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googva's Issues

Incorrect blocks when END position in INFO field

When the end position of a genomic region is specified in the INFO field of the VCF file it causes reference loci to be incorrectly blocked by gvcf-mapper-cl.py.

Input:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	400470164
1	1	.	N	<NON_REF>	.	.	END=10033	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
1	10034	.	C	<NON_REF>	.	.	END=10035	GT:DP:GQ:MIN_DP:PL	0/0:94:6:91:0,6,90
1	10036	.	C	<NON_REF>	.	.	END=10036	GT:DP:GQ:MIN_DP:PL	0/0:96:9:96:0,9,135
1	10037	.	T	<NON_REF>	.	.	END=10037	GT:DP:GQ:MIN_DP:PL	0/0:99:12:99:0,12,180
1	10038	.	A	<NON_REF>	.	.	END=10038	GT:DP:GQ:MIN_DP:PL	0/0:104:0:104:0,0,2807
1	10039	.	A	<NON_REF>	.	.	END=10039	GT:DP:GQ:MIN_DP:PL	0/0:106:18:106:0,18,270
1	10040	.	C	<NON_REF>	.	.	END=10041	GT:DP:GQ:MIN_DP:PL	0/0:111:24:110:0,24,360
1	10042	.	C	<NON_REF>	.	.	END=10043	GT:DP:GQ:MIN_DP:PL	0/0:117:33:115:0,33,495
1	10044	.	A	<NON_REF>	.	.	END=10044	GT:DP:GQ:MIN_DP:PL	0/0:120:36:120:0,36,540

Output:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	400470164
1	1	.	N	<NON_REF>	.	.	END=1	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
1	10034	.	C	<NON_REF>	.	.	END=10040	GT:DP:GQ:MIN_DP:PL	0/0:94:6:91:0,6,90
1	10042	.	C	<NON_REF>	.	.	END=10045	GT:DP:GQ:MIN_DP:PL	0/0:117:33:115:0,33,495
1	10049	.	T	<NON_REF>	.	.	END=10050	GT:DP:GQ:MIN_DP:PL	0/0:129:45:129:0,45,675

Negative interval issue

(Adding issue here for the sake of logging)

End position incorrectly listed as 1 in some cases when using gvcf-mapper-cl.py. This throws error when trying to import into Google Genomics Variant Set.

$ gcloud alpha genomics operations describe operations/CJ3k0-yGHBCMn-DDBRiZ-5Hw3vP42kg
done: true
error:
  code: 2
  message: 'Invalid value for field "[variant.start, variant.end)": negative interval
    length, start > end for variant at start: 59118900 referenceName: "19"'
metadata:
  '@type': type.googleapis.com/google.genomics.v1.OperationMetadata
  clientId: ''
  createTime: '2017-01-12T23:21:48Z'
  endTime: '2017-01-12T23:40:35.737Z'
  events: []
  labels: {}
  projectId: gbsc-gcp-project-mvp
  request:
    '@type': type.googleapis.com/google.genomics.v1.ImportVariantsRequest
    format: FORMAT_VCF
    infoMergeConfig:
      FS: MOVE_TO_CALLS
      MQ: MOVE_TO_CALLS
      MQRankSum: MOVE_TO_CALLS
      PL: MOVE_TO_CALLS
      QD: MOVE_TO_CALLS
      ReadPosRankSum: MOVE_TO_CALLS
      VQSLOD: MOVE_TO_CALLS
      culprit: MOVE_TO_CALLS
    normalizeReferenceNames: false
    sourceUris:
    - gs://gbsc-gcp-project-mvp-group/test/dockerflow_test/bigquery_import/gvcf_mapper_out.vcf
    variantSetId: '8016995100636263441'
name: operations/CJ3k0-yGHBCMn-DDBRiZ-5Hw3vP42kg
$ grep '59118901' gvcf_mapper_out.vcf
14	59118900	.	T	<NON_REF>	.	.	END=59118901	GT:DP:GQ:MIN_DP:PL	0/0:40:96:40:0,96,1440
19	59118901	.	G	<NON_REF>	.	.	END=1	GT:DP:GQ:MIN_DP:PL	0/0:14:21:14:0,21,315

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