segfault on calls with larger alternates

[jwhitney31337]

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 1a0966684d8e37732a8352dff61e93ca2c860e93. 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

[reedacartwright]

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.