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ngsfilter: fixed critical bug where barcodes shorter than the forward

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primer would be missed
This commit is contained in:
MercierC
2021-03-16 15:09:28 +13:00
parent 8833110490
commit 10e5ebdbc0
1 changed files with 4 additions and 4 deletions
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8
python/obitools3/commands/ngsfilter.pyx
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@ -322,7 +322,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[0] = sequences[0][directmatch[1][2]:]
else:
sequences[1] = sequences[1][directmatch[1][2]:]
sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
if directmatch[0].forward:
@ -369,7 +369,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[0] = sequences[0][:r[1]]
else:
sequences[1] = sequences[1][:r[1]]
sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
# do the same on the other seq
if first_match_first_seq:
@ -394,7 +394,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
seq_to_match = sequences[0]
reversematch = []
# Compute begin
begin=directmatch[1][2]+1 # end of match + 1 on the same sequence
#begin=directmatch[1][2]+1 # end of match + 1 on the same sequence -- No, already cut out forward primer
# Try reverse matching on the other sequence:
new_seq = True
pattern = 0
@ -408,7 +408,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
primer=p
# Saving original primer as 4th member of the tuple to serve as correct key in infos dict even if it might have been reversed complemented
# (3rd member already used by directmatch)
reversematch.append((primer, primer(seq_to_match, same_sequence=not new_seq, pattern=pattern, begin=begin), None, p))
reversematch.append((primer, primer(seq_to_match, same_sequence=not new_seq, pattern=pattern, begin=0), None, p))
new_seq = False
pattern+=1
# Choose match closer to the end of the sequence