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Fix problem when annotating Delly2 VCF files (#88)
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Closes: #88
Related-Issue: #88
Projected-Results-Impact: none
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@holtgrewe
holtgrewe committed Dec 30, 2022
1 parent f226257 commit a564569
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Showing 8 changed files with 48 additions and 52 deletions.
2 changes: 1 addition & 1 deletion tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
release chromosome chromosome_no bin chromosome2 chromosome_no2 bin2 pe_orientation start end start_ci_left start_ci_right end_ci_left end_ci_right case_id set_id sv_uuid callers sv_type sv_sub_type info num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref genotype
GRCh37 22 22 89 22 22 89 3to5 17400000 17700000 -29 29 -29 29 . . UUID {"EMBL.DELLYv1.1.3"} DEL DEL {"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0} 0 2 1 0 0 {"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":["""LowQual"""],"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}
GRCh37 22 22 89 22 22 89 3to5 17400000 17700000 -29 29 -29 29 . . UUID {"DELLY2_SVv1.1.3"} DEL DEL {"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0} 0 2 1 0 0 {"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":["""LowQual"""],"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}
8 changes: 4 additions & 4 deletions ...-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java
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Original file line number Diff line number Diff line change
Expand Up @@ -628,18 +628,18 @@ private void annotateSvVcf(
// Get list of filter values to skip.
final ImmutableSet skipFilters = ImmutableSet.copyOf(args.getSkipFilters().split(","));

final String defaultSvMethod;
final String svMethod;
if (callerSupport.getSvCaller() == SvCaller.GENERIC && !args.getDefaultSvMethod().equals(".")) {
defaultSvMethod = args.getDefaultSvMethod();
svMethod = args.getDefaultSvMethod();
} else {
defaultSvMethod = callerSupport.getSvMethod(reader);
svMethod = callerSupport.getSvMethod(reader);
}

// Helpers for building record for `.gts.tsv` and `.feature-effects.tsv` records.
final GtRecordBuilder gtRecordBuilder =
new GtRecordBuilder(
args.getRelease(),
defaultSvMethod,
svMethod,
args.getOptOutFeatures(),
args.getCaseId(),
args.getSetId(),
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52 changes: 26 additions & 26 deletions ...t/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java
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2 changes: 1 addition & 1 deletion .../java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr22Test.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ void testWithTrio(boolean gzipOutput) throws IOException {
+ "GRCh37\tvarfish-annotator-db\tfor-testing\n";
final String expectedGts =
"release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcallers\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n"
+ "GRCh37\t22\t22\t89\t22\t22\t89\t3to5\t17400000\t17700000\t-29\t29\t-29\t29\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"EMBL.DELLYv1.1.3\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"Case_1_father-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"ft\"\"\":[\"\"\"LowQual\"\"\"],\"\"\"gq\"\"\":14,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":34,\"\"\"srv\"\"\":4},\"\"\"Case_1_index-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":35,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":29,\"\"\"srv\"\"\":2},\"\"\"Case_1_mother-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":67,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":32,\"\"\"srv\"\"\":1}}\n";
+ "GRCh37\t22\t22\t89\t22\t22\t89\t3to5\t17400000\t17700000\t-29\t29\t-29\t29\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"DELLY2_SVv1.1.3\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"Case_1_father-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"ft\"\"\":[\"\"\"LowQual\"\"\"],\"\"\"gq\"\"\":14,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":34,\"\"\"srv\"\"\":4},\"\"\"Case_1_index-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":35,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":29,\"\"\"srv\"\"\":2},\"\"\"Case_1_mother-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":67,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":32,\"\"\"srv\"\"\":1}}\n";
final String expectedFeatureEffects =
"case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"
+ ".\t.\t00000000-0000-0000-0000-000000000000\t51816\tNM_017424.2\tTRUE\t{\"transcript_ablation\",\"coding_transcript_variant\"}\tENSG00000093072\tENST00000262607.3\tTRUE\t{\"transcript_ablation\",\"coding_transcript_variant\"}\n"
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20 changes: 10 additions & 10 deletions ...t/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf38Chr1Test.java
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Original file line number Diff line number Diff line change
Expand Up @@ -117,11 +117,11 @@ void testWithSingleton(boolean gzipOutput) throws IOException {
+ "GRCh38\thgmd_public\tensembl_r104\n";
final String expectedGts =
"release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcallers\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n"
+ "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"
+ "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.DELLYv0.8.5\"}\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n"
+ "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n";
+ "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"DELLY2_SVv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\t{\"DELLY2_SVv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"DELLY2_SVv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"
+ "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"DELLY2_SVv0.8.5\"}\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n"
+ "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\t{\"DELLY2_SVv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n";
final String expectedFeatureEffects =
"case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n";
runTest(
Expand All @@ -146,11 +146,11 @@ void testWithTrio(boolean gzipOutput) throws IOException {
+ "GRCh38\thgmd_public\tensembl_r104\n";
final String expectedGts =
"release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcallers\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n"
+ "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":57,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"
+ "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.DELLYv0.8.5\"}\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":157,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n"
+ "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n";
+ "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"DELLY2_SVv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":57,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\t{\"DELLY2_SVv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+ "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"DELLY2_SVv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"
+ "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"DELLY2_SVv0.8.5\"}\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":[\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":157,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n"
+ "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\t{\"DELLY2_SVv0.8.5\"}\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n";
final String expectedFeatureEffects =
"case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n";
runTest(
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