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VCF genotype Number=A attribute throws ArrayIndexOutOfBoundsException #1562

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heuermh opened this issue Jun 9, 2017 · 0 comments
Closed

VCF genotype Number=A attribute throws ArrayIndexOutOfBoundsException #1562

heuermh opened this issue Jun 9, 2017 · 0 comments
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@heuermh
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@heuermh heuermh commented Jun 9, 2017

Given a VCF with genotype Number=A attribute

...
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1
q	186	.	T	C	340.765	.	AB=0.390244;ABP=7.30028;AC=1;AF=0.5;AN=2;AO=16;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.55317;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.464;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=588;QR=953;RO=25;RPL=4;RPP=11.6962;RPPR=10.0459;RPR=12;RUN=1;SAF=11;SAP=7.89611;SAR=5;SRF=9;SRP=7.26639;SRR=16;TYPE=snp;technology.ILLUMINA=1	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:25,16:25:953:16:588:-40.8962,0,-73.7281

loadVcf results in ArrayIndexOutOfBoundsException

org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): java.lang.ArrayIndexOutOfBoundsException: 1
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$fromArrayExtractor$2.apply(VariantContextConverter.scala:1167)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$fromArrayExtractor$2.apply(VariantContextConverter.scala:1167)
	at scala.Option.map(Option.scala:145)
	at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$fromArrayExtractor(VariantContextConverter.scala:1167)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToGenotypeExtractor$5.apply(VariantContextConverter.scala:1372)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToGenotypeExtractor$5.apply(VariantContextConverter.scala:1369)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$82.apply(VariantContextConverter.scala:1561)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$82.apply(VariantContextConverter.scala:1561)
	at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:251)
	at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:251)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
	at scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:251)
	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:105)
	at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$convert$2(VariantContextConverter.scala:1561)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$makeGenotypeFormatFn$1.apply(VariantContextConverter.scala:1579)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$makeGenotypeFormatFn$1.apply(VariantContextConverter.scala:1579)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$3.apply(VariantContextConverter.scala:211)
	at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$3.apply(VariantContextConverter.scala:210)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
	at scala.collection.AbstractTraversable.map(Traversable.scala:105)
	at org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:210)
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