From 181c0bea5869503820b8330bf670c4f3ae25fc51 Mon Sep 17 00:00:00 2001 From: Kyle Ferriter Date: Thu, 29 Jan 2026 11:55:19 -0500 Subject: [PATCH] Treat all empty/none as '.' in string fields even though pysam does not --- src/ga4gh/vrs/extras/annotator/vcf.py | 31 ++++++++++++++++--- .../test_vcf_expected_altsonly_output.vcf | 6 ++-- .../extras/data/test_vcf_expected_output.vcf | 6 ++-- .../test_vcf_expected_output_no_vrs_attrs.vcf | 4 +-- 4 files changed, 34 insertions(+), 13 deletions(-) diff --git a/src/ga4gh/vrs/extras/annotator/vcf.py b/src/ga4gh/vrs/extras/annotator/vcf.py index 37f0d475..3dd70dcf 100644 --- a/src/ga4gh/vrs/extras/annotator/vcf.py +++ b/src/ga4gh/vrs/extras/annotator/vcf.py @@ -41,6 +41,18 @@ class FieldName(str, Enum): ERROR_FIELD = "VRS_Error" +# String-typed INFO fields where pysam incorrectly converts None → b"" +# (empty bytes) instead of the VCF missing value ".". Integer/Float fields +# are unaffected because pysam uses proper BCF missing sentinels for those. +_STRING_FIELDS = frozenset( + { + FieldName.IDS_FIELD, + FieldName.STATES_FIELD, + FieldName.ERROR_FIELD, + } +) + + # VCF character escape map VCF_ESCAPE_MAP = str.maketrans( { @@ -293,11 +305,20 @@ def annotate( if output_vcf_path and vcf_out: for k in additional_info_fields: - # Convert "" and None values (but not 0) to None. - # Pysam outputs "." for missing values. - record.info[k.value] = [ - None if v in ("", None) else v for v in vrs_field_data[k.value] - ] + # pysam correctly converts None → "." for Integer/Float + # INFO fields, but for String fields it converts None → + # "" (empty bytes), violating the VCF spec. Work around + # by using the literal string "." for String-typed fields. + if k in _STRING_FIELDS: + record.info[k.value] = [ + "." if v in ("", None) else v + for v in vrs_field_data[k.value] + ] + else: + record.info[k.value] = [ + None if v in ("", None) else v + for v in vrs_field_data[k.value] + ] vcf_out.write(record) vcf.close() diff --git a/tests/extras/data/test_vcf_expected_altsonly_output.vcf b/tests/extras/data/test_vcf_expected_altsonly_output.vcf index 8d74d7ca..3b7f2ab5 100644 --- a/tests/extras/data/test_vcf_expected_altsonly_output.vcf +++ b/tests/extras/data/test_vcf_expected_altsonly_output.vcf @@ -240,7 +240,7 @@ chr19 82664 . C T 50 PASS platforms=2;platformnames=10X,PacBio;datasets=2;datase chr19 284350 . CA C 50 PASS platforms=4;platformnames=Illumina,10X,PacBio,CG;datasets=4;datasetnames=HiSeqPE300x,10XChromiumLR,CCS15kb_20kb,CGnormal;callsets=5;callsetnames=HiSeqPE300xGATK,10XLRGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=CCS15kb_20kb,IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;difficultregion=GRCh38_AllHomopolymers_gt6bp_imperfectgt10bp_slop5,GRCh38_SimpleRepeat_imperfecthomopolgt10_slop5;VRS_Allele_IDs=ga4gh:VA.a04jFsNg0bS0RMIWjKWSbwJS4_vp7S6x;VRS_Starts=284350;VRS_Ends=284366;VRS_States=AAAAAAAAAAAAAAA;VRS_Lengths=15;VRS_RepeatSubunitLengths=1 GT:PS:DP:ADALL:AD:GQ 0/1:.:422:117,101:81,75:356 chr19 289464 . T TCACGCCTGTAATCC 50 PASS platforms=4;platformnames=Illumina,PacBio,CG,10X;datasets=4;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;callsets=6;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.ySvDptXfHB_9WEfu78v32DzBXJfwGgO7;VRS_Starts=289464;VRS_Ends=289466;VRS_States=CACGCCTGTAATCCCA;VRS_Lengths=.;VRS_RepeatSubunitLengths=. GT:PS:DP:ADALL:AD:GQ 0/1:.:518:94,98:116,137:785 chr19 28946400 . T C 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.uV5O4M9zpiwk6sftOd-EDvtw_pkSAvdf;VRS_Starts=28946399;VRS_Ends=28946400;VRS_States=C;VRS_Lengths=.;VRS_RepeatSubunitLengths=. GT:PS:DP:ADALL:AD:GQ 1/1:.:874:0,275:115,378:502 -chr19 490414 . ACT A 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt;VRS_Allele_IDs=ga4gh:VA.lok7a3lot_cvUyw626otpJi4yxk0X07v;VRS_Starts=490414;VRS_Ends=490416;VRS_States;VRS_Lengths=0;VRS_RepeatSubunitLengths=2 GT:PS:DP:ADALL:AD:GQ 0/1:.:821:163,158:239,220:1004 -chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1;VRS_Starts=.,54220023;VRS_Ends=.,54220024;VRS_States=,A;VRS_Lengths=.,.;VRS_RepeatSubunitLengths=.,. GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 +chr19 490414 . ACT A 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt;VRS_Allele_IDs=ga4gh:VA.lok7a3lot_cvUyw626otpJi4yxk0X07v;VRS_Starts=490414;VRS_Ends=490416;VRS_States=.;VRS_Lengths=0;VRS_RepeatSubunitLengths=2 GT:PS:DP:ADALL:AD:GQ 0/1:.:821:163,158:239,220:1004 +chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=.,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1;VRS_Starts=.,54220023;VRS_Ends=.,54220024;VRS_States=.,A;VRS_Lengths=.,.;VRS_RepeatSubunitLengths=.,. GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 chr19 54220999 . A T 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Error=Reference mismatch at GRCh38:chr19 position 54220998-54220999 (input gave 'A' but correct ref is 'T') GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 -chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu,;VRS_Starts=54221653,.;VRS_Ends=54221654,.;VRS_States=A,;VRS_Lengths=.,.;VRS_RepeatSubunitLengths=.,. GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 +chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu,.;VRS_Starts=54221653,.;VRS_Ends=54221654,.;VRS_States=A,.;VRS_Lengths=.,.;VRS_RepeatSubunitLengths=.,. GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 diff --git a/tests/extras/data/test_vcf_expected_output.vcf b/tests/extras/data/test_vcf_expected_output.vcf index fd781c5a..da94feb4 100644 --- a/tests/extras/data/test_vcf_expected_output.vcf +++ b/tests/extras/data/test_vcf_expected_output.vcf @@ -240,7 +240,7 @@ chr19 82664 . C T 50 PASS platforms=2;platformnames=10X,PacBio;datasets=2;datase chr19 284350 . CA C 50 PASS platforms=4;platformnames=Illumina,10X,PacBio,CG;datasets=4;datasetnames=HiSeqPE300x,10XChromiumLR,CCS15kb_20kb,CGnormal;callsets=5;callsetnames=HiSeqPE300xGATK,10XLRGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=CCS15kb_20kb,IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;difficultregion=GRCh38_AllHomopolymers_gt6bp_imperfectgt10bp_slop5,GRCh38_SimpleRepeat_imperfecthomopolgt10_slop5;VRS_Allele_IDs=ga4gh:VA.xgtXGA3ZkV1WgMc6eD9l64fX27S_TScW,ga4gh:VA.a04jFsNg0bS0RMIWjKWSbwJS4_vp7S6x;VRS_Starts=284349,284350;VRS_Ends=284351,284366;VRS_States=CA,AAAAAAAAAAAAAAA;VRS_Lengths=2,15;VRS_RepeatSubunitLengths=2,1 GT:PS:DP:ADALL:AD:GQ 0/1:.:422:117,101:81,75:356 chr19 289464 . T TCACGCCTGTAATCC 50 PASS platforms=4;platformnames=Illumina,PacBio,CG,10X;datasets=4;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;callsets=6;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.nqqTUy-a2gssemOmJb4CJv-HNuFAmGrO,ga4gh:VA.ySvDptXfHB_9WEfu78v32DzBXJfwGgO7;VRS_Starts=289463,289464;VRS_Ends=289464,289466;VRS_States=T,CACGCCTGTAATCCCA;VRS_Lengths=1,.;VRS_RepeatSubunitLengths=1,. GT:PS:DP:ADALL:AD:GQ 0/1:.:518:94,98:116,137:785 chr19 28946400 . T C 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.yPr2pVvJeWHDHarhzAvOCb5Cn9UMF6a5,ga4gh:VA.uV5O4M9zpiwk6sftOd-EDvtw_pkSAvdf;VRS_Starts=28946399,28946399;VRS_Ends=28946400,28946400;VRS_States=T,C;VRS_Lengths=1,.;VRS_RepeatSubunitLengths=1,. GT:PS:DP:ADALL:AD:GQ 1/1:.:874:0,275:115,378:502 -chr19 490414 . ACT A 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt;VRS_Allele_IDs=ga4gh:VA.aje4-hx7eihWndAwfhzNq_7CZV3bRMXf,ga4gh:VA.lok7a3lot_cvUyw626otpJi4yxk0X07v;VRS_Starts=490413,490414;VRS_Ends=490416,490416;VRS_States=ACT,;VRS_Lengths=3,0;VRS_RepeatSubunitLengths=3,2 GT:PS:DP:ADALL:AD:GQ 0/1:.:821:163,158:239,220:1004 -chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.LlmfhAC3gQlVQUwXWYiYjrn5V_K8vBz1,,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1;VRS_Starts=54220023,.,54220023;VRS_Ends=54220024,.,54220024;VRS_States=G,,A;VRS_Lengths=1,.,.;VRS_RepeatSubunitLengths=1,.,. GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 +chr19 490414 . ACT A 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt;VRS_Allele_IDs=ga4gh:VA.aje4-hx7eihWndAwfhzNq_7CZV3bRMXf,ga4gh:VA.lok7a3lot_cvUyw626otpJi4yxk0X07v;VRS_Starts=490413,490414;VRS_Ends=490416,490416;VRS_States=ACT,.;VRS_Lengths=3,0;VRS_RepeatSubunitLengths=3,2 GT:PS:DP:ADALL:AD:GQ 0/1:.:821:163,158:239,220:1004 +chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.LlmfhAC3gQlVQUwXWYiYjrn5V_K8vBz1,.,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1;VRS_Starts=54220023,.,54220023;VRS_Ends=54220024,.,54220024;VRS_States=G,.,A;VRS_Lengths=1,.,.;VRS_RepeatSubunitLengths=1,.,. GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 chr19 54220999 . A T 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Error=Reference mismatch at GRCh38:chr19 position 54220998-54220999 (input gave 'A' but correct ref is 'T') GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 -chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.kea5G-J1teg0iHMbgUELy-4L9lbJkgoj,ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu,;VRS_Starts=54221653,54221653,.;VRS_Ends=54221654,54221654,.;VRS_States=T,A,;VRS_Lengths=1,.,.;VRS_RepeatSubunitLengths=1,.,. GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 +chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.kea5G-J1teg0iHMbgUELy-4L9lbJkgoj,ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu,.;VRS_Starts=54221653,54221653,.;VRS_Ends=54221654,54221654,.;VRS_States=T,A,.;VRS_Lengths=1,.,.;VRS_RepeatSubunitLengths=1,.,. GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 diff --git a/tests/extras/data/test_vcf_expected_output_no_vrs_attrs.vcf b/tests/extras/data/test_vcf_expected_output_no_vrs_attrs.vcf index c81bb519..9a50b61f 100644 --- a/tests/extras/data/test_vcf_expected_output_no_vrs_attrs.vcf +++ b/tests/extras/data/test_vcf_expected_output_no_vrs_attrs.vcf @@ -236,6 +236,6 @@ chr19 284350 . CA C 50 PASS platforms=4;platformnames=Illumina,10X,PacBio,CG;dat chr19 289464 . T TCACGCCTGTAATCC 50 PASS platforms=4;platformnames=Illumina,PacBio,CG,10X;datasets=4;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;callsets=6;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.nqqTUy-a2gssemOmJb4CJv-HNuFAmGrO,ga4gh:VA.ySvDptXfHB_9WEfu78v32DzBXJfwGgO7 GT:PS:DP:ADALL:AD:GQ 0/1:.:518:94,98:116,137:785 chr19 28946400 . T C 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;VRS_Allele_IDs=ga4gh:VA.yPr2pVvJeWHDHarhzAvOCb5Cn9UMF6a5,ga4gh:VA.uV5O4M9zpiwk6sftOd-EDvtw_pkSAvdf GT:PS:DP:ADALL:AD:GQ 1/1:.:874:0,275:115,378:502 chr19 490414 . ACT A 50 PASS platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt;VRS_Allele_IDs=ga4gh:VA.aje4-hx7eihWndAwfhzNq_7CZV3bRMXf,ga4gh:VA.lok7a3lot_cvUyw626otpJi4yxk0X07v GT:PS:DP:ADALL:AD:GQ 0/1:.:821:163,158:239,220:1004 -chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.LlmfhAC3gQlVQUwXWYiYjrn5V_K8vBz1,,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1 GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 +chr19 54220024 . G *,A 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.LlmfhAC3gQlVQUwXWYiYjrn5V_K8vBz1,.,ga4gh:VA.I7J3i1B36BACEUINcTwEh7uMv3I-PXT1 GT:PS:DP:ADALL:AD:GQ 1/2:.:45:0,20,25:0,20,25:99 chr19 54220999 . A T 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Error=Reference mismatch at GRCh38:chr19 position 54220998-54220999 (input gave 'A' but correct ref is 'T') GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 -chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.kea5G-J1teg0iHMbgUELy-4L9lbJkgoj,ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu, GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99 +chr19 54221654 . T A,P 50 PASS platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.kea5G-J1teg0iHMbgUELy-4L9lbJkgoj,ga4gh:VA.Zzlc24htmBV1HZZzWYgPD2_GfMInkrZu,. GT:PS:DP:ADALL:AD:GQ 0/1:.:45:0,20,25:0,20,25:99