Bump version and brings Changes up to date

Changes

@@ -1,3 +1,36 @@
+1.5.3
+  bam_stats C - changed array for khash in insert size calculations in order to make code more robust.
+  Header RG line reading now reads anything not a tab or newline as it should when determining what the values of tags are.
+1.5.2
+  bamToBw.pl fixes
+  * Pull actual binaries from jkent_util not html page associated
+  * process name corrections in bamToBw.pm command line args
+1.5.1
+  bam_stats c now has CRAM support.
+  Also dropped need for samtools v1.x api as can be handled by htslib on it's own.
+1.5.0
+  bamToBw.pl and new biobambam dep
+  No changes to old tools, just additions and prep for handling CRAM input.
+1.4.0
+  bam_stats in C, less than 2 hours to generate stats on a sample level BAM file of ~120GB.
+1.3.0
+  bam_stats.pl is now multi-threaded, can get ~50% runtime reduction with 3-4 threads, memory still <500MB.
+  Upgrades biobambam to 0.0.185 (and dependencies).
+1.2.3
+  xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile, #54
+1.2.2
+  Fixed bug in bwa_mem.pl when using '-f' option on paired fastq.
+1.2.1
+  Makes xml_to_bas.pl more robust on AWS. Retrieved XML was being truncated on some network configurations.
+1.2.0
+  Modifications made to the bwa_mem.pl code to split a lane of data into fragments to reduce failure recovery time. Primarily added to handle X10 data better.
+  Also updated samtools to 0.1.20, last version that is currently compatible with Bio::DB::Sam.
+1.1.1
+  Fix missing dependancy and build a relocatable version of biobambam suitable for use in artifactory.
+1.1.0
+  Minor enhancement to bwa_mem.pl to automatically generate the *.bas file.
+  Added xml_to_bas.pl for pancancer users, see the wiki for details.
+  Fixed a few minor issues, #36, #37, #39
 1.0.4
   Install biobambam 0.0.142 to prevent over-counting of duplicates when multiple
   libraries, also required libmaus 0.0.124.

MANIFEST

@@ -12,6 +12,7 @@ c/bam_access.c
 c/bam_access.h
 c/bam_stats.c
 c/dbg.h
+c/khash.h
 Changes
 dists/snappy-1.1.2.tar.gz
 docs.tar.gz

MYMETA.json

@@ -4,7 +4,7 @@
       "unknown"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
    "license" : [
       "gpl_2"
    ],
@@ -55,5 +55,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.5.2"
+   "version" : "v1.5.3"
 }

MYMETA.yml

@@ -3,38 +3,38 @@ abstract: unknown
 author:
   - unknown
 build_requires:
-  ExtUtils::MakeMaker: '0'
+  ExtUtils::MakeMaker: 0
 configure_requires:
-  ExtUtils::MakeMaker: '0'
+  ExtUtils::MakeMaker: 0
 dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560'
 license: gpl
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: '1.4'
+  version: 1.4
 name: PCAP
 no_index:
   directory:
     - t
     - inc
 requires:
-  Bio::DB::Sam: '1.39'
-  Bio::Root::Version: '1.006923'
-  Capture::Tiny: '0.24'
-  Const::Fast: '0.014'
-  Data::UUID: '1.219'
-  Devel::Cover: '1.09'
-  File::Which: '0.05'
-  GD: '2.52'
-  IPC::System::Simple: '1.25'
-  List::Util: '1.38'
-  Math::Gradient: '0.04'
-  Module::Build: '0.42'
-  Pod::Coverage: '0.23'
-  Proc::ProcessTable: '0.5'
-  Sub::Exporter::Progressive: '0.001011'
-  Term::UI: '0.42'
-  Test::Fatal: '0.013'
-  Try::Tiny: '0.19'
-  XML::Simple: '2.2'
-version: v1.5.2
+  Bio::DB::Sam: 1.39
+  Bio::Root::Version: 1.006923
+  Capture::Tiny: 0.24
+  Const::Fast: 0.014
+  Data::UUID: 1.219
+  Devel::Cover: 1.09
+  File::Which: 0.05
+  GD: 2.52
+  IPC::System::Simple: 1.25
+  List::Util: 1.38
+  Math::Gradient: 0.04
+  Module::Build: 0.42
+  Pod::Coverage: 0.23
+  Proc::ProcessTable: 0.5
+  Sub::Exporter::Progressive: 0.001011
+  Term::UI: 0.42
+  Test::Fatal: 0.013
+  Try::Tiny: 0.19
+  XML::Simple: 2.2
+version: v1.5.3

c/Makefile

@@ -1,4 +1,4 @@
-VERSION=1.5.2
+VERSION=1.5.3
 
 #Compiler
 CC = gcc -O3 -DVERSION='"$(VERSION)"' -g

lib/PCAP.pm

@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.5.2';
+our $VERSION = '1.5.3';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -55,6 +55,9 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,bwa,samtools',
                             '1.3.0'  => 'biobambam',
                             '1.4.0'  => 'biobambam',
                             '1.5.0'  => '',
+                            '1.5.1'  => '',
+                            '1.5.2'  => '',
+                            '1.5.3'  => '',
                           );
 
 sub license {