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Made the OBITools3 more 'empty file friendly'

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This commit is contained in:
MercierC
2021-03-15 16:25:41 +13:00
parent d48aed38d4
commit 425fe25bd2
4 changed files with 90 additions and 73 deletions
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28
python/obitools3/commands/alignpairedend.pyx
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@ -205,19 +205,25 @@ def run(config):
if type(entries) == list:
forward = entries[0]
reverse = entries[1]
aligner = Kmer_similarity(forward, \
view2=reverse, \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=None)
if len(forward) == 0 or len(reverse) == 0:
aligner = None
else:
aligner = Kmer_similarity(forward, \
view2=reverse, \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=None)
else:
aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQUENCE_COLUMN], \
qual_column2=entries[REVERSE_QUALITY_COLUMN], \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
if len(entries) == 0:
aligner = None
else:
aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQUENCE_COLUMN], \
qual_column2=entries[REVERSE_QUALITY_COLUMN], \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
ba = alignmentIterator(entries, aligner)
i = 0
for ali in ba:
@ -251,7 +257,7 @@ def run(config):
pb(i, force=True)
print("", file=sys.stderr)
if kmer_ali :
if kmer_ali and aligner is not None:
aligner.free()
# Save command config in View and DMS comments