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Cython API: fixed a bug where the quality format would not be read

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properly from the configuration values
This commit is contained in:
Celine Mercier
2018-02-12 14:42:30 +01:00
parent 370fb9272c
commit 00993d4215
2 changed files with 11 additions and 8 deletions
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9
python/obitools3/commands/alignpairedend.pyx
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@ -96,11 +96,11 @@ def run(config):
logger("info", "obi alignpairedend")
# Open the input
finput = open_uri(config["alignpairedend"]["forward"], config)
finput = open_uri(config["alignpairedend"]["forward"])
if finput is None:
raise Exception("Could not open forward reads")
forward = finput[1]
rinput = open_uri(config["alignpairedend"]["reverse"], config)
rinput = open_uri(config["alignpairedend"]["reverse"])
if rinput is None:
raise Exception("Could not open reverse reads")
reverse = rinput[1]
@ -108,14 +108,13 @@ def run(config):
if len(forward) != len(reverse):
raise Exception("Error: the number of forward and reverse reads are different")
if "index" in config["alignpairedend"]:
index = open_uri(config["alignpairedend"]["index"], config)
if "index" in config["alignpairedend"]: # TODO
index = open_uri(config["alignpairedend"]["index"])
else:
index = None
# Open the output
output = open_uri(config['obi']['outputURI'],
config,
input=False,
newviewtype=View_NUC_SEQS)
if output is None: