Merge branch 'release/v4.1.0'

CHANGES.md

@@ -1,3 +1,6 @@
+### 4.1.0
+* Modified to use new >= 3.3.0 allelecounter code with dense SNP functionality
+
 ### 2.1.2
 * Minor fix to usage typo
 
@@ -6,4 +9,4 @@
 * Supports CRAM
 * Allele count phase is now threaded.
 
-NOTE: Individual scripts called by `ascat.pl` have been renamed to prevent potential namespace clashes.
+NOTE: Individual scripts called by `ascat.pl` have been renamed to prevent potential namespace clashes.

perl/lib/Sanger/CGP/Ascat.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '4.0.1';
+our $VERSION = '4.1.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

perl/lib/Sanger/CGP/Ascat/Implement.pm

@@ -49,7 +49,7 @@ const my $FAILED_SAMPLE_STATISTICS => qq{## WARNING ASCAT failed to %s ##\nNorma
 
 const my $ALLELE_COUNT_GENDER => ' -o %s -b %s -l %s -r %s -g ';
 
-const my $ALLELE_COUNT_PARA => ' -b %s -o %s -l %s -c %s -r %s ';
+const my $ALLELE_COUNT_PARA => ' -b %s -o %s -l %s -c %s -r %s -d ';
 
 const my $GREP_ALLELE_COUNTS => q{grep -v '^#' %s >> %s};
 

setup.sh

@@ -23,6 +23,11 @@
 
 # v2.4.3
 ASCAT_SRC="https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/6d40e69a2919ddfc1cda870310203c772bf846ce/ASCAT/R/ascat.R"
+EXP_ACV="3.3.0"
+
+version_gt () {
+  test $(printf '%s\n' $@ | sort -V | head -n 1) == "$1";
+}
 
 done_message () {
     if [ $? -eq 0 ]; then
@@ -123,9 +128,17 @@ fi
 
 AC=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::AlleleCount`
 if [[ "x$AC" == "x" ]] ; then
-  echo "PREREQUISITE: Please install alleleCount before proceeding:"
+  echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding:"
   echo "  https://github.com/cancerit/alleleCount/releases"
   exit 1;
+else
+  if version_gt $AC $EXP_ACV; then
+    echo "  alleleCounter version is good ($AC)"
+  else
+    echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding (Found version $AC):"
+    echo "  https://github.com/cancerit/alleleCount/releases"
+    exit 1;
+  fi
 fi
 
 VCF=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vcf`