java.lang.NumberFormatException

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  • GATK | GATK | Tagged #variantannotator
    via by Unknown author,
  • Getting total amount in a column
    via Stack Overflow by pmaingi
    ,
    • java.lang.NumberFormatException: For input string: "." at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1250) at java.lang.Double.parseDouble(Double.java:540) at htsjdk.variant.variantcontext.GenotypeLikelihoods.parseDeprecatedGLString(GenotypeLikelihoods.java:251) at htsjdk.variant.variantcontext.GenotypeLikelihoods.fromGLField(GenotypeLikelihoods.java:81) at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:715) at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128) at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:347) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:40) at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502) at htsjdk.tribble.index.IndexFactory$FeatureIterator.<init>(IndexFactory.java:403) at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:312) at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:401) at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:287) at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:224) at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:147) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:208) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:88) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:1047) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:828) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

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