From e099a16624c0533b27cebea54ef57bc0cc600b0e Mon Sep 17 00:00:00 2001 From: MercierC Date: Wed, 7 Apr 2021 10:28:02 +1200 Subject: [PATCH] small fixes --- python/obitools3/commands/import.pyx | 2 +- python/obitools3/commands/ngsfilter.pyx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index d5eb1ba..56b1cce 100755 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -430,7 +430,7 @@ def run(config): if pb is not None: pb(i, force=True) print("", file=sys.stderr) - logger("info", "Imported %d entries", i) + logger("info", "Imported %d entries", len(view)) # Save command config in View and DMS comments command_line = " ".join(sys.argv[1:]) diff --git a/python/obitools3/commands/ngsfilter.pyx b/python/obitools3/commands/ngsfilter.pyx index 22c6c6e..131201c 100644 --- a/python/obitools3/commands/ngsfilter.pyx +++ b/python/obitools3/commands/ngsfilter.pyx @@ -450,7 +450,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False): sequences[1] = sequences[1][reversematch[1][2]:] if not directmatch[0].forward: sequences[1] = sequences[1].reverse_complement - sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool + sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool else: sequences[0] = sequences[0][reversematch[1][2]:]