Merge pull request #93 from wtsi-npg/devel

merge to master for release 50.12

.travis.yml

@@ -11,6 +11,7 @@ language: perl
 
 perl:
   - "5.16"
+  - "5.22-shrplib"
 
 env:
   global:

Build.PL

@@ -30,13 +30,14 @@ my $requires = {
                 'Math::Round'                     => '0.06',
                 'MIME::Lite'                      => '3.024',
                 'Moose'                           => '0.93',
+                'Moose::Meta::Class'              => '0',
                 'Moose::Role'                     => '0.93',
                 'Moose::Util::TypeConstraints'    => 0,
                 'MooseX::ClassAttribute'          => 0,
                 'MooseX::Storage'                 => 0,
-                'MooseX::StrictConstructor'       => '0.08',
                 'Parallel::ForkManager'           => 0,
                 'Perl6::Slurp'                    => '0.03',
+                'Pod::Usage'                      => '0',
                 'POSIX'                           => '1.09',
                 'Readonly'                        => '1.03',
                 'Readonly::XS'                    => 0,

Changes

@@ -1,5 +1,15 @@
 LIST OF CHANGES
 
+  - RefMaker: added extra dict symlink for RNA SeQc
+  - code changes to reduce number of warnings under Perl 5.22.2
+
+release 50.11
+  - seqchksum_merge.pl:
+      updated to generate chksums on the fly is given a bam file
+      added new column class (partition) to partition data when merging.
+      modified and extended tests. N.B. running the script on multiple bam files 
+      should generate the same values as bamcat + bamseqchksum but the
+      order is no longer guaranteed to be the same
   - RefMaker: added function for longranger mkref and extended test
 
 release 50.10

MANIFEST

@@ -57,6 +57,9 @@ t/data/fastq_split/2518_2_5_merge_part.sam
 t/data/fastq_split/Homo_sapiens.NCBI36.48.dna.all.fa
 t/data/fastq_split/seq_ids.txt
 t/data/good.sam
+t/data/seqchksum_merge/merged.different.seqchksum
+t/data/seqchksum_merge/group1.seqchksum
+t/data/seqchksum_merge/group2.seqchksum
 t/data/java
 t/data/mixed.sam
 t/data/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa

bin/FastaFormat

@@ -29,7 +29,7 @@ foreach (@ARGV) {
         next;
     }
 
-    ( -e $_ )
+    ( -e )
         ? ( push @fasta_list, $_ )
         : ( warn "$_ not found. Skipping...\n" );
 }

bin/Ref_Maker

@@ -150,21 +150,15 @@ sub main { ##no critic (Subroutines::ProhibitExcessComplexity)
     # samtools requires its index file to be in the same directory as the fasta
     # Check first that the samtools command worked above.
     if ($build{'samtools'}) {
-        eval {
-            my $source = "samtools/$files[0].fai";
-            my $target = "fasta/$files[0].fai";
-            croak 'samtools .fai file not found' if !-e $source;
-
-            # This can fail if $target is a broken link.
-            ( -e $target ) && ( unlink $target );
-
-            symlink qq{../$source}, $target;
-            1;
-        } or do {
-            carp "Error symlinking fai file: $EVAL_ERROR $SKIP_STRING";
-        };
+        create_symlink("samtools/$files[0].fai","fasta/$files[0].fai");
+    }
+
+    # RNA SeQc requires dict file in same directory as the fasta
+    if ($build{'picard'}) {
+        create_symlink("picard/$files[0].dict","fasta/$files[0].dict");
     }
 
+
     if (@failed) {
         my $message = 'WARNING: Task(s) failed, see Ref_Maker output for '.
             'details: '.join(', ', @failed)."\n";
@@ -337,6 +331,26 @@ sub log_timestamp {
     return;
 }
 
+
+sub create_symlink{
+
+    my($source,$target) = @_;
+
+    eval {
+        croak qq{$source file not found} if !-e $source;
+
+        # This can fail if $target is a broken link.
+        ( -e $target ) && ( unlink $target );
+
+        symlink qq{../$source}, $target;
+        1;
+    } or do {
+        carp "Error symlinking $target file: $EVAL_ERROR $SKIP_STRING";
+    };
+
+    return;
+}
+
 sub _get_rm {
     my $rm_class = Moose::Meta::Class->create_anon_class(
         roles => [qw/npg_common::roles::software_location/]);
@@ -437,6 +451,10 @@ Delete and previous version/attempt and create a fresh directory.
 
 Log a timestamp for the start or end (normal or aborted) of an aligner job.
 
+=head2 create_symlink
+
+Create a symlink between a source and target
+
 =head1 REQUIRED ARGUMENTS
 
 =head1 OPTIONS