small fixes
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@ -430,7 +430,7 @@ def run(config):
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if pb is not None:
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if pb is not None:
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pb(i, force=True)
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pb(i, force=True)
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print("", file=sys.stderr)
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print("", file=sys.stderr)
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logger("info", "Imported %d entries", i)
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logger("info", "Imported %d entries", len(view))
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# Save command config in View and DMS comments
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# Save command config in View and DMS comments
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command_line = " ".join(sys.argv[1:])
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command_line = " ".join(sys.argv[1:])
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@ -450,7 +450,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
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sequences[1] = sequences[1][reversematch[1][2]:]
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sequences[1] = sequences[1][reversematch[1][2]:]
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if not directmatch[0].forward:
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if not directmatch[0].forward:
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sequences[1] = sequences[1].reverse_complement
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sequences[1] = sequences[1].reverse_complement
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sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
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sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
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sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
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sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
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else:
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else:
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sequences[0] = sequences[0][reversematch[1][2]:]
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sequences[0] = sequences[0][reversematch[1][2]:]
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