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Remove check on PL values when computing local alleles #285

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Remove check on PL values when computing local alleles #285

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30 changes: 0 additions & 30 deletions bio2zarr/vcf2zarr/icf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -540,36 +540,6 @@ def bincount_nonzero(arr, *, minlength):
bincount_nonzero, axis=1, arr=depths, minlength=allele_count
)
allele_counts += depths_allele_counts
if "PL" in variant.FORMAT:
likelihoods = variant.format("PL")
likelihoods.clip(0, None, out=likelihoods)
# n is the indices of the nonzero likelihoods
n = np.tile(np.arange(likelihoods.shape[1]), (likelihoods.shape[0], 1))
assert n.shape == likelihoods.shape
n[likelihoods <= 0] = 0
ploidy = variant.ploidy

if ploidy == 1:
a = n
b = np.zeros_like(a)
elif ploidy == 2:
# We have n = b(b+1) / 2 + a
# We need to compute a and b
b = np.ceil(np.sqrt(2 * n + 9 / 4) - 3 / 2).astype(int)
a = (n - b * (b + 1) / 2).astype(int)
else:
# TODO: Handle all possible ploidy
raise ValueError(f"Cannot handle ploidy = {ploidy}")

a_counts = np.apply_along_axis(
np.bincount, axis=1, arr=a, minlength=allele_count
)
b_counts = np.apply_along_axis(
np.bincount, axis=1, arr=b, minlength=allele_count
)
assert a_counts.shape == b_counts.shape == allele_counts.shape
allele_counts += a_counts
allele_counts += b_counts

allele_counts[:, 0] = 0 # We don't count the reference allele
max_row_length = 1
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