Merge branch 'hotfix/v3.0.3'

cancerit · Oct 24, 2018 · 41fa2a9 · 41fa2a9
2 parents 27c0916 + 2442a61
commit 41fa2a9
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Showing 6 changed files with 43 additions and 31 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -21,13 +21,17 @@ addons:
    - unzip
    - libpng12-dev
    - libexpat1-dev
+   - libgoogle-perftools-dev
+   - lsof
+   - libbz2-dev
+   - liblzma-dev
 
 install: true
 
 language: perl
 
 perl:
- - "5.22"
+ - "5.22-shrplib"
 
 script:
  - set -e
@@ -36,12 +40,12 @@ script:
  - cd cgpBigWig
  - ./setup.sh $HOME/PCAP-opt
  - cd ../
- - git clone --depth 1 --single-branch --branch dev https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git
+ - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/PCAP-core.git
  - cd PCAP-core
  - ./setup.sh $HOME/PCAP-opt
  - cd ../
  - git clone --depth 1 --single-branch --branch dev https://github.com/cancerit/cgpVcf.git
  - cd cgpVcf
- - ./setup.sh $HOME/cgpVcf-opt $HOME/PCAP-opt
+ - ./setup.sh $HOME/PCAP-opt
  - cd ../
- - ./setup.sh $HOME/cgpPindel-opt $HOME/cgpVcf-opt $HOME/PCAP-opt
+ - ./setup.sh $HOME/PCAP-opt
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 3.0.3
+
+Changes to how germline filter determined resulted in dummy germline bed file not being generated as previously.
+This release reinstates the old behaviour.
+
 ## 3.0.2
 
 * Correct example rule files for *Fragment.lst files to use FFnnn filter types

diff --git a/perl/bin/pindel_germ_bed.pl b/perl/bin/pindel_germ_bed.pl
@@ -61,23 +61,28 @@ BEGIN
 $vcf->parse_header();
 
 my @segments;
-while(my $x = $vcf->next_data_array){
-  next unless(";$x->[6];" =~ m/;$flag;/); # skip things that don't have this flag value
-  my ($ref, $start, $alt) = (@{$x})[0,1,4];
-  my $end = $start + length $alt;
-  if(scalar @segments == 0) {
-    push @segments, [$ref, $start, $end];
-    next;
-  }
-  if($ref ne $segments[-1][0]) {
+if($flag eq 'NA') {
+  warn "Flag not applied, generating dummy bed file.\n";
+}
+else {
+  while(my $x = $vcf->next_data_array){
+    next unless(";$x->[6];" =~ m/;$flag;/); # skip things that don't have this flag value
+    my ($ref, $start, $alt) = (@{$x})[0,1,4];
+    my $end = $start + length $alt;
+    if(scalar @segments == 0) {
+      push @segments, [$ref, $start, $end];
+      next;
+    }
+    if($ref ne $segments[-1][0]) {
+      push @segments, [$ref, $start, $end];
+      next;
+    }
+    if($start >= $segments[-1][1] && $start <= $segments[-1][2]) {
+      $segments[-1][2] = $end if($end > $segments[-1][2]); # as only sorted by start pos
+      next;
+    }
     push @segments, [$ref, $start, $end];
-    next;
-  }
-  if($start >= $segments[-1][1] && $start <= $segments[-1][2]) {
-    $segments[-1][2] = $end if($end > $segments[-1][2]); # as only sorted by start pos
-    next;
   }
-  push @segments, [$ref, $start, $end];
 }
 
 if(scalar @segments == 0) {

diff --git a/perl/lib/Sanger/CGP/Pindel.pm b/perl/lib/Sanger/CGP/Pindel.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.0.2';
+our $VERSION = '3.0.3';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/perl/lib/Sanger/CGP/Pindel/Implement.pm b/perl/lib/Sanger/CGP/Pindel/Implement.pm
@@ -282,14 +282,11 @@ sub flag {
 
   my @commands = ($command, $bgzip, $tabix);
 
-  my $germ_rule = find_germline_rule($options);
-  if(defined $germ_rule) {
-    my $germ_bed = "$stub.germline.bed";
-    my $germ = "$^X ";
-    $germ .= _which('pindel_germ_bed.pl');
-    $germ .= sprintf $PIN_GERM, find_germline_rule($options), $vcf_gz, $germ_bed;
-    push @commands, $germ;
-  }
+  my $germ_bed = "$stub.germline.bed";
+  my $germ = "$^X ";
+  $germ .= _which('pindel_germ_bed.pl');
+  $germ .= sprintf $PIN_GERM, find_germline_rule($options), $vcf_gz, $germ_bed;
+  push @commands, $germ;
 
   PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, 0);
 
@@ -309,6 +306,7 @@ sub find_germline_rule {
     }
   }
   close $ffh;
+  $filter = 'NA' unless($filter);
   return $filter;
 }
 

diff --git a/setup.sh b/setup.sh
@@ -47,8 +47,8 @@ if [[ ($# -ne 1 && $# -ne 2) ]] ; then
   echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
   echo "  ./setup.sh /opt/myBundle"
   echo "OR all elements versioned:"
-  echo "  ./setup.sh /opt/cgpVcf-X.X.X /opt/PCAP-X.X.X/lib/perl"
-  exit 0
+  echo "  ./setup.sh /opt/cgpPinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core-X.X.X/lib/perl"
+  exit 1
 fi
 
 INST_PATH=$1
@@ -108,7 +108,7 @@ echo $CPANM
 PCAP=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' PCAP`
 if [[ "x$PCAP" == "x" ]] ; then
   echo "PREREQUISITE: Please install PCAP-core before proceeding:"
-  echo "  https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases"
+  echo "  https://github.com/cancerit/PCAP-core/releases"
   exit 1;
 fi