Merge branch 'hotfix/v1.1.1'

cancerit · Aug 20, 2015 · 93cbe2b · 93cbe2b
2 parents 0a05193 + de0e054
commit 93cbe2b
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Showing 8 changed files with 11 additions and 11 deletions.
diff --git a/MYMETA.json b/MYMETA.json
@@ -45,5 +45,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.1.0"
+   "version" : "v1.1.1"
 }
diff --git a/MYMETA.yml b/MYMETA.yml
@@ -27,4 +27,4 @@ requires:
   Pod::Coverage: '0.23'
   Sub::Exporter::Progressive: '0.001011'
   Try::Tiny: '0.19'
-version: v1.1.0
+version: v1.1.1
diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/Sanger/CGP/Grass.pm b/lib/Sanger/CGP/Grass.pm
@@ -25,6 +25,6 @@ package Sanger::CGP::Grass;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.1.0';
+our $VERSION = '1.1.1';
 
 1;
diff --git a/setup.sh b/setup.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 ##########LICENCE##########
-#  Copyright (c) 2014 Genome Research Ltd.
+#  Copyright (c) 2014,2015 Genome Research Ltd.
 #
 #  Author: Lucy Stebbings <[email protected]>
 #
@@ -95,7 +95,7 @@ echo > $INIT_DIR/setup.log
 
 VCF=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vcf`
 if [[ "x$VCF" == "x" ]] ; then
-  echo "PREREQUISITE: Please install Sanger::CGP::Vagrent before proceeding: https://github.com/cancerit/cgpVcf/releases"
+  echo "PREREQUISITE: Please install Sanger::CGP::Vcf before proceeding: https://github.com/cancerit/cgpVcf/releases"
   exit 1;
 fi
 

diff --git a/testData/test_VcfConverterII_ann.vcf b/testData/test_VcfConverterII_ann.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=VcfConverter.t_v1.1.0
+##source_20140512.1=VcfConverter.t_v1.1.1
 ##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=<1.1.0>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.1>>
 ##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

diff --git a/testData/test_VcfConverter_ann.vcf b/testData/test_VcfConverter_ann.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=VcfConverter.t_v1.1.0
+##source_20140512.1=VcfConverter.t_v1.1.1
 ##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=<1.1.0>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.1>>
 ##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

diff --git a/testData/testout_Brass_ann.vcf b/testData/testout_Brass_ann.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.1
 ##fileDate=20140512
-##source_20140512.1=grass.pl_v1.1.0
+##source_20140512.1=grass.pl_v1.1.1
 ##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=<1.1.0>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<grass.pl>,InputVCFVer=<1.1.1>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",SampleName=>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",SampleName=>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR