Potentially incorrect NT_POS output

[nahanoo]

Hi Torsten Seemann, Thanks a lot for developing and maintaining snippy!

I'm using your tool to study deletions. While investigating the output for deletions I realized that I ether don't understand the NT_POS output or it's incorrect (very well possible that it's and understanding issue on my side).

Interestingly the output is only wrong in my opinion for the + strand. Here is an example snps.tab (shortened for readability):

CHROM	POS	TYPE	REF	ALT	STRAND	NT_POS
AGTU001.0001.c01	251174	del	TC	T	+	1425/1545

According to the used reference.gbk this feature has following start and end positions: 249758..251302

They way I would determine the NT_POS for the + strand is NT_POS = POS - feature_start_position so 251174 -249758 = 1416
This doesn't match the output of snippy. Am I missing something? I have plenty of other examples that I'm happy to share if this could be a bug. I can also guarantee that the reference.gbk is the same I used for snippy and for doublechecking.

For the - strand I would calculate the NT_POS as NT_POS = feature_end_position - POS which matches the snippy output.

I'm using snippy 4.6.0 Thank in advance and best regards, Eric