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uniq: added forced deletion of reverse sequence quality

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Celine Mercier
2019-12-12 17:02:36 +01:00
parent 6bfd7441f3
commit d75e54a078
1 changed files with 6 additions and 2 deletions
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6
python/obitools3/commands/uniq.pyx
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@ -25,6 +25,8 @@ from cpython.exc cimport PyErr_CheckSignals
__title__="Group sequence records together" __title__="Group sequence records together"
REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY" # TODO from ngsfilter, move to C
def addOptions(parser): def addOptions(parser):
@ -491,9 +493,11 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
o_idx += 1 o_idx += 1
# Deletes quality column if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not) # Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
if QUALITY_COLUMN in view: if QUALITY_COLUMN in view:
o_view.delete_column(QUALITY_COLUMN) o_view.delete_column(QUALITY_COLUMN)
if REVERSE_QUALITY_COLUMN_NAME in view:
o_view.delete_column(REVERSE_QUALITY_COLUMN_NAME)
if taxonomy is not None: if taxonomy is not None:
print("") # TODO because in the middle of progress bar. Better solution? print("") # TODO because in the middle of progress bar. Better solution?