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[MERGE] fix divide by zero issue in MinHash.contained_by #572

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merged 2 commits into from
Dec 5, 2018
Merged

[MERGE] fix divide by zero issue in MinHash.contained_by #572

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30870c0
fix divide by zero issue in contained_by
ctb Dec 5, 2018
93b8343
fix per luiz
ctb Dec 5, 2018
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2 changes: 2 additions & 0 deletions sourmash/_minhash.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -364,6 +364,8 @@ cdef class MinHash(object):
"""\
Calculate how much of self is contained by other.
"""
if not self.get_mins():
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Suggested change
if not self.get_mins():
if len(self) == 0:

will avoid building mins (len() check the underlying mins in C++ without having to build it)

return 0.0
return self.count_common(other) / len(self.get_mins())

def similarity_ignore_maxhash(self, MinHash other):
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20 changes: 20 additions & 0 deletions tests/test__minhash.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,26 @@ def test_basic_dna(track_abundance):
assert len(b) == 1


def test_div_zero(track_abundance):
# verify that empty MHs do not yield divide by zero errors for similarity
mh = MinHash(1, 4, track_abundance=track_abundance)
mh2 = mh.copy_and_clear()

mh.add_sequence('ATGC')
assert mh.similarity(mh2) == 0
assert mh2.similarity(mh) == 0


def test_div_zero_contained(track_abundance):
# verify that empty MHs do not yield divide by zero errors for contained_by
mh = MinHash(1, 4, track_abundance=track_abundance)
mh2 = mh.copy_and_clear()

mh.add_sequence('ATGC')
assert mh.contained_by(mh2) == 0
assert mh2.contained_by(mh) == 0


def test_bytes_dna(track_abundance):
mh = MinHash(1, 4, track_abundance=track_abundance)
mh.add_sequence('ATGC')
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