Haploid geno

[jydu]

Hi Stephan,

I modified the multiHepSep file to work with haploid genomes. One just has to add the --haploid argument, and it will read only the first genotype (and consider it "phased").
I have not tried in combination with the trios option... I doubt it makes sense; one should probably add a test so that both are not used simultaneously.

Cheers,

Julien.

[stschiff]

OK, I looked through the code. Looks all reasonable. Have you tested it with toy data? If so, do you think you can perhaps add some test data into this repo, perhaps into a new folder testData and a readme on how to test it? I don't need to go full-scale unit-testing here, but with more contributors it probably makes sense to establish some simple non-automatic tests so that one can at least try it out in a minimal way. Thanks!

[jydu]

Hi Stephan, I tested it on real data, but it is unpublished. But I can make a test, for instance splitting a human phased diploid into haploids, and show that it give the same results... I put it on the TODO list.