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Fix array indexing bug in uint8_to_bed_parallel.py #26

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Fix array indexing bug in uint8_to_bed_parallel.py #26

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14 changes: 7 additions & 7 deletions umap/uint8_to_bed_parallel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,14 +366,14 @@ def write_as_wig(self, uint_path, out_path, kmer, chrom):
unimap_diff = np.diff(np.array(ar_quant > 0, dtype=int))
poses_start, = np.where(unimap_diff == 1)
poses_end, = np.where(unimap_diff == -1)
if len(poses_start) != len(poses_end):
if len(poses_start) > len(poses_end):
poses_end = np.append(poses_end, [len(uniquely_mappable)])
else:
poses_start = np.append([0], poses_start)
elif uniquely_mappable[0] == 1:
if uniquely_mappable[0] > 0:
# If the first element of uniquely_mappable is nonzero,
# then poses_start is missing the start position of the first "run"
poses_start = np.append([0], poses_start)
poses_end = np.append(poses_end, [len(uniquely_mappable)])
if uniquely_mappable[-1] > 0:
# If the last element of uniquely_mappable is nonzero,
# then poses_end is missing the end position of the last "run".
poses_end = np.append(poses_end, [len(uniquely_mappable) - 1])
for ind_st in range(len(poses_start)):
pos_st = poses_start[ind_st] + 1
pos_end = poses_end[ind_st] + 1
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