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##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)
The text was updated successfully, but these errors were encountered:
Given a VCF with genotype Number=A attribute
loadVcf
results in ArrayIndexOutOfBoundsExceptionThe text was updated successfully, but these errors were encountered: