Updates to LiftoverVcf break on indel that span two chain blocks

[yfarjoun]

thanks to the user who reported this error.

The resulting error message looks like this:

Exception in thread "main" java.lang.IllegalStateException: BUG: GenomeLoc 1:1634405-1634409 has a size == 5 but the variation reference allele has length 2 this = [VC Unknown @ 1:1634405-1634409 Q. of type=INDEL
        at htsjdk.variant.variantcontext.VariantContext.validateStop(VariantContext.java:1327)
        at htsjdk.variant.variantcontext.VariantContext.validate(VariantContext.java:1294)
        at htsjdk.variant.variantcontext.VariantContext.<init>(VariantContext.java:401)
        at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:494)
        at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:488)
        at picard.vcf.LiftoverVcf.liftSnp(LiftoverVcf.java:359)
        at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:245)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
        at edu.mit.broad.picard.cmdline.PicardPrivateCommandLine.main(PicardPrivateCommandLine.java:24)

I know what the problem is. I think I fixed it already, but I'm trying to build a test that covers this case.