Updated coding function for multiallelics #12
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collapses multiple SNP records for same site from multiple records to one tped row. somewhat experimental; this commit may break things.
…c is specified rows with duplicate positions are now only written out if --considerMultiAllelic is specified
genotype coding function can now specified in a separate python file via the —codingFunctionClassFile, containing a GenoCoder class with a coding_function(current_value, reference_allele, ancestral_allele) that returns an array of “0” and “1” for selscan. The method used to combine coded output for each allele of a multiallelic site is a bitwise operator, now specified via the hidden —multiAllelicMergeFunction argument. It accepts OR, AND, XOR. It is currently set to a default of OR, though I believe it should perhaps be AND.
BABY'S FIRST TIME USING GIT, hope I don't do any irreparable damage~* trying to pass the index of the alternate allele to the coding function so that the coding function can then take into account whether it's a 1 or a 2
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tomkinsc
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Jul 2, 2015
Updated coding function for multiallelics
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Altered coding function to correctly handle variants coded as "2" or "3", as well as multiallelics split across multiple lines (merged by bitwise "OR").