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Fix wrong band width calculation under some circumstances #723

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Dec 22, 2024
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Fix wrong band width calculation under some circumstances #723

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10 changes: 5 additions & 5 deletions src/biotite/sequence/align/banded.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -214,9 +214,6 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
else:
is_swapped = False
lower_diag, upper_diag = min(band), max(band)
band_width = upper_diag - lower_diag + 1
if band_width < 1:
raise ValueError("The width of the band is 0")
if len(seq1) + upper_diag <= 0 or lower_diag >= len(seq2):
raise ValueError(
"Alignment band is out of range, the band allows no overlap "
Expand All @@ -226,6 +223,9 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
# covers the search space of an unbanded alignment
lower_diag = max(lower_diag, -len(seq1)+1)
upper_diag = min(upper_diag, len(seq2)-1)
band_width = upper_diag - lower_diag + 1
if band_width < 1:
raise ValueError("The width of the band is 0")

# This implementation uses transposed tables in comparison
# to the common visualization
Expand All @@ -249,12 +249,12 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
###############

# A score value that signals that the respective direction in the
# dynamic programming matrix should not be used since, it would be
# dynamic programming matrix should not be used, since it would be
# outside the band
# It is the 'worst' score available, so the trace table will never
# include such a direction
neg_inf = np.iinfo(np.int32).min
# Correct the 'negative infinity' integer, by making it more positve
# Correct the 'negative infinity' integer, by making it more positive
# This prevents an integer underflow when the gap penalty or
# match score is added to this value
neg_inf -= min(gap_penalty) if affine_penalty else gap_penalty
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