obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

small fixes

Browse Source
This commit is contained in:
MercierC
2021-04-07 10:28:02 +12:00
parent 847c9c816d
commit e099a16624
2 changed files with 2 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
python/obitools3/commands/import.pyx
View File

@ -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:])

2
python/obitools3/commands/ngsfilter.pyx
View File

@ -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]:]