Merge branch 'hotfix/v1.1.5'

MYMETA.json

@@ -45,5 +45,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.1.4"
+   "version" : "v1.1.5"
 }

MYMETA.yml

@@ -27,4 +27,4 @@ requires:
   Pod::Coverage: '0.23'
   Sub::Exporter::Progressive: '0.001011'
   Try::Tiny: '0.19'
-version: v1.1.4
+version: v1.1.5

lib/Sanger/CGP/Grass.pm

@@ -25,6 +25,6 @@ package Sanger::CGP::Grass;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.1.4';
+our $VERSION = '1.1.5';
 
 1;

lib/Sanger/CGP/Grass/Annotation/RGcombinationAnnotator.pm

@@ -2,21 +2,21 @@ package Sanger::CGP::Grass::Annotation::RGcombinationAnnotator;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Lucy Stebbings <[email protected]>
-# 
+#
 # This file is part of grass.
-# 
+#
 # grass is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -276,7 +276,7 @@ sub combine {
     # return the combined RGanno object
 
     # combine the annopoint and H/L type data into one object
-    if ($self->{anno1}->id_rg && ($self->{anno1}->id_rg =~ /^d+$/)) { unless ($self->{anno1}->id_rg == $self->{anno2}->id_rg) {  die "ALERT: id_rgs dont match $!"; } }
+    if ($self->{anno1}->id_rg && ($self->{anno1}->id_rg =~ /^d+$/)) { unless ($self->{anno1}->id_rg == $self->{anno2}->id_rg) {  die "ALERT: id_rgs dont match\n"; } }
 
     # do I need to swap them over if both genes are on the reverse strand and the product is currently on the plus strand?
     # need to mess around with the end_phase and phase if so

lib/Sanger/CGP/Grass/FlankingBases.pm

@@ -292,8 +292,8 @@ sub _read_data {
 	my $Hstring = "$chr2:" . $Hbase_pos . "-" . $Hbase_pos;
 	if ($self->{debug}) { print "L $Lstring, H $Hstring\n"; }
 
-	if ($self->{data}->{$name}->{1}) { die "duplicate entry $name in infile. Exiting.\n $!"; }
-	if ($self->{data}->{$name}->{2}) { die "duplicate entry $name in infile. Exiting.\n $!"; }
+	if ($self->{data}->{$name}->{1}) { die "duplicate entry $name in infile. Exiting.\n"; }
+	if ($self->{data}->{$name}->{2}) { die "duplicate entry $name in infile. Exiting.\n"; }
 
 	$self->{data}->{$name}->{1} = $fai->fetch("$Lstring");
 	$self->{data}->{$name}->{2} = $fai->fetch("$Hstring");

testData/test_VcfConverterII_ann.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=VcfConverter.t_v1.1.4
+##source_20140512.1=VcfConverter.t_v1.1.5
 ##reference=/nfs/users/nfs_l/las/CGP_github/grass/t/../testData/genome.fa
 ##contig=<ID=1,assembly=GRC37,length=249250621,species=HUMAN>
 ##contig=<ID=2,assembly=GRC37,length=243199373,species=HUMAN>
@@ -59,7 +59,7 @@
 ##INFO=<ID=TRDS,Number=.,Type=String,Description="Reads from the tumour sample (PD1234a) that contribute to this rearrangement">
 ##INFO=<ID=NRDS,Number=.,Type=String,Description="Reads from the normal sample (PD1234b) that contribute to this rearrangement">
 ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Count of countributing reads">
-##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.4>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.5>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",Accession=45,Platform=HiSeq,Protocol=genomic,SampleName=PD1234b,Source=ID_SAMPLE_COSMIC,Study=12346>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",Accession=123,Platform=HiSeq,Protocol=genomic,SampleName=PD1234a,Source=ID_SAMPLE_COSMIC,Study=12345>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR

testData/test_VcfConverter_ann.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=VcfConverter.t_v1.1.4
+##source_20140512.1=VcfConverter.t_v1.1.5
 ##reference=/nfs/users/nfs_l/las/CGP_github/grass/t/../testData/genome.fa
 ##contig=<ID=1,assembly=GRC37,length=249250621,species=HUMAN>
 ##contig=<ID=2,assembly=GRC37,length=243199373,species=HUMAN>
@@ -59,7 +59,7 @@
 ##INFO=<ID=TRDS,Number=.,Type=String,Description="Reads from the tumour sample (PD1234a) that contribute to this rearrangement">
 ##INFO=<ID=NRDS,Number=.,Type=String,Description="Reads from the normal sample (PD1234b) that contribute to this rearrangement">
 ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Count of countributing reads">
-##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.4>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.5>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",Accession=45,Platform=HiSeq,Protocol=genomic,SampleName=PD1234b,Source=ID_SAMPLE_COSMIC,Study=12346>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",Accession=123,Platform=HiSeq,Protocol=genomic,SampleName=PD1234a,Source=ID_SAMPLE_COSMIC,Study=12345>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR

testData/testout_Brass_ann.vcf

@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=grass.pl_v1.1.4
+##source_20140512.1=grass.pl_v1.1.5
 ##reference=/nfs/cancer_ref01/human/37/genome.fa
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant. (All sequence is on the plus strand and in the forward direction).">
 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend">
@@ -34,7 +34,7 @@
 ##INFO=<ID=TRDS,Number=.,Type=String,Description="Reads from the tumour sample () that contribute to this rearrangement">
 ##INFO=<ID=NRDS,Number=.,Type=String,Description="Reads from the normal sample () that contribute to this rearrangement">
 ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Count of countributing reads">
-##vcfProcessLog_20140512.1=<InputVCFSource=<grass.pl>,InputVCFVer=<1.1.4>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<grass.pl>,InputVCFVer=<1.1.5>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",SampleName=>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",SampleName=>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR