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nakib103nakib103
committed
Merge branch 'postreleasefix/113' into release/113
2 parents 68350e1 + fcc5262 commit eb55c22

22 files changed

+59
-33
lines changed

Diff for: ‎.travis.yml

+1-3
Original file line numberDiff line numberDiff line change
@@ -57,9 +57,7 @@ install:
5757
- cd $DEPS
5858
- $CWD/travisci/build_c.sh
5959
- cd $CWD
60-
- cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
61-
- cpanm --quiet --installdeps --with-recommends --notest .
62-
- if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]; then cpanm --quiet -n Devel::Cover::Report::Coveralls; fi
60+
- $CWD/travisci/install_dependencies.sh
6361
- cp travisci/MultiTestDB.conf.travisci t/MultiTestDB.conf
6462

6563
script: "./travisci/harness.sh"

Diff for: ‎modules/Bio/EnsEMBL/VEP/Constants.pm

+6-5
Original file line numberDiff line numberDiff line change
@@ -116,9 +116,9 @@ our @FLAG_FIELDS = (
116116
# frequency stuff
117117
{ flag => 'af', fields => ['AF'] },
118118
{ flag => 'af_1kg', fields => ['AF','AFR_AF','AMR_AF','EAS_AF','EUR_AF','SAS_AF'] },
119-
{ 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'] },
120-
{ 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'] },
121-
{ 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'] },
119+
{ 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'] },
120+
{ 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'] },
121+
{ 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'] },
122122
{ flag => 'max_af', fields => ['MAX_AF', 'MAX_AF_POPS'] },
123123
{ flag => 'check_frequency', fields => ['FREQS'] },
124124

@@ -217,8 +217,9 @@ our %FIELD_DESCRIPTIONS = (
217217
'gnomADe_ASJ_AF', => 'Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population',
218218
'gnomADe_EAS_AF', => 'Frequency of existing variant in gnomAD exomes East Asian population',
219219
'gnomADe_FIN_AF', => 'Frequency of existing variant in gnomAD exomes Finnish population',
220+
'gnomADe_MID_AF', => 'Frequency of existing variant in gnomAD exomes Mid-eastern population',
220221
'gnomADe_NFE_AF', => 'Frequency of existing variant in gnomAD exomes Non-Finnish European population',
221-
'gnomADe_OTH_AF', => 'Frequency of existing variant in gnomAD exomes other combined populations',
222+
'gnomADe_REMAINING_AF', => 'Frequency of existing variant in gnomAD exomes remaining combined populations',
222223
'gnomADe_SAS_AF', => 'Frequency of existing variant in gnomAD exomes South Asian population',
223224
'gnomADg_AF', => 'Frequency of existing variant in gnomAD genomes combined population',
224225
'gnomADg_AFR_AF', => 'Frequency of existing variant in gnomAD genomes African/American population',
@@ -229,7 +230,7 @@ our %FIELD_DESCRIPTIONS = (
229230
'gnomADg_FIN_AF', => 'Frequency of existing variant in gnomAD genomes Finnish population',
230231
'gnomADg_MID_AF', => 'Frequency of existing variant in gnomAD genomes Mid-eastern population',
231232
'gnomADg_NFE_AF', => 'Frequency of existing variant in gnomAD genomes Non-Finnish European population',
232-
'gnomADg_OTH_AF', => 'Frequency of existing variant in gnomAD genomes other combined populations',
233+
'gnomADg_REMAINING_AF', => 'Frequency of existing variant in gnomAD genomes remaining combined populations',
233234
'gnomADg_SAS_AF', => 'Frequency of existing variant in gnomAD genomes South Asian population',
234235
'MAX_AF', => 'Maximum observed allele frequency in 1000 Genomes, ESP and ExAC/gnomAD',
235236
'MAX_AF_POPS' => 'Populations in which maximum allele frequency was observed',

Diff for: ‎modules/Bio/EnsEMBL/VEP/OutputFactory.pm

+3-3
Original file line numberDiff line numberDiff line change
@@ -107,9 +107,9 @@ my %DISTANCE_CONS = (upstream_gene_variant => 1, downstream_gene_variant => 1);
107107
my %FREQUENCY_KEYS = (
108108
af => ['AF'],
109109
af_1kg => [qw(AF AFR AMR ASN EAS EUR SAS)],
110-
af_gnomad => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))],
111-
af_gnomade => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN NFE OTH SAS))],
112-
af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE OTH SAS))],
110+
af_gnomad => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))],
111+
af_gnomade => [('gnomADe', map {'gnomADe_'.$_} qw(AFR AMR ASJ EAS FIN MID NFE REMAINING SAS))],
112+
af_gnomadg => [('gnomADg', map {'gnomADg_'.$_} qw(AFR AMI AMR ASJ EAS FIN MID NFE REMAINING SAS))],
113113
);
114114

115115

Diff for: ‎modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm

+2-2
Original file line numberDiff line numberDiff line change
@@ -129,8 +129,8 @@ my @FREQ_FIELDS = qw(
129129
AF AFR AMR ASN EAS SAS EUR
130130
AA EA
131131
ExAC ExAC_Adj ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS
132-
gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS
133-
gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_OTH gnomADg_SAS
132+
gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS
133+
gnomADg gnomADg_AFR gnomADg_AMI gnomADg_AMR gnomADg_ASJ gnomADg_EAS gnomADg_FIN gnomADg_MID gnomADg_NFE gnomADg_REMAINING gnomADg_SAS
134134
);
135135

136136

Diff for: ‎modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm

+1-1
Original file line numberDiff line numberDiff line change
@@ -583,7 +583,7 @@ sub human_frequency_checks {
583583
af_gnomad => 1,
584584
af_gnomade => 1,
585585
af_gnomadg => 1,
586-
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',
586+
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',
587587
buffer_size => 1,
588588
pick => 1,
589589
failed => 1,

Diff for: ‎t/AnnotationSource_Cache_Variation.t

+4-2
Original file line numberDiff line numberDiff line change
@@ -296,12 +296,13 @@ is_deeply($vf->{existing}, [
296296
'gnomADe_AFR' => 'T:0.004643',
297297
'minor_allele_freq' => '0.0010',
298298
'AMR' => 'T:0.0014',
299-
'gnomADe_OTH' => 'T:0',
299+
'gnomADe_REMAINING' => 'T:0',
300300
'gnomADe_EAS' => 'T:0',
301301
'EUR' => 'T:0',
302302
'clin_sig' => '',
303303
'EAS' => 'T:0',
304304
'end' => 25585733,
305+
'gnomADe_MID' => 'T:0',
305306
'gnomADe_NFE' => 'T:1.886e-05',
306307
'variation_name' => 'rs142513484',
307308
'minor_allele' => 'T',
@@ -352,12 +353,13 @@ is_deeply(
352353
'gnomADe_AFR' => 'T:0',
353354
'minor_allele_freq' => '0.0002',
354355
'AMR' => 'T:0.0014',
355-
'gnomADe_OTH' => 'T:0.0001823',
356+
'gnomADe_REMAINING' => 'T:0.0001823',
356357
'gnomADe_EAS' => 'T:0',
357358
'EUR' => 'T:0',
358359
'clin_sig' => 'uncertain_significance,not_provided,pathogenic',
359360
'EAS' => 'T:0',
360361
'end' => 25891796,
362+
'gnomADe_MID' => 'T:0',
361363
'gnomADe_NFE' => 'T:2.687e-05',
362364
'variation_name' => 'rs63750066',
363365
'minor_allele' => 'T',

Diff for: ‎t/AnnotationSource_Cache_VariationTabix.t

+6-3
Original file line numberDiff line numberDiff line change
@@ -80,12 +80,13 @@ my $exp = [{
8080
'minor_allele_freq' => '0.0010',
8181
'AMR' => 'T:0.0014',
8282
'chr' => '21',
83-
'gnomADe_OTH' => 'T:0',
83+
'gnomADe_REMAINING' => 'T:0',
8484
'gnomADe_EAS' => 'T:0',
8585
'EUR' => 'T:0',
8686
'clin_sig' => undef,
8787
'EAS' => 'T:0',
8888
'end' => 25585733,
89+
'gnomADe_MID' => 'T:0',
8990
'gnomADe_NFE' => 'T:1.886e-05',
9091
'variation_name' => 'rs142513484',
9192
'minor_allele' => 'T',
@@ -197,12 +198,13 @@ SKIP: {
197198
'minor_allele_freq' => undef,
198199
'AMR' => undef,
199200
'chr' => '21',
200-
'gnomADe_OTH' => undef,
201+
'gnomADe_REMAINING' => undef,
201202
'gnomADe_EAS' => undef,
202203
'EUR' => undef,
203204
'clin_sig' => undef,
204205
'EAS' => undef,
205206
'end' => 25891796,
207+
'gnomADe_MID' => undef,
206208
'gnomADe_NFE' => undef,
207209
'variation_name' => 'CM930033',
208210
'minor_allele' => undef,
@@ -228,12 +230,13 @@ SKIP: {
228230
'minor_allele_freq' => '0.0002',
229231
'AMR' => 'T:0.0014',
230232
'chr' => '21',
231-
'gnomADe_OTH' => 'T:0.0001823',
233+
'gnomADe_REMAINING' => 'T:0.0001823',
232234
'gnomADe_EAS' => 'T:0',
233235
'EUR' => 'T:0',
234236
'clin_sig' => 'not_provided,pathogenic',
235237
'EAS' => 'T:0',
236238
'end' => 25891796,
239+
'gnomADe_MID' => 'T:0',
237240
'gnomADe_NFE' => 'T:2.687e-05',
238241
'variation_name' => 'rs63750066',
239242
'minor_allele' => 'T',

Diff for: ‎t/CacheDir.t

+2-1
Original file line numberDiff line numberDiff line change
@@ -210,8 +210,9 @@ is_deeply(
210210
'gnomADe_ASJ',
211211
'gnomADe_EAS',
212212
'gnomADe_FIN',
213+
'gnomADe_MID',
213214
'gnomADe_NFE',
214-
'gnomADe_OTH',
215+
'gnomADe_REMAINING',
215216
'gnomADe_SAS',
216217
'var_synonyms',
217218
'AF'

Diff for: ‎t/OutputFactory.t

+4-1
Original file line numberDiff line numberDiff line change
@@ -772,7 +772,7 @@ is_deeply(
772772
'gnomADe_AF' => [
773773
'9.75e-05'
774774
],
775-
'gnomADe_OTH_AF' => [
775+
'gnomADe_REMAINING_AF' => [
776776
'0.0001823'
777777
],
778778
'gnomADe_AFR_AF' => [
@@ -792,6 +792,9 @@ is_deeply(
792792
],
793793
'gnomADe_ASJ_AF' => [
794794
'0'
795+
],
796+
'gnomADe_MID_AF' => [
797+
'0'
795798
]
796799
},
797800
'add_colocated_frequency_data - af_gnomad',

Diff for: ‎t/OutputFactory_JSON.t

+7-4
Original file line numberDiff line numberDiff line change
@@ -133,7 +133,7 @@ SKIP: {
133133
'amr' => '0.0014',
134134
'gnomade_sas' => '0',
135135
'gnomade' => '0.0003478',
136-
'gnomade_oth' => '0',
136+
'gnomade_remaining' => '0',
137137
'gnomade_asj' => '0',
138138
'gnomade_nfe' => '1.886e-05',
139139
'gnomade_afr' => '0.004643',
@@ -142,6 +142,7 @@ SKIP: {
142142
'gnomade_fin' => '0',
143143
'sas' => '0',
144144
'gnomade_eas' => '0',
145+
'gnomade_mid' => '0',
145146
'eur' => '0',
146147
'eas' => '0'
147148
}
@@ -201,10 +202,11 @@ SKIP: {
201202
'gnomade_fin' => '0',
202203
'gnomade_amr' => '0',
203204
'gnomade' => '7.313e-05',
204-
'gnomade_oth' => '0',
205+
'gnomade_remaining' => '0',
205206
'gnomade_asj' => '0',
206207
'gnomade_eas' => '0',
207-
'gnomade_nfe' => '0.0001433'
208+
'gnomade_nfe' => '0.0001433',
209+
'gnomade_mid' => '0'
208210
}
209211
},
210212
'end' => '25891785',
@@ -319,7 +321,7 @@ SKIP: {
319321
'amr' => 0.0014,
320322
'gnomade_sas' => 0,
321323
'gnomade' => 0.0003478,
322-
'gnomade_oth' => 0,
324+
'gnomade_remaining' => 0,
323325
'gnomade_asj' => 0,
324326
'gnomade_nfe' => 1.886e-05,
325327
'gnomade_afr' => 0.004643,
@@ -328,6 +330,7 @@ SKIP: {
328330
'gnomade_fin' => 0,
329331
'sas' => 0,
330332
'gnomade_eas' => 0,
333+
'gnomade_mid' => 0,
331334
'eur' => 0,
332335
'eas' => 0
333336
}

Diff for: ‎t/OutputFactory_Tab.t

+1-1
Original file line numberDiff line numberDiff line change
@@ -256,7 +256,7 @@ is(
256256
"-\t-\t-\t-\trs142513484\tMODIFIER\t-\t-1\t-\tSNV\tMRPL39\tHGNC\tHGNC:14027\tprotein_coding\tYES\t-\t-\t-\t5\t-\t".
257257
"CCDS33522.1\tENSP00000305682\tQ9NYK5\t-\tUPI00001AEAC0\t-\t-\t-\t-\t11/11\t-\t-\t-\tENST00000307301.11:c.*18G>A\t".
258258
"-\t-\t0.0010\t0.003\t0.0014\t0\t0\t0\t".
259-
"0.0003478\t0.004643\t0.0003236\t0\t0\t0\t1.886e-05\t0\t0\t".
259+
"0.0003478\t0.004643\t0.0003236\t0\t0\t0\t0\t1.886e-05\t0\t0\t".
260260
"-\t-\t-\t-\t-\t-\t-\t-\t-\t".
261261
"-\t-\t0.004643\tgnomADe_AFR\t-\t-\t-\t-\t-\t-\t-\t-\t-",
262262
'get_all_lines_by_InputBuffer - everything'

Diff for: ‎t/OutputFactory_VCF.t

+3-3
Original file line numberDiff line numberDiff line change
@@ -351,14 +351,14 @@ is(
351351
'21 25585733 rs142513484 C T . . CSQ=T|3_prime_UTR_variant'.
352352
'|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|11/11||ENST00000307301.11:c.*18G>A||1122|'.
353353
'||||rs142513484||-1||SNV|HGNC|HGNC:14027|YES||||5||CCDS33522.1|ENSP00000305682|Q9NYK5||UPI00001AEAC0|'.
354-
'|||||||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||'.
354+
'|||||||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||'.
355355
'|||||||,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|10/10|'.
356356
'|ENST00000352957.8:c.991G>A|ENSP00000284967.6:p.Ala331Thr|1033|991|331|A/T|Gca/Aca|rs142513484||-1||SNV|HGNC'.
357357
'|HGNC:14027|||||1|P1|CCDS13573.1|ENSP00000284967|Q9NYK5||UPI00001AEE66|||tolerated_low_confidence(0.17)|benign(0.001)'.
358-
'||||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'.
358+
'||||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'.
359359
'|upstream_gene_variant|MODIFIER|AP000223.1|ENSG00000260583|Transcript|ENST00000567517|antisense||||||||||rs142513484'.
360360
'|2407|-1||SNV|Clone_based_ensembl_gene||YES||||||||||||||||||0.0010|0.003|0.0014|0|0|0|0.0003478|0.004643'.
361-
'|0.0003236|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||||||||| GT 0|0'
361+
'|0.0003236|0|0|0|0|1.886e-05|0|0||||||||||||0.004643|gnomADe_AFR||||||||| GT 0|0'
362362
,'get_all_lines_by_InputBuffer - everything'
363363
);
364364

Diff for: ‎t/OutputFactory_VEP_output.t

+1-1
Original file line numberDiff line numberDiff line change
@@ -217,7 +217,7 @@ is(
217217
'HGVSc=ENST00000307301.11:c.*18G>A;'.
218218
'AF=0.0010;AFR_AF=0.003;AMR_AF=0.0014;EAS_AF=0;EUR_AF=0;SAS_AF=0;'.
219219
'gnomADe_AF=0.0003478;gnomADe_AFR_AF=0.004643;gnomADe_AMR_AF=0.0003236;gnomADe_ASJ_AF=0;'.
220-
'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',
220+
'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',
221221
'get_all_lines_by_InputBuffer - everything'
222222
);
223223

Diff for: ‎t/VEPTestingConfig.pm

+1-1
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ our %DEFAULTS = (
3535
allele_string strand minor_allele minor_allele_freq
3636
clin_sig phenotype_or_disease pubmed
3737
AFR AMR EAS EUR SAS AA EA
38-
gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_NFE gnomADe_OTH gnomADe_SAS
38+
gnomADe gnomADe_AFR gnomADe_AMR gnomADe_ASJ gnomADe_EAS gnomADe_FIN gnomADe_MID gnomADe_NFE gnomADe_REMAINING gnomADe_SAS
3939
)],
4040

4141
chr_synonyms => $Bin.'/testdata/chr_synonyms.txt',

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Diff for: ‎t/testdata/cache/homo_sapiens/84_GRCh38/info.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ source_gencode GENCODE 24
1212
source_genebuild 2014-07
1313
source_regbuild 13.0
1414
source_assembly GRCh38.p5
15-
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
15+
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
1616
source_COSMIC 80
1717
source_HGMD-PUBLIC 20164
1818
source_ESP 20141103

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+1-1
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ source_gencode GENCODE 24
1313
source_genebuild 2014-07
1414
source_regbuild 13.0
1515
source_assembly GRCh38.p5
16-
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
16+
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
1717
var_type tabix
1818
source_COSMIC 80
1919
source_HGMD-PUBLIC 20164

Diff for: ‎travisci/install_dependencies.sh

+15
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
#!/bin/bash
2+
3+
if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]
4+
then
5+
sed -i '/Devel::Cover/d' ensembl/cpanfile
6+
sed -i '/Devel::Cover/d' cpanfile
7+
fi
8+
9+
cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
10+
cpanm --quiet --installdeps --with-recommends --notest .
11+
12+
if [[ "$COVERALLS" = 'true' && ! "${TRAVIS_PERL_VERSION}" =~ '5.10' ]]
13+
then
14+
cpanm --quiet -n Devel::Cover::Report::Coveralls
15+
fi

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