Commit a13e9bdd by Eric Coissac

Refactoring & debugging

parent b330de3e
......@@ -19,7 +19,9 @@ default_config = { 'circular' : False,
'format' : "fasta",
"fscaffold": [],
"path" : None,
"contigs" : False
"contigs" : False,
'tags' : None,
'extension' : None
}
def addOptions(parser):
......@@ -79,7 +81,7 @@ def addOptions(parser):
help='the number of bases taken at the end of '
'contigs to jump with paired-ends [default: <estimated>]')
parser.add_argument('--set-tag','-S', dest ='fasta:tags',
parser.add_argument('--set-tag','-S', dest ='unfold:tags',
metavar='tag',
action='append',
default=[],
......@@ -225,14 +227,14 @@ def run(config):
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
tags=config['unfold']['tags'])
if config['unfold']['format']=="sam":
fa = path2sam(asm,cg,path,
identifier="%s_%d" % (seqid,c),
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
tags=config['unfold']['tags'])
print(fa,file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
......@@ -36,7 +36,7 @@ def addOptions(parser):
help='the number of bases taken at the end of '
'contigs to jump with pared-ends [default: <estimated>]')
parser.add_argument('--set-tag','-S', dest ='fasta:tags',
parser.add_argument('--set-tag','-S', dest ='unfold:tags',
metavar='tag',
action='append',
default=[],
......@@ -129,7 +129,7 @@ def run(config):
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
tags=config['tags']['tags'])
print(fa, file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
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