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alignpairedend: improved/fixed the output tags for the alignment score

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and lengths. Removed minimum score option
This commit is contained in:
Celine Mercier
2020-07-13 15:59:50 +02:00
parent ed9549acfb
commit 9672f01c6a
4 changed files with 24 additions and 21 deletions
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24
python/obitools3/commands/alignpairedend.pyx
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@ -39,12 +39,13 @@ def addOptions(parser):
type=str,
help="URI to the reverse reads if they are in a different view than the forward reads")
group.add_argument('--score-min',
action="store", dest="alignpairedend:smin",
metavar="#.###",
default=None,
type=float,
help="Minimum score for keeping alignments")
# group.add_argument('--score-min',
# action="store", dest="alignpairedend:smin",
# metavar="#.###",
# default=None,
# type=float,
# help="Minimum score for keeping alignments. "
# "(for kmer alignment) The score is an approximation of the number of nucleotides matching in the overlap of the alignment.")
# group.add_argument('-A', '--true-ali',
# action="store_true", dest="alignpairedend:trueali",
@ -174,11 +175,6 @@ def run(config):
Column.new_column(view, QUALITY_COLUMN, OBI_QUAL) #TODO output URI quality option?
if 'smin' in config['alignpairedend']:
smin = config['alignpairedend']['smin']
else:
smin = 0
# Initialize the progress bar
pb = ProgressBar(entries_len, config, seconde=5)
@ -217,7 +213,7 @@ def run(config):
else:
seqF = forward[i]
if ali.score > smin and ali.consensus_len > 0 :
if ali.overlap_len > 0 :
buildConsensus(ali, consensus, seqF)
else:
if not two_views:
@ -225,9 +221,7 @@ def run(config):
else:
seqR = reverse[i]
buildJoinedSequence(ali, seqR, consensus, forward=seqF)
consensus[b"smin"] = smin
if kmer_ali :
ali.free()