Range error in version 0.2

[naumenko-sa]

Hi @brentp !

Thanks for supporting duphold! We are using it to annotate calls made by CNVkit in bcbio.

Since the latest update to 0.2 one of our tests fails (duphold 0.1.4 works just fine given the same input). I tracked the variant which causes the failure:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  H-2_sorted
chr7    500     .       N       <DEL>   .       .       IMPRECISE;SVTYPE=DEL;END=33440015;SVLEN=-33439515;FOLD_CHANGE=0.621507;FOLD_CHANGE_LOG=-0.686157;PROBES=50;

We call duphold this way:

#!/bin/bash
duphold --threads 4 \
--vcf test.vcf.gz \
--bam test.bam \
--fasta /path/genomes/Hsapiens/hg38/seq/hg38.fa \
-o test_sorted-call-effects-duphold.vcf.gz

The error message:

fatal.nim(39)            sysFatal
Error: unhandled exception: value out of range [RangeError]

Could you please take a look, why it breaks?

Sergey