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Cython: rearranged input and output format options to have both and

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updated commands accordingly
This commit is contained in:
Celine Mercier
2018-10-17 11:19:48 +02:00
parent e6bbe13d81
commit 58589e04be
11 changed files with 120 additions and 77 deletions
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4
python/obitools3/commands/clean.pyx
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@ -5,7 +5,7 @@ from obitools3.dms.dms cimport DMS
from obitools3.dms.capi.obidms cimport OBIDMS_p
from obitools3.dms.view import RollbackException
from obitools3.dms.capi.obiclean cimport obi_clean
from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
@ -20,7 +20,7 @@ __title__="Tag a set of sequences for PCR and sequencing errors identification"
def addOptions(parser):
addSequenceInputOption(parser)
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
group = parser.add_argument_group('obi clean specific options')