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More fixes for type annotations #129

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merged 3 commits into from
Nov 1, 2023
Merged

More fixes for type annotations #129

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d270a9c
remove redundant test cases
fabianegli Nov 1, 2023
40fb154
use correct test case result
fabianegli Nov 1, 2023
693aceb
fix too many unpackings and zips
fabianegli Nov 1, 2023
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12 changes: 2 additions & 10 deletions bin/diann_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1234,7 +1234,7 @@ def calculate_coverage(ref_sequence: str, sequences: Set[str]):

Examples:
>>> calculate_coverage("WATEROVERTHEDUCKSBACK", {"WATER", "DUCK"})
0.45
0.42857142857142855
>>> calculate_coverage("DUCKDUCKDUCK", {"DUCK"})
1.0
>>> calculate_coverage("WATEROVERTHEDUCK", {"DUCK"})
Expand All @@ -1243,14 +1243,6 @@ def calculate_coverage(ref_sequence: str, sequences: Set[str]):
1.0
>>> calculate_coverage("WATERGLASS", {"WAT", "TER"})
0.5
>>> calculate_coverage("WATER", {"WAT", "TER"})
1.0
>>> calculate_coverage("WATERGLASS", {"WAT", "TER"})
0.5
>>> calculate_coverage("WATER", {"WAT", "TER"})
1.0
>>> calculate_coverage("WATERGLASS", {"WAT", "TER"})
0.5
"""
starts = []
lengths = []
Expand All @@ -1267,7 +1259,7 @@ def calculate_coverage(ref_sequence: str, sequences: Set[str]):
# merge overlapping intervals
merged_starts: list = []
merged_lengths: list = []
for start, length in zip(*sorted(zip(starts, lengths))):
for start, length in sorted(zip(starts, lengths)):
if merged_starts and merged_starts[-1] + merged_lengths[-1] >= start:
merged_lengths[-1] = max(merged_starts[-1] + merged_lengths[-1], start + length) - merged_starts[-1]
else:
Expand Down