Upgrade biobambam version and minor enhancements

ICGC-TCGA-PanCancer · Apr 25, 2014 · 3fbdc8e · 3fbdc8e
1 parent 046acd3
commit 3fbdc8e
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Showing 7 changed files with 18 additions and 9 deletions.
diff --git a/Changes b/Changes
@@ -1,3 +1,11 @@
+1.0.1
+  Upgrade install to pull biobambam 0.0.135
+    - fastqtobam supports Casava v1.8
+    - bamsort supports NM/MD correction during sam->bam/merge process
+  Minor enhancement to BAS reader module
+  Sample name from command line passed through to SM of RG header in bwa_mem.pl
+  SRA.pm - check that rg id is unique within run of code (thanks to Junjun Zhang)
+  Threads.pm - join interval is now configurable.
 1.0.0
   bam_stats.pl actually installed now.
   Basic *.bas perl access module.

diff --git a/MYMETA.json b/MYMETA.json
@@ -53,5 +53,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.0.0"
+   "version" : "v1.0.1"
 }
diff --git a/MYMETA.yml b/MYMETA.yml
@@ -35,4 +35,4 @@ requires:
   Term::UI: 0.42
   Test::Fatal: 0.013
   Try::Tiny: 0.19
-version: v1.0.0
+version: v1.0.1
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 = '1.0.0';
+our $VERSION = '1.0.1';
 
 const my $LICENSE =>
 "#################
@@ -39,7 +39,8 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,samtools,bwa',
                             '0.2.0'  => 'biobambam',
                             '0.2.99' => 'biobambam',
                             '0.3.0'  => 'biobambam',
-                            '1.0.0'  => '',
+                            '1.0.0'  => 'biobambam',
+                            '1.0.1'  => '',
                           );
 
 sub license {

diff --git a/setup.sh b/setup.sh
@@ -3,8 +3,8 @@
 SOURCE_BWA="https://github.com/lh3/bwa/archive/0.7.7.tar.gz"
 SOURCE_SNAPPY="https://snappy.googlecode.com/files/snappy-1.1.1.tar.gz"
 SOURCE_IOLIB="http://downloads.sourceforge.net/project/staden/io_lib/1.13.4/io_lib-1.13.4.tar.gz"
-SOURCE_LIBMAUS="https://github.com/gt1/libmaus/archive/0.0.112-release-20140411095503.tar.gz"
-SOURCE_BIOBAMBAM="https://github.com/gt1/biobambam/archive/0.0.131-release-20140411101450.tar.gz"
+SOURCE_LIBMAUS="https://github.com/gt1/libmaus/archive/0.0.115-release-20140423163910.tar.gz"
+SOURCE_BIOBAMBAM="https://github.com/gt1/biobambam/archive/0.0.135-release-20140423164503.tar.gz"
 SOURCE_SAMTOOLS="https://github.com/samtools/samtools/archive/0.1.19.tar.gz"
 
 done_message () {

diff --git a/t/3_external_progs.t b/t/3_external_progs.t
@@ -17,15 +17,15 @@ my %EXPECTED_VERSION = (
                         'bamcollate2'       => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.131']},
+                              'version'       => ['0.0.135']},
                         'bammarkduplicates' => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.131']},
+                              'version'       => ['0.0.135']},
                         'bamsort'           => {
                               'get'   => q{ -h},
                               'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => ['0.0.131']},
+                              'version'       => ['0.0.135']},
                         'bwa'           => {
                               'get'   => q{},
                               'match' => qr/Version: ([[:digit:]\.]+[[:alpha:]]?)/, # we don't care about the revision number