Commit 1d3d4616 by Eric Coissac

Fix issue #8 by substituing all occurrences of Bruinj by Bruijn in

source code and documentation
parent 3b0d5f95
......@@ -4,7 +4,7 @@ The :program:`buildgraph` command
=================================
The :ref:`organelle assembler <oa>`'s :program:`buildgraph`
realizes the assembling of the reads by building the De Bruinj Graph which
realizes the assembling of the reads by building the De Bruijn Graph which
is the central data structure used by the :ref:`organelle assembler <oa>`.
.. figure:: ../oa-buildgraph.*
......
......@@ -172,7 +172,7 @@ is a variable three-letters extension.
.. code-block:: bash
2015-08-17 12:05:24,808 [INFO ] Building De Bruinj Graph
2015-08-17 12:05:24,808 [INFO ] Building De Bruijn Graph
2015-08-17 12:05:24,808 [INFO ] Minimum overlap between read: 50
The first lines printed recall the current operation and the minimum length of
......
......@@ -31,6 +31,7 @@ default_config = {
'seeds' : None,
'seedmincov' : 1,
'kup' : None,
'version' : False,
'progress' : True
}
......@@ -39,9 +40,10 @@ default_config = {
from orgasm import command
from orgasm.version import version
__all__ = []
__version__ = 0.1
__version__ = version
__date__ = '2014-09-28'
__updated__ = '2014-09-28'
......@@ -122,6 +124,11 @@ def getLogger(config):
def buildArgumentParser():
parser = argparse.ArgumentParser()
parser.add_argument('--version', dest='orgasm:version',
action='store_true',
default=False,
help='Print the version of the Organelle Assembler')
parser.add_argument('--no-log', dest='orgasm:log',
action='store_false',
default=None,
......@@ -190,6 +197,11 @@ def getConfiguration():
if options[k] is not None:
s[key]=options[k]
if config['orgasm']['version']:
print("The Organelle Assembler - Version %s" % __version__)
sys.exit(0)
if config['orgasm']['outputfilename'] is None:
config['orgasm']['outputfilename']=config['orgasm']['indexfilename']
......@@ -202,7 +214,8 @@ def getConfiguration():
if __name__ =="__main__":
config = getConfiguration()
config = getConfiguration()
config['orgasm']['module'].run(config)
......@@ -167,7 +167,7 @@ def run(config):
snp=config['buildgraph']['snp']
assmax = config['buildgraph']['assmax']*2
logger.info("Building De Bruinj Graph")
logger.info("Building De Bruijn Graph")
minoverlap = config['buildgraph']['minoverlap']
......
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