Merge branch 'hotfix/5.3.6'

cancerit · May 15, 2018 · d532dfb · d532dfb
2 parents 41875ed + e7bfa18
commit d532dfb
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Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## v5.3.6
+* Correct query_full to ensure `undef` return is caught.
+* vaf output precison raised from two to four decimal places.
+
 ## v5.3.5
 * Update `samtols` and `hstlib` to v1.7
 * Update `Bio::DB::HTS` to v2.10

diff --git a/perl/lib/Sanger/CGP/Vaf.pm b/perl/lib/Sanger/CGP/Vaf.pm
@@ -2,7 +2,7 @@ package Sanger::CGP::Vaf;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '5.3.5';
+our $VERSION = '5.3.6';
 
 const my $LICENSE =>
 "#################

diff --git a/perl/lib/Sanger/CGP/Vaf/Process/Variant.pm b/perl/lib/Sanger/CGP/Vaf/Process/Variant.pm
@@ -134,7 +134,7 @@ sub storeResults {
 	my $WTR = $g_pu->{'ref_p'} + $g_pu->{'ref_n'};
 	my $VAF;
 	eval {$VAF = $MTR/($MTR+$WTR);};
-	$VAF=defined $VAF?sprintf("%.2f",$VAF):'0.0';
+	$VAF=defined $VAF?sprintf("%.4f",$VAF):'0.0';
  	if ($self->getVarLine=~/BEDFILE/) {
 	    my $bed_line=$g_pu->{'chr'}."\t".
 	    						 $g_pu->{'start'}."\t".
@@ -391,13 +391,15 @@ sub _check_hdr_overlap {
 	###
 		my $i=0;
 		my $res = $tabix->query_full($chr,$zero_start,$one_end);
-		while(my $record=$res->next) {
-			if($record) {
-				$i=1;
-				return $i;
-			}
-		}
-	$i;	
+    if(defined($res)){
+		  while(my $record=$res->next) {
+			   if($record) {
+				    $i=1;
+				    return $i;
+			   }
+		  }
+    }
+	$i;
 }
 
 
@@ -934,7 +936,7 @@ sub addNormalCount {
 						$g_pu->{'normal_MTR'}=$g_pu->{'alt_p'} + $g_pu->{'alt_n'};
 						$g_pu->{'normal_WTR'}=$g_pu->{'ref_p'} + $g_pu->{'ref_n'};
 						eval{$VAF=$g_pu->{'normal_MTR'}/($g_pu->{'normal_WTR'}+$g_pu->{'normal_MTR'}); };
-						$g_pu->{'normal_VAF'}=defined $VAF?sprintf("%.2f",$VAF):'0.00';
+						$g_pu->{'normal_VAF'}=defined $VAF?sprintf("%.4f",$VAF):'0.00';
 						$g_pu->{'normal_UNK'}=$g_pu->{'unk'};
 						$g_pu->{'normal_AMB'}=$g_pu->{'amb'};
 
@@ -1061,7 +1063,7 @@ sub formatResults {
 
 	my $VAF;
 	eval {$VAF = $MTR/($MTR+$WTR);};
-	$VAF=defined $VAF?sprintf("%.2f",$VAF):'0.0';
+	$VAF=defined $VAF?sprintf("%.4f",$VAF):'0.0';
 
 	if($self->getVarType ne 'indel') {
 	$pileup_results={

diff --git a/setup.sh b/setup.sh
@@ -134,7 +134,7 @@ perlmods=( "File::ShareDir" "File::ShareDir::Install" "Bio::Root::Version@1.0069
 (
 set -e
 for i in "${perlmods[@]}" ; do
-  echo -n "Installing build prerequisite $i..."
+  echo "Installing build prerequisite $i..."
 
     set -x
     $INIT_DIR/perl/bin/cpanm -v --mirror http://cpan.metacpan.org -l $INST_PATH $i
@@ -166,7 +166,7 @@ else
   ) >>$INIT_DIR/setup.log 2>&1
 
 
-  echo -n "Building htslib ..."
+  echo "Building htslib ..."
   (
   if [ -e $SETUP_DIR/htslib.success ]; then
     echo " previously installed ...";
@@ -188,7 +188,7 @@ else
 
   (
   if [[ ",$COMPILE," == *,samtools,* ]] ; then
-    echo -n "Building samtools ..."
+    echo "Building samtools ..."
     if [ -e $SETUP_DIR/samtools.success ]; then
       echo " previously installed ...";
     else
@@ -210,7 +210,7 @@ else
   fi
   ) >>$INIT_DIR/setup.log 2>&1
 
-  echo -n "Building Bio::DB::HTS ..."
+  echo "Building Bio::DB::HTS ..."
   (
   if [ -e $SETUP_DIR/biohts.success ]; then
     echo " previously installed ...";