Definition of TS_boundary and TS_contained regions

[ofonov]

Hi,

I could not find in the documentation of hap.py how TS_boundary and TS_contained regions are assigned to various variant locations. Could you please give an explanation to that, and perhaps add it to the documentation? In particular, it is not clear to me in which cases TS_boundary flag is assigned to a variant. Does it have to be exactly on the boundary of the high confidence region, or does it have to be within a certain distance to the left/right from the boundary of the high confidence region?

[pkrusche]

TS_boundary would capture all variants that overlap with but aren't fully contained within the confident regions. TS_contained has all variants that are fully contained within the confident regions. For insertions, the variant region includes both the preceding and the following position of the inserted sequence (padding left and right).