vcf entry crashes mehari

[xiamaz]

When using mehari the following vcf entry crashes mehari:

X       2733841 .       T       TACACACACACAC   133.77  PASS    AC=2;AF=0.667;AN=3;DP=76;FS=0;MQ=197.58;QD=0.88;SOR=0.552       GT:AD:AF:DP:GQ:FT:F1R2:F2R1:PL:GP:PP:DN 1:0,10:1:10:80:PASS:0,7:0,3:86,0:79.797,4.5512e-08:177,0:Inherited      .:13,13:0.5:26:0:LowGQ:.:.:.:.:.:.      0/1:14,14:0.5:28:46:PASS:6,5:8,9:56,0,47:48.634,0.00010291,50:427,57,0:.

with the following error message:

Error: invalid GT value

[xiamaz]

This might be caused by mehari not playing well with '.' genotype records, e.g. no-call.

For the following print:

println!("{record:?} {sample:?} {name:?} {value:?}");

Record { chromosome: Name("X"), position: Position(2733841), ids: Ids({}), reference_bases: ReferenceBases([T]), alternate_bases: AlternateBases([Bases([T, A, C, A, C, A, C, A, C, A, C, A, C])]), quality_score: Some(QualityScore(133.77)), filters: Some(Pass), info: Info({Standard(AlleleCount): Some(Array(Integer([Some(2)]))), Standard(AlleleFrequencies): Some(Array(Float([Some(0.667)]))), Standard(TotalAlleleCount): Some(Integer(3)), Standard(TotalDepth): Some(Integer(76)), Other(Other("FS")): Some(Float(0.0)), Standard(MappingQuality): Some(Float(197.58)), Other(Other("QD")): Some(Float(0.88)), Other(Other("SOR")): Some(Float(0.552)), Other(Other("ANN")): Some(Array(String([Some("TACACACACACAC|3_prime_UTR_variant|MODIFIER|XG|HGNC:12806|transcript|NM_001141919.2|Coding|11/11|c.*1431_*1442dupACACACACACAC|p.?|2254/2943|1431/588||-1438|"), Some("TACACACACACAC|3_prime_UTR_variant|MODIFIER|XG|HGNC:12806|transcript|NM_001141920.2|Coding|10/10|c.*1431_*1442dupACACACACACAC|p.?|2212/2901|1431/546||-1438|"), Some("TACACACACACAC|3_prime_UTR_variant|MODIFIER|XG|HGNC:12806|transcript|NM_175569.3|Coding|10/10|c.*1431_*1442dupACACACACACAC|p.?|2209/2898|1431/543||-1438|")])))}), genotypes: Genotypes { keys: Keys({Standard(Genotype), Standard(ReadDepths), Other(Other("AF")), Standard(ReadDepth), Standard(ConditionalGenotypeQuality), Standard(Filter), Other(Other("F1R2")), Other(Other("F2R1")), Standard(RoundedGenotypeLikelihoods), Standard(GenotypePosteriorProbabilities), Standard(RoundedGenotypePosteriorProbabilities), Other(Other("DN"))}), values: [[Some(String("1")), Some(Array(Integer([Some(0), Some(10)]))), Some(Array(Float([Some(1.0)]))), Some(Integer(10)), Some(Integer(80)), Some(String("PASS")), Some(Array(Integer([Some(0), Some(7)]))), Some(Array(Integer([Some(0), Some(3)]))), Some(Array(Integer([Some(86), Some(0)]))), Some(Array(Float([Some(79.797), Some(4.5512e-8)]))), Some(Array(Integer([Some(177), Some(0)]))), Some(String("Inherited"))], [None, Some(Array(Integer([Some(13), Some(13)]))), Some(Array(Float([Some(0.5)]))), Some(Integer(26)), Some(Integer(0)), Some(String("LowGQ")), None, None, None, None, None, None], [Some(String("0/1")), Some(Array(Integer([Some(14), Some(14)]))), Some(Array(Float([Some(0.5)]))), Some(Integer(28)), Some(Integer(46)), Some(String("PASS")), Some(Array(Integer([Some(6), Some(5)]))), Some(Array(Integer([Some(8), Some(9)]))), Some(Array(Integer([Some(56), Some(0), Some(47)]))), Some(Array(Float([Some(48.634), Some(0.00010291), Some(50.0)]))), Some(Array(Integer([Some(427), Some(57), Some(0)]))), None]] } } Sample { keys: Keys({Standard(Genotype), Standard(ReadDepths), Other(Other("AF")), Standard(ReadDepth), Standard(ConditionalGenotypeQuality), Standard(Filter), Other(Other("F1R2")), Other(Other("F2R1")), Standard(RoundedGenotypeLikelihoods), Standard(GenotypePosteriorProbabilities), Standard(RoundedGenotypePosteriorProbabilities), Other(Other("DN"))}), values: [None, Some(Array(Integer([Some(13), Some(13)]))), Some(Array(Float([Some(0.5)]))), Some(Integer(26)), Some(Integer(0)), Some(String("LowGQ")), None, None, None, None, None, None] } "LB23_2763" None
Error: invalid GT value

[xiamaz]

Somehow this only occurs when attempting to output tsv instead of vcf