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Merged
grexor merged 2 commits into from
Sep 4, 2025
Merged

Dev #103

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64946ab
Merge pull request #98 from bedapub/main
grexor Mar 20, 2025
95c9032
At very very very rare cases, it happens that there is a short insert…
grexor Sep 4, 2025
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15 changes: 13 additions & 2 deletions splicekit/core/junctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,8 +168,19 @@ def detect_junctions(database, positions, cigar, read, pair=None, stats=False):
num_junctions += 1
cigar_left = cigar[index-1]
cigar_right = cigar[index+1]
assert(cigar_left[0]==0)
assert(cigar_right[0]==0)

# @ very very very rare cases, it happens that there is a short insertion or deletion on the acceptor side, and there is always a match after (index+2 with type 0)
# examples:
# [(4, 12), (0, 114), *(3, 821), (1, 2), (0, 22)]
# [(0, 61), (3, 97), (0, 65), *(3, 7174), (2, 3), (0, 24)]
if cigar_right[0] in [1,2]:
cigar_right = cigar[index+2]

try:
assert(cigar_left[0]==0)
assert(cigar_right[0]==0)
except:
print("problems parsing cigar string part:", cigar)
coverage_left = cigar_left[1]
coverage_right = cigar_right[1]
junction_size = v
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