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alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences

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where only the forward sequence was kept
This commit is contained in:
Celine Mercier
2020-06-05 16:06:43 +02:00
parent 359a9fe237
commit 5fbbb6d304
1 changed files with 14 additions and 4 deletions
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16
python/obitools3/libalign/_solexapairend.pyx
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@ -188,7 +188,7 @@ def buildConsensus(ali, seq, ref_tags=None):
seq[b'shift']=ali.shift seq[b'shift']=ali.shift
else: else:
if len(ali[0])>999: # TODO why? if len(ali[0])>999: # TODO why?
raise AssertionError,"Too long alignemnt" raise AssertionError,"Too long alignment"
ic=IterOnConsensus(ali) ic=IterOnConsensus(ali)
@ -250,11 +250,21 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
quality.extend(reverse.quality) quality.extend(reverse.quality)
seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality) seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
seq[b"score"]=ali.score seq[b"score"]=ali.score
seq[b"ali_direction"]=ali.direction if len(ali.direction) > 0:
seq[b"ali_direction"]=ali.direction
else:
seq[b"ali_direction"]=None
seq[b"mode"]=b"joined" seq[b"mode"]=b"joined"
seq[b"pairedend_limit"]=len(forward) seq[b"pairedend_limit"]=len(forward)
seq[b"ali_length"] = ali.consensus_len
if ali.consensus_len > 0:
seq[b"score_norm"]=float(ali.score)/ali.consensus_len
else:
seq[b"score_norm"]=0.0
for tag in forward: for tag in forward:
if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN: if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = forward[tag] seq[tag] = forward[tag]
return seq return seq