Merge branch 'hotfix/v3.0.1'

cancerit · Mar 26, 2018 · 3a1e1b7 · 3a1e1b7
2 parents c40f376 + f641ec5
commit 3a1e1b7
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Showing 5 changed files with 12 additions and 8 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.0.1
+
+* Update tabix calls to directly use query_full (solves GRCh38 contig name issues).
+
 ## 3.0.0
 
 * Germline bed file is now merged for adjacent regions (#31)

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 = '3.0.0';
+our $VERSION = '3.0.1';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/perl/lib/Sanger/CGP/Pindel/InputGen/Read.pm b/perl/lib/Sanger/CGP/Pindel/InputGen/Read.pm
@@ -156,7 +156,7 @@ sub _good_anchor {
 
 sub _tabix_hit {
   my $self = shift;
-  my $iter = $self->{'tabix'}->query(sprintf '%s:%d-%d', $self->{'rname'}, $self->{'pos'}, $self->{'pos'});
+  my $iter = $self->{'tabix'}->query_full($self->{'rname'}, $self->{'pos'}, $self->{'pos'});
   return 0 unless(defined $iter);
   while(my $ret = $iter->next){
     return 1;

diff --git a/perl/lib/Sanger/CGP/PindelPostProcessing/FilterRules.pm b/perl/lib/Sanger/CGP/PindelPostProcessing/FilterRules.pm
@@ -305,7 +305,7 @@ sub flag_009 {
 
   my $ret = eval{
     # as vcf POS for indels is the previous base pos is 0-based, but the new TABIX requires 1-based
-    my $iter = $main::VCF_IS_CODING_TABIX->query(sprintf '%s:%d-%d', $CHROM,$POS+1,($POS+$MATCH));
+    my $iter = $main::VCF_IS_CODING_TABIX->query_full($CHROM,$POS+1,($POS+$MATCH));
     return $FAIL if(!defined $iter); # no valid entries (chromosome not in index) so must FAIL
     while($iter->next){
       return $PASS;
@@ -337,7 +337,7 @@ sub flag_010 {
   $to += $length_off;
 
   my $ret = eval{
-    my $iter = $vcf_flagging_unmatched_normals_tabix->query(sprintf '%s:%d-%d', $CHROM,$from,$to);
+    my $iter = $vcf_flagging_unmatched_normals_tabix->query_full($CHROM,$from,$to);
     return $PASS if(!defined $iter); # no valid entries (chromosome not in index) so must pass
     while($iter->next){
       return $FAIL;
@@ -427,7 +427,7 @@ sub flag_017 {
 
   my $ret = eval{
     # as vcf POS for indels is the previous base pos is 0-based, but the new TABIX requires 1-based
-    my $iter = $vcf_flagging_repeats_tabix->query(sprintf '%s:%d-%d', $CHROM,$from,$to);
+    my $iter = $vcf_flagging_repeats_tabix->query_full($CHROM,$from,$to);
     return $PASS if(!defined $iter); # no valid entries (chromosome not in index) so must pass
     while($iter->next){
       return $FAIL;

diff --git a/perl/lib/Sanger/CGP/PindelPostProcessing/FragmentFilterRules.pm b/perl/lib/Sanger/CGP/PindelPostProcessing/FragmentFilterRules.pm
@@ -305,7 +305,7 @@ sub flag_009 {
 
   my $ret = eval{
     # as vcf POS for indels is the previous base pos is 0-based, but the new TABIX requires 1-based
-    my $iter = $main::VCF_IS_CODING_TABIX->query(sprintf '%s:%d-%d', $CHROM,$POS+1,($POS+$MATCH));
+    my $iter = $main::VCF_IS_CODING_TABIX->query_full($CHROM,$POS+1,($POS+$MATCH));
     return $FAIL if(!defined $iter); # no valid entries (chromosome not in index) so must FAIL
     while($iter->next){
       return $PASS;
@@ -337,7 +337,7 @@ sub flag_010 {
   $to += $length_off;
 
   my $ret = eval{
-    my $iter = $vcf_flagging_unmatched_normals_tabix->query(sprintf '%s:%d-%d', $CHROM,$from,$to);
+    my $iter = $vcf_flagging_unmatched_normals_tabix->query_full($CHROM,$from,$to);
     return $PASS if(!defined $iter); # no valid entries (chromosome not in index) so must pass
     while($iter->next){
       return $FAIL;
@@ -423,7 +423,7 @@ sub flag_017 {
 
   my $ret = eval{
     # as vcf POS for indels is the previous base pos is 0-based, but the new TABIX requires 1-based
-    my $iter = $vcf_flagging_repeats_tabix->query(sprintf '%s:%d-%d', $CHROM,$from,$to);
+    my $iter = $vcf_flagging_repeats_tabix->query_full($CHROM,$from,$to);
     return $PASS if(!defined $iter); # no valid entries (chromosome not in index) so must pass
     while($iter->next){
       return $FAIL;