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bdgdiff: do not truncate region scores to integers (fixes #715) #739

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Merged
taoliu merged 1 commit into from
Sep 18, 2026
Merged

bdgdiff: do not truncate region scores to integers (fixes #715) #739

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4 changes: 2 additions & 2 deletions MACS3/Signal/ScoreTrack.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1935,8 +1935,8 @@ def mean_from_peakcontent(self,
tmp_s: cython.int
tmp_e: cython.int
ln: cython.int
tmp_v: cython.long
sum_v: cython.long # for better precision
tmp_v: cython.double
sum_v: cython.double # for better precision
r: cython.float
i: cython.int

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33 changes: 29 additions & 4 deletions test/test_ScoreTrack.py
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Expand Up @@ -23,12 +23,12 @@ def setUp(self):
(b"chrY", 75, 90, 35.0, 6.00),
(b"chrY", 90, 150, 10.0, 15.00)]
for a in self.test_regions1:
self.t1bdg.safe_add_loc(a[0], a[1], a[2], a[3])
self.c1bdg.safe_add_loc(a[0], a[1], a[2], a[4])
self.t1bdg.add_loc(a[0], a[1], a[2], a[3])
self.c1bdg.add_loc(a[0], a[1], a[2], a[4])

for a in self.test_regions2:
self.t2bdg.safe_add_loc(a[0], a[1], a[2], a[3])
self.c2bdg.safe_add_loc(a[0], a[1], a[2], a[4])
self.t2bdg.add_loc(a[0], a[1], a[2], a[3])
self.c2bdg.add_loc(a[0], a[1], a[2], a[4])

self.twoconditionscore = TwoConditionScores(self.t1bdg,
self.c1bdg,
Expand All @@ -40,6 +40,31 @@ def setUp(self):
self.twoconditionscore.finalize()
(self.cat1, self.cat2, self.cat3) = self.twoconditionscore.call_peaks(min_length=10, max_gap=10, cutoff=3)

def test_call_peaks_score_is_mean_logLR(self):
# Regression test for issue #715: the score of a bdgdiff region
# must be the length-weighted mean of the log10 likelihood
# ratios of its intervals, not the mean of their integer parts.
# Two adjacent cond1 intervals of equal length with
# log10LR(t1 vs t2) = 0.3271 and 6.1784 (pseudocount 0.01)
# must give (0.3271 + 6.1784) / 2 = 3.2527, whereas truncating
# each value to an integer gives (0 + 6) / 2 = 3.0.
regions = [(0, 1000, 20.0, 2.0, 18.0, 2.0),
(1000, 2000, 20.0, 2.0, 15.0, 2.0),
(2000, 3000, 40.0, 2.0, 15.0, 2.0),
(3000, 4000, 2.0, 2.0, 2.0, 2.0)]
bdgs = [bedGraphTrackI() for i in range(4)]
for (s, e, t1, c1, t2, c2) in regions:
for (bdg, v) in zip(bdgs, (t1, c1, t2, c2)):
bdg.add_loc(b"chr1", s, e, v)
tcs = TwoConditionScores(bdgs[0], bdgs[1], bdgs[2], bdgs[3], 1.0, 1.0)
tcs.build()
tcs.finalize()
(cat1, cat2, _cat3) = tcs.call_peaks(min_length=200, max_gap=100, cutoff=0.2)
self.assertEqual(cat1.total, 1)
self.assertEqual(cat2.total, 0)
peaks = cat1.get_data_from_chrom(b"chr1")
self.assertAlmostEqual(peaks[0]["score"], 3.2527, places=3)


class Test_ScoreTrackII(unittest.TestCase):

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