Variant at start of chromosome, illegal storage access

[chapmanb]

Brent;
Thanks for all the work and fixes with duphold. The 0.0.3 version is running cleanly on most of our samples now and I'm starting to try and build up test cases so we can look at including filters based on the annotations.

I ran into one edge case that's causing duphold to fail with:

SIGSEGV: Illegal storage access. (Attempt to read from nil?)

This appears to happen with reads right at the start of a chromosome and I have a reproducible test case here:

https://s3.amazonaws.com/chapmanb/testcases/duphold_sisegv_storage_access.tar.gz

It contains the variant and BAM files, you'll just need to adjust REF in the shell script to point to a GRCh37.fa reference.

This fails in the same way with both 0.0.3 and the 0.0.4 release from yesterday. Please let me know if I can provide anything else to help with debugging and thanks again.

[brentp]

thanks Brad, I have a fix for this. It occurred when there was a variant within ~15 bases of the start of the chrom which usually doesn't happen. I'll make a new release today or tomorrow. There might be a couple of other ones like this, but I think we're closing in on a stable release. Thanks for persisting.

[brentp]

new release with a fix for this issue: https://github.com/brentp/duphold/releases/tag/v0.0.5

thanks again.