Merge branch 'hotfix/v3.3.1'

CHANGES.md

@@ -1,24 +1,31 @@
-### 3.3.0
+# CHANGES
+
+## 3.3.1
+* `samtools` and `htslib` updated to 1.7
+* `Bio::DB::HTS` updated to 2.10, fixes error with GRCh38 contig names in Tabix.
+* Update tabix query to use `query_full`
+
+## 3.3.0
 * Complete re-write of the reference generation code
 
-### 3.2.2
+## 3.2.2
 * Add bedtools2 to `setup.sh`
 * Added bedtools2 to `README.md`
 * Changes `Bio::DB::HTS`, `samtools` and `HTSlib` install methods.
 * Corrected condition indicating sort is required.
 * Fixes #23 Changed from vcf-sort to normal linux sort to ensure multiple indels with
 same start coord are sorted in a stable way.
 
-### 3.2.0
+## 3.2.0
 * Allows use of ensemblgenomes.org as a datasource
 * Handle genes without names, and give more useful error message
 * Ensure an error code is emmitted on failure
 
-### 3.1.0
+## 3.1.0
 * Adds travis testing
 * Cleans up install script and adds multi versioned paths to options
 
-### 3.0.0
+## 3.0.0
 * Removed use of legacy Tabix codebase and switches to samtools 1.2+
 * Switches to gihub version of vcftools and makes several patches unnecessary
 * Several bugfixes

lib/Sanger/CGP/Vagrent.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.3.0';
+our $VERSION = '3.3.1';
 our @EXPORT = qw($VERSION);
 
 1;

lib/Sanger/CGP/Vagrent/TranscriptSource/FileBasedTranscriptSource.pm

@@ -128,7 +128,7 @@ sub _getTranscriptsFromCache {
   } else {
     $min = ($gp->getMinPos - $SEARCH_BUFFER);
   }
-  my $iter = $self->{_cache_tbx}->query(sprintf '%s:%d-%d', $gp->getChr(),$min,$max);
+  my $iter = $self->{_cache_tbx}->query_full($gp->getChr(),$min,$max);
   return undef unless defined $iter;
   my $out = undef;
   while(my $ret = $iter->next){

setup.sh

@@ -21,9 +21,9 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
 
-SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2"
-SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.3.tar.gz"
+SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.7.tar.bz2"
+SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.7.tar.bz2"
+SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.10.tar.gz"
 SOURCE_VCFTOOLS="https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"
 # Warning bedtools 2.24.0 and 2.25.0 have a swapped usage in coverageBed
 # No upgrades until [this ticket](https://github.com/arq5x/bedtools2/issues/319) is resolved