segfault on calls with larger alternates
Opened this issue · 1 comments
We encountered an issue where dng-dnm will segfault on certain VCF inputs. I isolated a single call that elicits this problem - it is an unusually large insert, so presumably an issue with allocating a buffer of insufficient size somewhere? This was reproduced with the latest develop branch commit 1a09666.
Command (using files from attached segfault.zip ):
dng-dnm auto --ped segfault.ped --vcf segfault.vcf -w output.vcf
Output:
Created SNP lookup table
First mrate: 1 last: 1
First code: 6 last: 6
First target string: AA/AA/AA last: TT/TT/TT
First tref: 0.0002388 last: 0.99301
Created indel lookup table First code: 6 last: 6
First target string: RR/RR/RR last: DD/DD/DD
First prior: 0.05 last: 0.114
Created paired lookup table
First target string: AA/AA last: TT/TT
First prior 1 last: 1
Segmentation fault (core dumped)
We're hoping this is a relatively easy fix, as we'd like to use a recent build of denovogear for a large project but need to move forward quickly.
Please let me know if there's anything else I can provide to help diagnose.
-Joe
This project currently does not have the personale to maintain the legacy code in dng-dnm. I recommend seeing if dng-call suits your needs.