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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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python/obitools3/commands/alignpairedend.pyx
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@ -8,7 +8,7 @@ from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column, Column_line
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
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.align._qsassemble import QSolexaReverseAssemble
@ -29,7 +29,7 @@ __title__="Aligns paired-ended reads"
def addOptions(parser):
addSequenceInputOption(parser)
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
group = parser.add_argument_group('obi alignpairedend specific options')