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Liftover gVCFs with indels

See original GitHub issue

I think that LiftoverVcf isn’t working with a gVCF and indel allele in a reference block when trying to left-align indels.

Changing this line to catch if a.length == 0 gets me farther (back to this issue https://github.com/broadinstitute/picard/issues/1258): https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/util/LiftoverUtils.java#L370

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
    at picard.util.LiftoverUtils.lambda$leftAlignVariant$3(LiftoverUtils.java:370)
    at java.util.stream.Collectors.lambda$groupingBy$45(Collectors.java:907)
    at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
    at java.util.HashMap$ValueSpliterator.forEachRemaining(HashMap.java:1620)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
    at picard.util.LiftoverUtils.leftAlignVariant(LiftoverUtils.java:370)
    at picard.util.LiftoverUtils.reverseComplementVariantContext(LiftoverUtils.java:172)
    at picard.util.LiftoverUtils.liftVariant(LiftoverUtils.java:81)
    at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:396)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

Issue Analytics

State:
Created 5 years ago
Comments:9 (4 by maintainers)

Top GitHub Comments

1reaction

yfarjouncommented, Feb 18, 2020

thanks for the test case @nh13

makes it much easier to debug!

0reactions

yfarjouncommented, Feb 18, 2020

thanks @nh13

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