiny: 0.19
-version: v0.3.0
+version: v1.0.0

docs.tar.gz

@@ -23,7 +23,7 @@ package PCAP;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '0.3.0';
+our $VERSION = '1.0.0';
 
 const my $LICENSE =>
 "#################
@@ -33,11 +33,13 @@ const my $LICENSE =>
 #################";
 
 const my $DEFAULT_PATH => 'biobambam,samtools,bwa';
-const my %UPGRADE_PATH => ( '0.1.0' => 'biobambam,samtools,bwa',
-                            '0.1.1' => 'biobambam,bwa',
-                            '0.1.2' => 'biobambam',
-                            '0.2.0' => 'biobambam',
-                            '0.3.0' => '',
+const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,samtools,bwa',
+                            '0.1.1'  => 'biobambam,bwa',
+                            '0.1.2'  => 'biobambam',
+                            '0.2.0'  => 'biobambam',
+                            '0.2.99' => 'biobambam',
+                            '0.3.0'  => 'biobambam',
+                            '1.0.0'  => '',
                           );
 
 sub license {