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alignpairedend: fixed the worst memory leak and the handling of the case

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where 0 common kmers are found
This commit is contained in:
Celine Mercier
2019-03-29 11:16:25 +01:00
parent ceaafca427
commit ee9947217c
5 changed files with 46 additions and 43 deletions
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28
python/obitools3/commands/alignpairedend.pyx
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@ -2,7 +2,6 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view import RollbackException
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
@ -201,26 +200,23 @@ def run(config):
pb(i)
consensus = view[i]
if not two_views:
seqF = entries[i]
else:
seqF = forward[i]
if smin > 0:
if (ali.score > smin) :
buildConsensus(ali, consensus, seqF)
else:
if not two_views:
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
else:
seqR = reverse[i]
buildJoinedSequence(ali, seqR, consensus, forward=seqF)
consensus[b"smin"] = smin
else:
if ali.score > smin and ali.consensus_len > 0 :
buildConsensus(ali, consensus, seqF)
else:
if not two_views:
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
else:
seqR = reverse[i]
buildJoinedSequence(ali, seqR, consensus, forward=seqF)
consensus[b"smin"] = smin
if kmer_ali :
ali.free()