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obi alignpairedend: fixed a bug where first seq was kept in result view

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instead of consensus seq
This commit is contained in:
Celine Mercier
2019-07-06 16:29:32 +02:00
parent a83bf43ab9
commit f765c6f41e
1 changed files with 3 additions and 2 deletions
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5
python/obitools3/libalign/_solexapairend.pyx
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@ -5,7 +5,7 @@ from cpython cimport array
from .solexapairend import iterOnAligment from .solexapairend import iterOnAligment
from .shifted_ali cimport Ali_shifted from .shifted_ali cimport Ali_shifted
from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, \ from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \ obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view obi_set_str_with_elt_idx_and_col_p_in_view
@ -233,7 +233,8 @@ def buildConsensus(ali, seq, ref_tags=None):
seq[b'mode']=b'alignment' seq[b'mode']=b'alignment'
for tag in ref_tags: for tag in ref_tags:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME: if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = ref_tags[tag] seq[tag] = ref_tags[tag]
return seq return seq