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Cleaner handling of reverse quality columns

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This commit is contained in:
Celine Mercier
2020-01-18 19:28:12 +01:00
parent ced82c4242
commit b4b2e62195
8 changed files with 85 additions and 46 deletions
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6
python/obitools3/libalign/_solexapairend.pyx
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@ -6,6 +6,7 @@ from .solexapairend import iterOnAligment
from .shifted_ali cimport Ali_shifted
from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \
REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
@ -13,7 +14,6 @@ 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
@ -233,7 +233,7 @@ def buildConsensus(ali, seq, ref_tags=None):
seq[b'mode']=b'alignment'
for tag in ref_tags:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME and \
if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = ref_tags[tag]
@ -254,7 +254,7 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
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:
if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN:
seq[tag] = forward[tag]
return seq