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Fix for floating point bug in heterozygosity_expected #274 #275

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Fix for floating point bug in heterozygosity_expected #274 #275

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b767e23
fix for floating point bug in heterozygosity_expected
timothymillar Jul 10, 2019
7de90cc
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timothymillar Jul 10, 2019
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3 changes: 2 additions & 1 deletion allel/stats/hw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,8 @@ def heterozygosity_expected(af, ploidy, fill=np.nan):
out = 1 - np.sum(np.power(af, ploidy), axis=1)

# fill values where allele frequencies could not be calculated
af_sum = np.sum(af, axis=1)
precision = np.finfo(af.dtype).precision
af_sum = np.round(np.sum(af, axis=1), precision)
with ignore_invalid():
out[(af_sum < 1) | np.isnan(af_sum)] = fill

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5 changes: 4 additions & 1 deletion allel/test/test_stats.py
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Expand Up @@ -425,7 +425,10 @@ def refimpl(f, ploidy, fill=0):
"""Limited reference implementation for testing purposes."""

# check allele frequencies sum to 1
af_sum = np.sum(f, axis=1)
# round to suitable precision for the dtype
af_sum = (np.sum(f, axis=1))
precision = np.finfo(af_sum.dtype).precision
af_sum = np.round(np.sum(f, axis=1), precision)

# assume three alleles
p = f[:, 0]
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