Fields lost from squeezed output if DP not present in input

[RussellTaylor]

I've been testing out spVCF with our product, the latest iteration of which is not writing the DP field. It's not fully clear to me from the spec whether DP is considered a mandatory field for squeezing, though there is an implication that it is. However, in the code its absence is handled except in one place: line 511 of spVCF.cc, where the loop starts from an index of 2 (i.e. assuming DP & GT are present), thus failing to write out one of the other fields.

The code should be updated to either explicitly reject input missing DP, or to handle its absence at the highlighted line.

[mlin]

Thanks for reporting! I put a probable fix on the main branch, will cut a release v1.1.1 once I use the opportunity to modernize the GitHub build a little.

[mlin]

@RussellTaylor Please check if v1.2.0 fixes the problem, thanks

[RussellTaylor]

@mlin Yes, that has fixed the issue of lost info that I was seeing. Thanks for addressing this so promptly!