Merge branch 'hotfix/v1.13.2'

ICGC-TCGA-PanCancer · Mar 15, 2016 · ab9aa4f · ab9aa4f
2 parents b33d81c + 445726d
commit ab9aa4f
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Showing 4 changed files with 6 additions and 2 deletions.
diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.13.1';
+our $VERSION = '1.13.2';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
@@ -103,6 +103,10 @@ sub mem_mapmax {
       next if($file =~ m/^\./);
       next if($file =~ m/^pairedfq2\.[[:digit:]]+/); # captured by 1.*
       next if($file =~ m/s[.]fq[.]gz_[[:digit:]]+[.]gz$/);
+      if($file =~ m/o[12][.]fq[.]gz_[[:digit:]]+[.]gz$/) {
+        warn "Orphan reads found, your input BAM appears to have had duplicates 'removed' rather than 'marked': $folder/$file\n\tWARNING: This will give a sub-optimal result\n";
+        next;
+      }
       push @files, File::Spec->catfile($folder, $file);
     }
     closedir($dh);

diff --git a/prerelease.sh b/prerelease.sh
@@ -22,7 +22,7 @@ cd $MY_PATH
 
 echo '### Running perl tests ###'
 
-export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-ignore,'t/.*\.t'
+export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-select='^lib/*\.pm$',-ignore,'^t/'
 rm -rf docs
 mkdir -p docs/reports_text
 prove --nocolor -w -I ./lib | sed 's/^/  /' # indent output of prove