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genomisc

Miscellaneous genomics tools and data structures in golang

HWE

go get github.com/carbocation/genomisc/hwe

HWE computes Exact or Approximate Hardy-Weinberg P value. Fast computes the approximate P value, then if it is significant according to your threshold, it computes the Exact P-value to be certain. This is a pure go implementation with naive algorithms, which can therefore be slow. It uses big.Int and can handle extremely large sample sizes (~hundreds of thousands).

RAMCSV

go get github.com/carbocation/genomisc/ramcsv

RAMCSV consumes a file handle and a csv.Reader (which exists only to provide your csv parsing settings) and allows you to seek back and forth through a CSV file to any line in the file, without having to actually keep the full file in memory.

PRSParser

go get github.com/carbocation/genomisc/prsparser

PRSParser consumes a variety of formats for polygenic scores.