From e509db7764989c1a830635c8a05414ed1e3b479e Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Mar 2018 10:18:33 +0100
Subject: [PATCH 1/4] VErsion bumped and CHANGES.md

---
 CHANGES.md            | 4 ++++
 perl/lib/Bio/Brass.pm | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index c45e545..44a2c9d 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,9 @@
 # Changes
 
+## v6.1.2
+
+* Change tabix->query to tabix->query_full
+
 ## v6.1.1
 
 * Reduce I/O for small cpu overhead in coverage step
diff --git a/perl/lib/Bio/Brass.pm b/perl/lib/Bio/Brass.pm
index d6f5b1d..ec33177 100644
--- a/perl/lib/Bio/Brass.pm
+++ b/perl/lib/Bio/Brass.pm
@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
 		 is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
 		 $VERSION);
 
-our $VERSION = '6.1.1';
+our $VERSION = '6.1.2';
 
 =head1 NAME
 

From 0d96ebff700db26cf4c428286a3e4fff7183ff0c Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Mar 2018 10:18:48 +0100
Subject: [PATCH 2/4] Update tabix->query to use tabix->query_full

---
 perl/lib/Bio/Brass/Merge.pm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/perl/lib/Bio/Brass/Merge.pm b/perl/lib/Bio/Brass/Merge.pm
index a6be3f7..951dc69 100644
--- a/perl/lib/Bio/Brass/Merge.pm
+++ b/perl/lib/Bio/Brass/Merge.pm
@@ -108,14 +108,16 @@ sub merge_records {
       # always clear the existing groups
       $n_grp->clear_group;
       # tabix BED now 1 based when queried
-      my $iter = $brass_np->query(sprintf '%s%s%s%s:%d-%d', $a_grp->low_chr, $a_grp->low_strand, $a_grp->high_chr, $a_grp->high_strand, $a_grp->low_5p, $a_grp->low_3p);
+      my $iter = $brass_np->query_full(sprintf('%s%s%s%s', $a_grp->low_chr, $a_grp->low_strand, $a_grp->high_chr, $a_grp->high_strand), $a_grp->low_5p, $a_grp->low_3p);
       my %overlaps;
       my $low_chr=$a_grp->low_chr;
-      while(my $record = $iter->next){
-        $record=~s/^[^\t]+/$low_chr/;
-        $n_grp->new_group($record);
-        next unless($a_grp->high_3p >= $n_grp->high_5p && $a_grp->high_5p <= $n_grp->high_3p);
-        $overlaps{"@{$n_grp->{_loc_data}}"} = $record;
+      if(defined($iter)){
+        while(my $record = $iter->next){
+          $record=~s/^[^\t]+/$low_chr/;
+          $n_grp->new_group($record);
+          next unless($a_grp->high_3p >= $n_grp->high_5p && $a_grp->high_5p <= $n_grp->high_3p);
+          $overlaps{"@{$n_grp->{_loc_data}}"} = $record;
+        }
       }
       my $overlap = filter_overlaps(\%overlaps, $n_grp->sample_count);
       if(defined $overlap) {

From 6d079c18807685997a947803ca5d370e244cac5a Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Mar 2018 12:48:16 +0100
Subject: [PATCH 3/4] Update to use the cancerit version of PCAP-Core

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index aaf3acb..126f00b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -35,7 +35,7 @@ install:
  - ./setup.sh $HOME/wtsi-opt
  - cd ../
  - rm -rf cgpBigWig
- - git clone --depth 1 --single-branch --branch dev https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git
+ - git clone --depth 1 --single-branch --branch dev https://github.com/cancerit/PCAP-core.git
  - cd PCAP-core
  - ./setup.sh $HOME/wtsi-opt
  - cd ../

From 798433e8c03e1445949ff1c38371dfbb9326cd16 Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Mar 2018 12:51:41 +0100
Subject: [PATCH 4/4] develop not dev branch of PCAP-core in `.travis.yml`

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 126f00b..2651715 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -35,7 +35,7 @@ install:
  - ./setup.sh $HOME/wtsi-opt
  - cd ../
  - rm -rf cgpBigWig
- - git clone --depth 1 --single-branch --branch dev https://github.com/cancerit/PCAP-core.git
+ - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/PCAP-core.git
  - cd PCAP-core
  - ./setup.sh $HOME/wtsi-opt
  - cd ../