Merge branch 'hotfix/v1.1.6'

cancerit · Feb 1, 2016 · d2efee7 · d2efee7
2 parents 24e4324 + 63aac63
commit d2efee7
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Showing 8 changed files with 28 additions and 102 deletions.
diff --git a/MYMETA.json b/MYMETA.json
diff --git a/MYMETA.yml b/MYMETA.yml
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 = '1.1.5';
+our $VERSION = '1.1.6';
 
 1;
diff --git a/t/RGcombinationAnnotator.t b/t/RGcombinationAnnotator.t
@@ -106,7 +106,7 @@ subtest 'Cache approach' => sub {
   is (($combi_cache->strand1()), $strand1 , "get strand1. Cache");
   is (($combi_cache->strand2()), $strand2 , "get strand2. Cache");
   is (($combi_cache->shard()), $shard , "get shard. Cache");
-  is ((Dumper($rganno_cache)), $res_74 , "get result. Cache");
+  is_deeply ($rganno_cache, $res_74 , "get result. Cache");
 };
 
 SKIP: {
@@ -146,14 +146,15 @@ SKIP: {
     is (($combi->strand1()), $strand1 , "get strand1. Ensembl");
     is (($combi->strand2()), $strand2 , "get strand2. Ensembl");
     is (($combi->shard()), $shard , "get shard. Ensembl");
-    is ((Dumper($rganno)), $res_74 , "get result. Ensembl");
+    is_deeply ($rganno, $res_74 , "get result. Ensembl");
   };
 };
 
 #------------------------------------------------------------------------------------------------#
 sub get_result_58 {
-    my $res = <<'END';
-$VAR1 = bless( {
+  my $res;
+    eval <<'END';
+$res = bless( {
                  'L5' => bless( {
                                   'gene_id' => 'TMCC1',
                                   'up2' => 'TT',
@@ -230,8 +231,9 @@ END
 }
 #------------------------------------------------------------------------------------------------#
 sub get_result_74 {
-    my $res = <<'END';
-$VAR1 = bless( {
+  my $res;
+    eval <<'END';
+$res = bless( {
                  'L5' => bless( {
                                   'gene_id' => 'TMCC1',
                                   'up2' => 'TT',

diff --git a/t/RGendAnnotator.t b/t/RGendAnnotator.t
@@ -123,7 +123,7 @@ subtest 'Cache approach' => sub {
   is (($End2->end()), $end , "get end");
   is (($End2->within()), $within , "get within");
   is (($End2->ccds_only()), 1 , "get ccds_only");
-  is ((Dumper($anns2)), $res , "get result cache");
+  is_deeply ($anns2, $res , "get result cache");
 
   # make a new object - plus strand
   my $End2_2 = new_ok('Sanger::CGP::Grass::Annotation::RGendAnnotator',
@@ -136,7 +136,7 @@ subtest 'Cache approach' => sub {
   is (($End2_2->end()), $end_2 , "get end (plus strand gene)");
   is (($End2_2->within()), $within_2 , "get within (plus strand gene)");
   is (($End2_2->ccds_only()), 1 , "get ccds_only (plus strand gene)");
-  is ((Dumper($anns2_2)), $res_2 , "get result cache (plus strand gene)");
+  is_deeply ($anns2_2, $res_2 , "get result cache (plus strand gene)");
 };
 
 
@@ -164,7 +164,7 @@ SKIP: {
     is (($End->end()), $end , "get end");
     is (($End->within()), $within , "get within");
     is (($End->ccds_only()), 1 , "get ccds_only");
-    is ((Dumper($anns)), $res , "get result ensembl");
+    is_deeply ($anns, $res , "get result ensembl");
 
     my $End_2 = new_ok('Sanger::CGP::Grass::Annotation::RGendAnnotator',
                [-entry   => $entry_2,
@@ -176,14 +176,15 @@ SKIP: {
     is (($End_2->end()), $end_2 , "get end (plus strand gene)");
     is (($End_2->within()), $within_2 , "get within (plus strand gene)");
     is (($End_2->ccds_only()), 1 , "get ccds_only (plus strand gene)");
-    is ((Dumper($anns_2)), $res_2 , "get result ensembl (plus strand gene)"); # has a putative coding transcript as well that is missing from the cache version
+    is_deeply ($anns_2, $res_2 , "get result ensembl (plus strand gene)"); # has a putative coding transcript as well that is missing from the cache version
   };
 };
 
 #------------------------------------------------------------------------------------------------#
 sub get_result_58 {
-    my $res = <<'END';
-$VAR1 = [
+    my $res;
+    eval <<'END';
+$res = [
           bless( {
                    'id_rg' => 'TEST',
                    'H5' => bless( {
@@ -321,8 +322,9 @@ END
 
 #------------------------------------------------------------------------------------------------#
 sub get_result_74 {
-    my $res = <<'END';
-$VAR1 = [
+    my $res;
+    eval <<'END';
+$res = [
           bless( {
                    'id_rg' => 'TEST',
                    'H5' => bless( {
@@ -366,8 +368,9 @@ END
 }
 #------------------------------------------------------------------------------------------------#
 sub get_result_74_2 {
-    my $res = <<'END';
-$VAR1 = [
+  my $res;
+    eval <<'END';
+$res = [
           bless( {
                    'L5' => bless( {
                                     'gene_id' => 'MIB2',

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_v1.1.5
+##source_20140512.1=VcfConverter.t_v1.1.6
 ##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=<1.1.5>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.6>>
 ##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_v1.1.5
+##source_20140512.1=VcfConverter.t_v1.1.6
 ##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=<1.1.5>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<VcfConverter.t>,InputVCFVer=<1.1.6>>
 ##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_v1.1.5
+##source_20140512.1=grass.pl_v1.1.6
 ##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=<1.1.5>>
+##vcfProcessLog_20140512.1=<InputVCFSource=<grass.pl>,InputVCFVer=<1.1.6>>
 ##SAMPLE=<ID=NORMAL,Description="Normal",SampleName=>
 ##SAMPLE=<ID=TUMOUR,Description="Mutant",SampleName=>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR