Merge branch 'hotfix/v1.1.2'

cancerit · Sep 8, 2015 · 054b5ab · 054b5ab
2 parents 93cbe2b + 43971b0
commit 054b5ab
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Showing 9 changed files with 12 additions and 12 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -101,7 +101,6 @@ MANIFEST			This list of files
 perltidy.LOG
 prerelease.sh
 README.md
-setup.log
 setup.sh
 t/1_pm_compile.t
 t/2_pl_compile.t

diff --git a/MYMETA.json b/MYMETA.json
@@ -4,7 +4,7 @@
       "unknown"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.143240",
    "license" : [
       "agpl_3"
    ],
@@ -45,5 +45,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.1.1"
+   "version" : "v1.1.2"
 }
diff --git a/MYMETA.yml b/MYMETA.yml
@@ -7,7 +7,7 @@ build_requires:
 configure_requires:
   ExtUtils::MakeMaker: '0'
 dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.143240'
 license: open_source
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -27,4 +27,4 @@ requires:
   Pod::Coverage: '0.23'
   Sub::Exporter::Progressive: '0.001011'
   Try::Tiny: '0.19'
-version: v1.1.1
+version: v1.1.2
diff --git a/bin/grass.pl b/bin/grass.pl
@@ -202,6 +202,7 @@ sub do_file {
 	}
 
 	my $entry_is_bedpe = do_data_line($fh_out, $line, $field, $is_refract, $list_between, $show_biotype, $genome_data);
+
 	if ($entry_is_bedpe) { $is_bedpe = 1; }
 	elsif(-s $infile == 0 && $infile =~ m/\.bedpe$/i) {
 	  $is_bedpe = 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 = '1.1.1';
+our $VERSION = '1.1.2';
 
 1;
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_v1.1.1
+##source_20140512.1=VcfConverter.t_v1.1.2
 ##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=<1.1.1>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.2>>
 ##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_v1.1.1
+##source_20140512.1=VcfConverter.t_v1.1.2
 ##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=<1.1.1>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.2>>
 ##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_v1.1.1
+##source_20140512.1=grass.pl_v1.1.2
 ##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=<1.1.1>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<grass.pl>,InputVCFVer=<1.1.2>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",SampleName=>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",SampleName=>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR