Minor test correction and version bump

CHANGES.md

@@ -1,3 +1,7 @@
+### 1.9.0
+* Fix bugs #52 and #53
+* Modified bwa_mem.pl to accept multi-readgroup BAM as input
+
 ### 1.7.1
 * Turns out BWA mem still requires fixmates to get proper isize distributions
 * bumped biobambam to [0.0.191](https://github.com/gt1/biobambam/releases/tag/0.0.191-release-20150401083643)

MYMETA.json

@@ -4,7 +4,7 @@
       "unknown"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
    "license" : [
       "gpl_2"
    ],
@@ -57,5 +57,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.8.2"
+   "version" : "v1.9.0"
 }

MYMETA.yml

@@ -3,40 +3,40 @@ 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 2.131560'
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
 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
-  Config::IniFiles: 2.83
-  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::PID::File: 1.27
-  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: v1.8.2
+  Bio::DB::Sam: '1.39'
+  Bio::Root::Version: '1.006923'
+  Capture::Tiny: '0.24'
+  Config::IniFiles: '2.83'
+  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::PID::File: '1.27'
+  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: v1.9.0

c/Makefile

@@ -1,4 +1,4 @@
-VERSION=1.8.2
+VERSION=1.9.0
 
 #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 = '1.8.2';
+our $VERSION = '1.9.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -68,6 +68,7 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,bwa,samtools',
                             '1.8.0'  => '',
                             '1.8.1'  => '',
                             '1.8.2'  => '',
+                            '1.9.0'  => '',
                           );
 
 sub license {

t/pcapBam.t

@@ -74,8 +74,11 @@ subtest 'rg line checks' => sub {
   my ($rg_line, $bio_db_sam) = PCAP::Bam::rg_line_for_output($test_bam);
   is($rg_line, $EXPECTED_RGLINE, 'Retreived single RG line');
   like(exception{ PCAP::Bam::rg_line_for_output($multi_bam) }
-      , qr/BAM file appears to contain data for multiple readgroups, not supported:/m
+      , qr/BAM file appears to contain data for multiple readgroups, not supported unless 'existing_rgid' is found:/m
       , 'Fail when multiple readgroups in BAM');
+
+  is((PCAP::Bam::rg_line_for_output($multi_bam, undef, undef, 1))[0], $EXPECTED_RGLINE, 'Correct RG from multiple RG header');
+
   my $obj = new_ok($MODULE => [$test_bam]);
   is($obj->single_rg_value('PL'), $EXPECTED_RG_PL, 'Tag successfully retrieved');
   $obj = new_ok($MODULE => [$multi_bam]);