diff --git a/.travis.yml b/.travis.yml index 2aac664ab..ecabb20c8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -57,9 +57,7 @@ install: - cd $DEPS - $CWD/travisci/build_c.sh - cd $CWD - - cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile . - - cpanm --quiet --installdeps --with-recommends --notest . - - if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]; then cpanm --quiet -n Devel::Cover::Report::Coveralls; fi + - $CWD/travisci/install_dependencies.sh - cp travisci/MultiTestDB.conf.travisci t/MultiTestDB.conf script: "./travisci/harness.sh" diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm index 954e3c135..369d09cbd 100755 --- a/modules/Bio/EnsEMBL/VEP/Constants.pm +++ b/modules/Bio/EnsEMBL/VEP/Constants.pm @@ -116,9 +116,9 @@ our @FLAG_FIELDS = ( # frequency stuff { flag => 'af', fields => ['AF'] }, { flag => 'af_1kg', fields => ['AF','AFR_AF','AMR_AF','EAS_AF','EUR_AF','SAS_AF'] }, - { flag => 'af_gnomad', fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF','gnomADe_NFE_AF','gnomADe_OTH_AF','gnomADe_SAS_AF'] }, - { flag => 'af_gnomade', fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF','gnomADe_NFE_AF','gnomADe_OTH_AF','gnomADe_SAS_AF'] }, - { flag => 'af_gnomadg', fields => ['gnomADg_AF','gnomADg_AFR_AF', ,'gnomADg_AMI_AF', 'gnomADg_AMR_AF','gnomADg_ASJ_AF','gnomADg_EAS_AF','gnomADg_FIN_AF','gnomADg_MID_AF','gnomADg_NFE_AF','gnomADg_OTH_AF','gnomADg_SAS_AF'] }, + { flag => 'af_gnomad', fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF', 'gnomADe_MID_AF', 'gnomADe_NFE_AF','gnomADe_REMAINING_AF','gnomADe_SAS_AF'] }, + { flag => 'af_gnomade', fields => ['gnomADe_AF','gnomADe_AFR_AF','gnomADe_AMR_AF','gnomADe_ASJ_AF','gnomADe_EAS_AF','gnomADe_FIN_AF', 'gnomADe_MID_AF', 'gnomADe_NFE_AF','gnomADe_REMAINING_AF','gnomADe_SAS_AF'] }, + { flag => 'af_gnomadg', fields => ['gnomADg_AF','gnomADg_AFR_AF', ,'gnomADg_AMI_AF', 'gnomADg_AMR_AF','gnomADg_ASJ_AF','gnomADg_EAS_AF','gnomADg_FIN_AF','gnomADg_MID_AF','gnomADg_NFE_AF','gnomADg_REMAINING_AF','gnomADg_SAS_AF'] }, { flag => 'max_af', fields => ['MAX_AF', 'MAX_AF_POPS'] }, { flag => 'check_frequency', fields => ['FREQS'] }, @@ -217,8 +217,9 @@ our %FIELD_DESCRIPTIONS = ( 'gnomADe_ASJ_AF', => 'Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population', 'gnomADe_EAS_AF', => 'Frequency of existing variant in gnomAD exomes East Asian population', 'gnomADe_FIN_AF', => 'Frequency of existing variant in gnomAD exomes Finnish population', + 'gnomADe_MID_AF', => 'Frequency of existing variant in gnomAD exomes Mid-eastern population', 'gnomADe_NFE_AF', => 'Frequency of existing variant in gnomAD exomes Non-Finnish European population', - 'gnomADe_OTH_AF', => 'Frequency of existing variant in gnomAD exomes other combined populations', + 'gnomADe_REMAINING_AF', => 'Frequency of existing variant in gnomAD exomes remaining combined populations', 'gnomADe_SAS_AF', => 'Frequency of existing variant in gnomAD exomes South Asian population', 'gnomADg_AF', => 'Frequency of existing variant in gnomAD genomes combined population', 'gnomADg_AFR_AF', => 'Frequency of existing variant in gnomAD genomes African/American population', @@ -229,7 +230,7 @@ our %FIELD_DESCRIPTIONS = ( 'gnomADg_FIN_AF', => 'Frequency of existing variant in gnomAD genomes Finnish population', 'gnomADg_MID_AF', => 'Frequency of existing variant in gnomAD genomes Mid-eastern population', 'gnomADg_NFE_AF', => 'Frequency of existing variant in gnomAD genomes Non-Finnish European population', - 'gnomADg_OTH_AF', => 'Frequency of existing variant in gnomAD genomes other combined populations', + 'gnomADg_REMAINING_AF', => 'Frequency of existing variant in gnomAD genomes remaining combined populations', 'gnomADg_SAS_AF', => 'Frequency of existing variant in gnomAD genomes South Asian population', 'MAX_AF', => 'Maximum observed allele frequency in 1000 Genomes, ESP and ExAC/gnomAD', 'MAX_AF_POPS' => 'Populations in which maximum allele frequency was observed', diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm index 4d79de891..cf98812a3 100755 --- a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm +++ b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm @@ -107,9 +107,9 @@ my %DISTANCE_CONS = (upstream_gene_variant => 1, downstream_gene_variant => 1); my %FREQUENCY_KEYS = ( af => ['AF'], af_1kg => [qw(AF AFR AMR ASN EAS EUR SAS)], - af_gnomad => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))], - af_gnomade => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))], - af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE OTH SAS))], + af_gnomad => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))], + af_gnomade => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))], + af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE REMAINING SAS))], ); diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm index 3cfd74803..49a92af21 100755 --- a/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm +++ b/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm @@ -129,8 +129,8 @@ my @FREQ_FIELDS = qw( AF AFR AMR ASN EAS SAS EUR AA EA ExAC ExAC_Adj ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS - gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS - gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_OTH gnomADg_SAS + gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS + gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_REMAINING gnomADg_SAS ); diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm index ad757dcf5..5154c625f 100644 --- a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm +++ b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm @@ -583,7 +583,7 @@ sub human_frequency_checks { af_gnomad => 1, af_gnomade => 1, af_gnomadg => 1, - fields => 'Uploaded_variation,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_NFE_AF,gnomADe_OTH_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AF,gnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_OTH_AF,gnomADg_SAS_AF', + fields => 'Uploaded_variation,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AF,gnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF', buffer_size => 1, pick => 1, failed => 1, diff --git a/t/AnnotationSource_Cache_Variation.t b/t/AnnotationSource_Cache_Variation.t index 86a43b695..a9bd639cf 100644 --- a/t/AnnotationSource_Cache_Variation.t +++ b/t/AnnotationSource_Cache_Variation.t @@ -296,12 +296,13 @@ is_deeply($vf->{existing}, [ 'gnomADe_AFR' => 'T:0.004643', 'minor_allele_freq' => '0.0010', 'AMR' => 'T:0.0014', - 'gnomADe_OTH' => 'T:0', + 'gnomADe_REMAINING' => 'T:0', 'gnomADe_EAS' => 'T:0', 'EUR' => 'T:0', 'clin_sig' => '', 'EAS' => 'T:0', 'end' => 25585733, + 'gnomADe_MID' => 'T:0', 'gnomADe_NFE' => 'T:1.886e-05', 'variation_name' => 'rs142513484', 'minor_allele' => 'T', @@ -352,12 +353,13 @@ is_deeply( 'gnomADe_AFR' => 'T:0', 'minor_allele_freq' => '0.0002', 'AMR' => 'T:0.0014', - 'gnomADe_OTH' => 'T:0.0001823', + 'gnomADe_REMAINING' => 'T:0.0001823', 'gnomADe_EAS' => 'T:0', 'EUR' => 'T:0', 'clin_sig' => 'uncertain_significance,not_provided,pathogenic', 'EAS' => 'T:0', 'end' => 25891796, + 'gnomADe_MID' => 'T:0', 'gnomADe_NFE' => 'T:2.687e-05', 'variation_name' => 'rs63750066', 'minor_allele' => 'T', diff --git a/t/AnnotationSource_Cache_VariationTabix.t b/t/AnnotationSource_Cache_VariationTabix.t index b3a44b55e..8c04263d7 100644 --- a/t/AnnotationSource_Cache_VariationTabix.t +++ b/t/AnnotationSource_Cache_VariationTabix.t @@ -80,12 +80,13 @@ my $exp = [{ 'minor_allele_freq' => '0.0010', 'AMR' => 'T:0.0014', 'chr' => '21', - 'gnomADe_OTH' => 'T:0', + 'gnomADe_REMAINING' => 'T:0', 'gnomADe_EAS' => 'T:0', 'EUR' => 'T:0', 'clin_sig' => undef, 'EAS' => 'T:0', 'end' => 25585733, + 'gnomADe_MID' => 'T:0', 'gnomADe_NFE' => 'T:1.886e-05', 'variation_name' => 'rs142513484', 'minor_allele' => 'T', @@ -197,12 +198,13 @@ SKIP: { 'minor_allele_freq' => undef, 'AMR' => undef, 'chr' => '21', - 'gnomADe_OTH' => undef, + 'gnomADe_REMAINING' => undef, 'gnomADe_EAS' => undef, 'EUR' => undef, 'clin_sig' => undef, 'EAS' => undef, 'end' => 25891796, + 'gnomADe_MID' => undef, 'gnomADe_NFE' => undef, 'variation_name' => 'CM930033', 'minor_allele' => undef, @@ -228,12 +230,13 @@ SKIP: { 'minor_allele_freq' => '0.0002', 'AMR' => 'T:0.0014', 'chr' => '21', - 'gnomADe_OTH' => 'T:0.0001823', + 'gnomADe_REMAINING' => 'T:0.0001823', 'gnomADe_EAS' => 'T:0', 'EUR' => 'T:0', 'clin_sig' => 'not_provided,pathogenic', 'EAS' => 'T:0', 'end' => 25891796, + 'gnomADe_MID' => 'T:0', 'gnomADe_NFE' => 'T:2.687e-05', 'variation_name' => 'rs63750066', 'minor_allele' => 'T', diff --git a/t/CacheDir.t b/t/CacheDir.t index b92e16813..38e3f52a8 100644 --- a/t/CacheDir.t +++ b/t/CacheDir.t @@ -210,8 +210,9 @@ is_deeply( 'gnomADe_ASJ', 'gnomADe_EAS', 'gnomADe_FIN', + 'gnomADe_MID', 'gnomADe_NFE', - 'gnomADe_OTH', + 'gnomADe_REMAINING', 'gnomADe_SAS', 'var_synonyms', 'AF' diff --git a/t/OutputFactory.t b/t/OutputFactory.t index a596a7434..665151aea 100644 --- a/t/OutputFactory.t +++ b/t/OutputFactory.t @@ -772,7 +772,7 @@ is_deeply( 'gnomADe_AF' => [ '9.75e-05' ], - 'gnomADe_OTH_AF' => [ + 'gnomADe_REMAINING_AF' => [ '0.0001823' ], 'gnomADe_AFR_AF' => [ @@ -792,6 +792,9 @@ is_deeply( ], 'gnomADe_ASJ_AF' => [ '0' + ], + 'gnomADe_MID_AF' => [ + '0' ] }, 'add_colocated_frequency_data - af_gnomad', diff --git a/t/OutputFactory_JSON.t b/t/OutputFactory_JSON.t index a38bea8cb..6ee7efd8a 100755 --- a/t/OutputFactory_JSON.t +++ b/t/OutputFactory_JSON.t @@ -133,7 +133,7 @@ SKIP: { 'amr' => '0.0014', 'gnomade_sas' => '0', 'gnomade' => '0.0003478', - 'gnomade_oth' => '0', + 'gnomade_remaining' => '0', 'gnomade_asj' => '0', 'gnomade_nfe' => '1.886e-05', 'gnomade_afr' => '0.004643', @@ -142,6 +142,7 @@ SKIP: { 'gnomade_fin' => '0', 'sas' => '0', 'gnomade_eas' => '0', + 'gnomade_mid' => '0', 'eur' => '0', 'eas' => '0' } @@ -201,10 +202,11 @@ SKIP: { 'gnomade_fin' => '0', 'gnomade_amr' => '0', 'gnomade' => '7.313e-05', - 'gnomade_oth' => '0', + 'gnomade_remaining' => '0', 'gnomade_asj' => '0', 'gnomade_eas' => '0', - 'gnomade_nfe' => '0.0001433' + 'gnomade_nfe' => '0.0001433', + 'gnomade_mid' => '0' } }, 'end' => '25891785', @@ -319,7 +321,7 @@ SKIP: { 'amr' => 0.0014, 'gnomade_sas' => 0, 'gnomade' => 0.0003478, - 'gnomade_oth' => 0, + 'gnomade_remaining' => 0, 'gnomade_asj' => 0, 'gnomade_nfe' => 1.886e-05, 'gnomade_afr' => 0.004643, @@ -328,6 +330,7 @@ SKIP: { 'gnomade_fin' => 0, 'sas' => 0, 'gnomade_eas' => 0, + 'gnomade_mid' => 0, 'eur' => 0, 'eas' => 0 } diff --git a/t/OutputFactory_Tab.t b/t/OutputFactory_Tab.t index f3406a74e..5ff586730 100644 --- a/t/OutputFactory_Tab.t +++ b/t/OutputFactory_Tab.t @@ -256,7 +256,7 @@ is( "-\t-\t-\t-\trs142513484\tMODIFIER\t-\t-1\t-\tSNV\tMRPL39\tHGNC\tHGNC:14027\tprotein_coding\tYES\t-\t-\t-\t5\t-\t". "CCDS33522.1\tENSP00000305682\tQ9NYK5\t-\tUPI00001AEAC0\t-\t-\t-\t-\t11/11\t-\t-\t-\tENST00000307301.11:c.*18G>A\t". "-\t-\t0.0010\t0.003\t0.0014\t0\t0\t0\t". - "0.0003478\t0.004643\t0.0003236\t0\t0\t0\t1.886e-05\t0\t0\t". + "0.0003478\t0.004643\t0.0003236\t0\t0\t0\t0\t1.886e-05\t0\t0\t". "-\t-\t-\t-\t-\t-\t-\t-\t-\t". "-\t-\t0.004643\tgnomADe_AFR\t-\t-\t-\t-\t-\t-\t-\t-\t-", 'get_all_lines_by_InputBuffer - everything' diff --git a/t/OutputFactory_VCF.t b/t/OutputFactory_VCF.t index 84a638112..1f1f7e1ff 100644 --- a/t/OutputFactory_VCF.t +++ b/t/OutputFactory_VCF.t @@ -351,14 +351,14 @@ is( '21 25585733 rs142513484 C T . . CSQ=T|3_prime_UTR_variant'. '|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|11/11||ENST00000307301.11:c.*18G>A||1122|'. '||||rs142513484||-1||SNV|HGNC|HGNC:14027|YES||||5||CCDS33522.1|ENSP00000305682|Q9NYK5||UPI00001AEAC0|'. -'|||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||'. +'|||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||'. '|||||||,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|10/10|'. '|ENST00000352957.8:c.991G>A|ENSP00000284967.6:p.Ala331Thr|1033|991|331|A/T|Gca/Aca|rs142513484||-1||SNV|HGNC'. '|HGNC:14027|||||1|P1|CCDS13573.1|ENSP00000284967|Q9NYK5||UPI00001AEE66|||tolerated_low_confidence(0.17)|benign(0.001)'. -'||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||,T'. +'||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR|||||||||,T'. '|upstream_gene_variant|MODIFIER|AP000223.1|ENSG00000260583|Transcript|ENST00000567517|antisense||||||||||rs142513484'. '|2407|-1||SNV|Clone_based_ensembl_gene||YES||||||||||||||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643'. -'|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||||||||| GT 0|0' +'|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||||||||| GT 0|0' ,'get_all_lines_by_InputBuffer - everything' ); diff --git a/t/OutputFactory_VEP_output.t b/t/OutputFactory_VEP_output.t index 098c9bd4b..068647c4c 100644 --- a/t/OutputFactory_VEP_output.t +++ b/t/OutputFactory_VEP_output.t @@ -217,7 +217,7 @@ is( 'HGVSc=ENST00000307301.11:c.*18G>A;'. 'AF=0.0010;AFR_AF=0.003;AMR_AF=0.0014;EAS_AF=0;EUR_AF=0;SAS_AF=0;'. 'gnomADe_AF=0.0003478;gnomADe_AFR_AF=0.004643;gnomADe_AMR_AF=0.0003236;gnomADe_ASJ_AF=0;'. - 'gnomADe_EAS_AF=0;gnomADe_FIN_AF=0;gnomADe_NFE_AF=1.886e-05;gnomADe_OTH_AF=0;gnomADe_SAS_AF=0;MAX_AF=0.004643;MAX_AF_POPS=gnomADe_AFR', + 'gnomADe_EAS_AF=0;gnomADe_FIN_AF=0;gnomADe_MID_AF=0;gnomADe_NFE_AF=1.886e-05;gnomADe_REMAINING_AF=0;gnomADe_SAS_AF=0;MAX_AF=0.004643;MAX_AF_POPS=gnomADe_AFR', 'get_all_lines_by_InputBuffer - everything' ); diff --git a/t/VEPTestingConfig.pm b/t/VEPTestingConfig.pm index 6a336895b..c26fd9be9 100644 --- a/t/VEPTestingConfig.pm +++ b/t/VEPTestingConfig.pm @@ -35,7 +35,7 @@ our %DEFAULTS = ( allele_string strand minor_allele minor_allele_freq clin_sig phenotype_or_disease pubmed AFR AMR EAS EUR SAS AA EA - gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS + gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS )], chr_synonyms => $Bin.'/testdata/chr_synonyms.txt', diff --git a/t/testdata/cache/homo_sapiens/84_GRCh38/21/25000001-26000000_var.gz b/t/testdata/cache/homo_sapiens/84_GRCh38/21/25000001-26000000_var.gz index b026f92ec..f0e429d36 100644 Binary files a/t/testdata/cache/homo_sapiens/84_GRCh38/21/25000001-26000000_var.gz and b/t/testdata/cache/homo_sapiens/84_GRCh38/21/25000001-26000000_var.gz differ diff --git a/t/testdata/cache/homo_sapiens/84_GRCh38/21/8000001-9000000_var.gz b/t/testdata/cache/homo_sapiens/84_GRCh38/21/8000001-9000000_var.gz index 5186d82b4..1a1bbe025 100644 Binary files a/t/testdata/cache/homo_sapiens/84_GRCh38/21/8000001-9000000_var.gz and b/t/testdata/cache/homo_sapiens/84_GRCh38/21/8000001-9000000_var.gz differ diff --git a/t/testdata/cache/homo_sapiens/84_GRCh38/LRG_485/1-1000000_var.gz b/t/testdata/cache/homo_sapiens/84_GRCh38/LRG_485/1-1000000_var.gz index 33f975d29..98cff2613 100644 Binary files a/t/testdata/cache/homo_sapiens/84_GRCh38/LRG_485/1-1000000_var.gz and b/t/testdata/cache/homo_sapiens/84_GRCh38/LRG_485/1-1000000_var.gz differ diff --git a/t/testdata/cache/homo_sapiens/84_GRCh38/info.txt b/t/testdata/cache/homo_sapiens/84_GRCh38/info.txt index bb4b7e281..4364a7bcf 100644 --- a/t/testdata/cache/homo_sapiens/84_GRCh38/info.txt +++ b/t/testdata/cache/homo_sapiens/84_GRCh38/info.txt @@ -12,7 +12,7 @@ source_gencode GENCODE 24 source_genebuild 2014-07 source_regbuild 13.0 source_assembly GRCh38.p5 -variation_cols variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomADe,gnomADe_AFR,gnomADe_AMR,gnomADe_ASJ,gnomADe_EAS,gnomADe_FIN,gnomADe_NFE,gnomADe_OTH,gnomADe_SAS,var_synonyms,AF +variation_cols variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomADe,gnomADe_AFR,gnomADe_AMR,gnomADe_ASJ,gnomADe_EAS,gnomADe_FIN,gnomADe_MID,gnomADe_NFE,gnomADe_REMAINING,gnomADe_SAS,var_synonyms,AF source_COSMIC 80 source_HGMD-PUBLIC 20164 source_ESP 20141103 diff --git a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz index d92aca5de..f6c2ca12e 100644 Binary files a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz and b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz differ diff --git a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz.tbi b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz.tbi index 74a124f54..eec02ecb2 100644 Binary files a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz.tbi and b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/21/all_vars.gz.tbi differ diff --git a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/info.txt b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/info.txt index fd52ee25a..86dce2615 100644 --- a/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/info.txt +++ b/t/testdata/cache/sereal/homo_sapiens/84_GRCh38/info.txt @@ -13,7 +13,7 @@ source_gencode GENCODE 24 source_genebuild 2014-07 source_regbuild 13.0 source_assembly GRCh38.p5 -variation_cols chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_NFE,gnomAD_OTH,gnomAD_SAS +variation_cols chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_MID,gnomAD_NFE,gnomAD_REMAINING,gnomAD_SAS var_type tabix source_COSMIC 80 source_HGMD-PUBLIC 20164 diff --git a/travisci/install_dependencies.sh b/travisci/install_dependencies.sh new file mode 100755 index 000000000..de9d8c1e9 --- /dev/null +++ b/travisci/install_dependencies.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]] +then + sed -i '/Devel::Cover/d' ensembl/cpanfile + sed -i '/Devel::Cover/d' cpanfile +fi + +cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile . +cpanm --quiet --installdeps --with-recommends --notest . + +if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]] +then + cpanm --quiet -n Devel::Cover::Report::Coveralls +fi