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Fixed the new alignpaired end to work after ngsfilter with the 9879847

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possible cases
This commit is contained in:
Celine Mercier
2019-02-17 18:32:35 +01:00
parent 4ddd1a1c37
commit e026e9ec83
9 changed files with 151 additions and 83 deletions
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19
python/obitools3/libalign/_solexapairend.pyx
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@ -13,7 +13,7 @@ from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.view.view cimport View
from obitools3.dms.column.column cimport Column
from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
from math import log10
@ -182,7 +182,7 @@ def buildConsensus(ali, seq, ref_tags=None):
col_p = column.pointer()
# 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, tags=ref_tags)
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'shift']=ali.shift
@ -208,7 +208,7 @@ def buildConsensus(ali, seq, ref_tags=None):
quality[i] = min(42, round(-10*log10(p)))
i+=1
seq.set(ali[0].wrapped.id+b"_CONS", sseq, quality=quality, tags=ali[0].wrapped)
seq.set(ali[0].wrapped.id+b"_CONS", sseq, quality=quality)
if hasattr(ali, "counter"):
seq[b'alignement_id']=ali.counter
@ -224,12 +224,18 @@ def buildConsensus(ali, seq, ref_tags=None):
seq[b'ali_length']=len(seq)-ic.seqASingle-ic.seqBSingle
if seq[b'ali_length']>0:
seq[b'score_norm']=float(ali.score)/seq[b'ali_length']
ref_tags = ali[0].wrapped
if hasattr(ali, "direction"):
seq[b'ali_direction']=ali.direction
seq[b'score']=ali.score
seq[b'mode']=b'alignment'
for tag in ref_tags:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME:
seq[tag] = ref_tags[tag]
return seq
@ -241,10 +247,13 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
s = forward.seq + reverse.seq
quality = forward.quality
quality.extend(reverse.quality)
seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality, tags=forward)
seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
seq[b"score"]=ali.score
seq[b"ali_direction"]=ali.direction
seq[b"mode"]=b"joined"
seq[b"pairedend_limit"]=len(forward)
for tag in forward:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME:
seq[tag] = forward[tag]
return seq