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alignpairedend: improved/fixed the output tags for the alignment score

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and lengths. Removed minimum score option
This commit is contained in:
Celine Mercier
2020-07-13 15:59:50 +02:00
parent ed9549acfb
commit 9672f01c6a
4 changed files with 24 additions and 21 deletions
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10
python/obitools3/libalign/_solexapairend.pyx
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@ -183,8 +183,9 @@ def buildConsensus(ali, seq, ref_tags=None):
# doesn't work because uint8_t* are forced into bytes by cython (nothing read/kept beyond 0 values)
#obi_set_qual_int_with_elt_idx_and_col_p_in_view(view_p, col_p, seq.index, 0, ali.consensus_qual, ali.consensus_len)
seq.set(ref_tags.id+b"_CONS", ali.consensus_seq, quality=ali.consensus_qual)
seq[b'ali_length'] = ali.consensus_len
seq[b'score_norm']=float(ali.score)/ali.consensus_len
seq[b"seq_length"] = ali.consensus_len
seq[b"overlap_length"] = ali.overlap_len
seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
seq[b'shift']=ali.shift
else:
if len(ali[0])>999: # TODO why?
@ -256,9 +257,10 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
seq[b"ali_direction"]=None
seq[b"mode"]=b"joined"
seq[b"pairedend_limit"]=len(forward)
seq[b"ali_length"] = ali.consensus_len
seq[b"seq_length"] = ali.consensus_len
seq[b"overlap_length"] = ali.overlap_len
if ali.consensus_len > 0:
seq[b"score_norm"]=float(ali.score)/ali.consensus_len
seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
else:
seq[b"score_norm"]=0.0