Release for 1.0.3

ICGC-TCGA-PanCancer · May 7, 2014 · a987ec4 · a987ec4
1 parent 8a1d61a
commit a987ec4
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Showing 6 changed files with 41 additions and 34 deletions.
diff --git a/Changes b/Changes
@@ -1,3 +1,9 @@
+1.0.3
+  Corrected issue from dynamic de-reference of hash, issue fort pre 5.14 perl
+  and potentially unstable in future.
+  Added missing project code to cv terms.
+  Bug-fixed upgrade path, still needs better solution.
+  Cleaned up messaging in Threaded module.
 1.0.2
   Upgrade install to pull biobambam 0.0.138
    - fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.

diff --git a/MANIFEST b/MANIFEST
@@ -29,6 +29,36 @@ share/cv_tables/ICGC/dcc_specimen_type.txt
 t/1_pm_compile.t
 t/2_pl_compile.t
 t/3_external_progs.t
+t/data/1.fq
+t/data/1_1.fq
+t/data/1_2.fq
+t/data/2_1.fq
+t/data/3_2.fq
+t/data/data.file
+t/data/empty.bam
+t/data/empty.bam.bas
+t/data/empty.file
+t/data/empty.fq
+t/data/empty_r1_1.fq
+t/data/empty_r1_2.fq
+t/data/empty_r2_1.fq
+t/data/empty_r2_2.fq
+t/data/header.bam
+t/data/header.sam
+t/data/malformed_head.bam
+t/data/malformed_head.sam
+t/data/md5.bam
+t/data/md5.bam.md5
+t/data/multi_sample.bam
+t/data/multi_sample.sam
+t/data/no_readgroups.bam
+t/data/no_readgroups.sam
+t/data/not_really_a.bam
+t/data/paired.bam
+t/data/Stats.bam
+t/data/Stats.bam.bas
+t/data/test.bam.bas
+t/data/unpaired.bam
 t/pcap.t
 t/pcapBam.t
 t/pcapBamBas.t
@@ -38,33 +68,3 @@ t/pcapBwaMeta.t
 t/pcapCli.t
 t/pcapSra.t
 t/pcapThreaded.t
-testData/1.fq
-testData/1_1.fq
-testData/1_2.fq
-testData/2_1.fq
-testData/3_2.fq
-testData/data.file
-testData/empty.bam
-testData/empty.bam.bas
-testData/empty.file
-testData/empty.fq
-testData/empty_r1_1.fq
-testData/empty_r1_2.fq
-testData/empty_r2_1.fq
-testData/empty_r2_2.fq
-testData/header.bam
-testData/header.sam
-testData/malformed_head.bam
-testData/malformed_head.sam
-testData/md5.bam
-testData/md5.bam.md5
-testData/multi_sample.bam
-testData/multi_sample.sam
-testData/no_readgroups.bam
-testData/no_readgroups.sam
-testData/not_really_a.bam
-testData/paired.bam
-testData/Stats.bam
-testData/Stats.bam.bas
-testData/test.bam.bas
-testData/unpaired.bam
diff --git a/MYMETA.json b/MYMETA.json
@@ -54,5 +54,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.0.1"
+   "version" : "v1.0.3"
 }
diff --git a/MYMETA.yml b/MYMETA.yml
@@ -36,4 +36,4 @@ requires:
   Term::UI: 0.42
   Test::Fatal: 0.013
   Try::Tiny: 0.19
-version: v1.0.1
+version: v1.0.3
diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -23,7 +23,7 @@ package PCAP;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.0.1';
+our $VERSION = '1.0.3';
 
 const my $LICENSE =>
 "#################
@@ -41,7 +41,8 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,samtools,bwa',
                             '0.3.0'  => 'biobambam,bwa',
                             '1.0.0'  => 'biobambam,bwa',
                             '1.0.1'  => 'biobambam,bwa',
-                            '1.0.2'  => '',
+                            '1.0.2'  => 'biobambam,bwa',
+                            '1.0.3'  => '',
                           );
 
 sub license {