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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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Could Selscan be faster? #50

Closed fengyq closed 3 years ago

fengyq commented 3 years ago

Hi, Thanks for this great software, but I found selscan is about >100 times slower than rehh and hapbin. Could you update it and make it faster?

szpiech commented 3 years ago

To match hapbin, selscan will need a re-implementation of the data structures to store genotypes bitwise and a re-implementation of haplotype comparison computations to operate similarly. This level of re-writing is too time intensive for me these days, but I welcome contributions attempting it or students/postdocs willing to take on a major re-write of the code.

However, implementation of new statistics and maintenance updates will continue.

fengyq commented 3 years ago

Thanks for your great efforts, Looking forward to the new statistics.