reconciling rec map in hapmap with actual chr sizes

[mufernando]

The recombination maps from HapMap do not span the full chromosome, but I am using the actual chromosome sizes to set simulations.

Deal with this discrepancy in windowed.snake. Check that last position in rec map is the end of the chr, if not, add another line with rec = 0.

[petrelharp]

Seems like you should set the chromosome length to the last position in the map?

[mufernando]

That's what I was doing before. But then it will be different than what is seen in the actual data and in the annotations.

The chunk that is missing is from the map is ~500kb for each chr.

[petrelharp]

Ok, but then maybe you should not use that bit of the real data, either? Unless we really think that 500Kb actually has no recombination.

[mufernando]

Ok, changed to get chr lens from the rec map! Thanks.