[libbio-samtools-perl] 01/01: Imported Upstream version 1.39

[Charles Plessy]

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plessy pushed a commit to annotated tag upstream/1.39
in repository libbio-samtools-perl.

commit cff6561503842aab0da01584b3d93098d5a1ad45
Author: Charles Plessy <plessy at debian.org>
Date:   Sun Sep 29 08:35:59 2013 +0900

    Imported Upstream version 1.39
---
 Changes                     |    5 +++++
 META.json                   |    6 +++---
 META.yml                    |    6 +++---
 lib/Bio/DB/Bam/Alignment.pm |    4 +---
 lib/Bio/DB/Sam.pm           |    2 +-
 5 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/Changes b/Changes
index 4b7f9ca..48746fb 100644
--- a/Changes
+++ b/Changes
@@ -1,3 +1,8 @@
+Version 1.39 
+
+   * Bio::DB::Bam::Alinment->strand() performance
+     patch from: https://rt.cpan.org/Ticket/Display.html?id=88203.
+
 Version 1.38
    * Add -lpthread to linker flags to allow to run with samtools 0.1.19.
 
diff --git a/META.json b/META.json
index 10057a8..29c0e93 100644
--- a/META.json
+++ b/META.json
@@ -4,7 +4,7 @@
       "Lincoln Stein <lincoln.stein at gmail.com>"
    ],
    "dynamic_config" : 1,
-   "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.112150",
+   "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.110440",
    "license" : [
       "perl_5"
    ],
@@ -74,7 +74,7 @@
       },
       "Bio::DB::Sam" : {
          "file" : "lib/Bio/DB/Sam.pm",
-         "version" : "1.38"
+         "version" : "1.39"
       },
       "Bio::DB::Sam::Constants" : {
          "file" : "lib/Bio/DB/Sam/Constants.pm",
@@ -107,5 +107,5 @@
          "http://dev.perl.org/licenses/"
       ]
    },
-   "version" : "1.38"
+   "version" : "1.39"
 }
diff --git a/META.yml b/META.yml
index 6fef4c1..3302c00 100644
--- a/META.yml
+++ b/META.yml
@@ -7,7 +7,7 @@ build_requires:
 configure_requires:
   Module::Build: 0.38
 dynamic_config: 1
-generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.112150'
+generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.110440'
 license: perl
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -46,7 +46,7 @@ provides:
     version: 0
   Bio::DB::Sam:
     file: lib/Bio/DB/Sam.pm
-    version: 1.38
+    version: 1.39
   Bio::DB::Sam::Constants:
     file: lib/Bio/DB/Sam/Constants.pm
     version: 0
@@ -70,4 +70,4 @@ requires:
   perl: 5.008
 resources:
   license: http://dev.perl.org/licenses/
-version: 1.38
+version: 1.39
diff --git a/lib/Bio/DB/Bam/Alignment.pm b/lib/Bio/DB/Bam/Alignment.pm
index 97aa502..487ca96 100644
--- a/lib/Bio/DB/Bam/Alignment.pm
+++ b/lib/Bio/DB/Bam/Alignment.pm
@@ -489,9 +489,7 @@ sub stop { shift->end }
 
 # in SAM format, alignment is always to the forward strand
 sub strand {
-    my $self     = shift;
-    return $self->reversed ? -1 : 1;
-#     return 1;
+    return shift->reversed ? -1 : 1;
 }
 
 sub abs_strand { shift->strand }
diff --git a/lib/Bio/DB/Sam.pm b/lib/Bio/DB/Sam.pm
index 9420a36..65be574 100644
--- a/lib/Bio/DB/Sam.pm
+++ b/lib/Bio/DB/Sam.pm
@@ -1,6 +1,6 @@
 package Bio::DB::Sam;
 
-our $VERSION = '1.38';
+our $VERSION = '1.39';
 
 =head1 NAME
 

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