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richarddurbin / pbwt

Implementation of Positional Burrows-Wheeler Transform for genetic data
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jl11 changes to pbwt code #5

Closed johnlees closed 10 years ago

johnlees commented 10 years ago

Some changes I've made that made it slightly easier to work with pbwt, particularly when looking at performance, you might like to include in your master:

pbwtImpute.c genotypeCompare no longer requires the sites to exactly match - if they don't it warns, and takes the intersection remove the warning when sum == 0 during imputation to allow imputation when lots of sites have no match

hash.c added type to constants to keep the compiler from producing warnings

makefile_icc a makefile (use make -f makefile_icc) that compiles with the intel compiler in an optimised way, giving 3x speedup to imputation

johnlees commented 10 years ago

I've also added a function to read phased haplotypes in impute2 .hap format, which is useful when shapeit2 has been run on the data first