Error at 'SnpSift filter proband' rule

[leahkemp]

Pipeline is erroring out at the SnpSift filter proband rule.

My error:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 4430 out of bounds for length 3
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:266)
        at java.base/java.util.Objects.checkIndex(Objects.java:359)
        at java.base/java.util.ArrayList.get(ArrayList.java:427)
        at org.snpeff.vcf.VcfEntry.getVcfGenotype(VcfEntry.java:768)
        at org.snpsift.lang.function.FunctionBoolGenotype.evalGenotype(FunctionBoolGenotype.java:30)
        at org.snpsift.lang.function.IsVariant.eval(IsVariant.java:21)
        at org.snpsift.SnpSiftCmdFilter.evaluate(SnpSiftCmdFilter.java:142)
        at org.snpsift.SnpSiftCmdFilter.annotate(SnpSiftCmdFilter.java:91)
        at org.snpsift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:355)
        at org.snpsift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:331)
        at org.snpsift.SnpSift.run(SnpSift.java:588)
        at org.snpsift.SnpSift.main(SnpSift.java:76)

As far as I understand, it seems like it's trying to parse the sample name "4430" as a number rather than a character value, given the vcf file I passed it was for a trio of "length 3" and the error suggests it's looking for something outside of that range (4430). Notably the error is resolved if I provide it with the sample name "DHB4430". So my hotfix was to do just that, use the pipeline on a vcf file named "DHB4430_raw_snps_indels.vcf" rather than "4430_raw_snps_indels.vcf".

I don't know if I'll get around to implementing a fix for this, but I'm recording the bug here in case others come across this issue and it hurts their heads. Others are more than welcome to pick up this issue and fix if you feel so inclined :)