def _loadReference(self, cmpH5):
logging.info("Loading reference")
err = reference.loadFromFile(options.referenceFilename, cmpH5)
if err:
die("Error loading reference")
# Grok the referenceWindow spec, if any.
if options.referenceWindowsAsString is None:
options.referenceWindows = ()
elif options.skipUnrecognizedContigs:
# This is a workaround for smrtpipe scatter/gather.
options.referenceWindows = []
for s in options.referenceWindowsAsString.split(","):
try:
win = reference.stringToWindow(s)
options.referenceWindows.append(win)
except:
pass
else:
options.referenceWindows = map(reference.stringToWindow,
options.referenceWindowsAsString.split(","))
def _loadReference(self, cmpH5):
logging.info("Loading reference")
err = reference.loadFromFile(options.referenceFilename, cmpH5)
if err:
die("Error loading reference")
# Grok the referenceWindow spec, if any.
if options.referenceWindowsAsString is None:
options.referenceWindows = ()
elif options.skipUnrecognizedContigs:
# This is a workaround for smrtpipe scatter/gather.
options.referenceWindows = []
for s in options.referenceWindowsAsString.split(","):
try:
win = reference.stringToWindow(s)
options.referenceWindows.append(win)
except:
pass
else:
options.referenceWindows = map(
reference.stringToWindow,
options.referenceWindowsAsString.split(","))
def _loadReference(self, alnFile):
logging.info("Loading reference")
reference.loadFromFile(options.referenceFilename, alnFile)
# Grok the referenceWindow spec, if any.
if options.referenceWindowsAsString is None:
options.referenceWindows = ()
elif options.skipUnrecognizedContigs:
# This is a workaround for smrtpipe scatter/gather.
options.referenceWindows = []
for s in options.referenceWindowsAsString.split(","):
try:
win = reference.stringToWindow(s)
options.referenceWindows.append(win)
except Exception:
msg = traceback.format_exc()
logging.debug(msg)
pass
else:
options.referenceWindows = map(reference.stringToWindow,
options.referenceWindowsAsString.split(","))
if options.referenceWindowsFromAlignment:
options.referenceWindows = alnFile.refWindows
def _loadReference(self, alnFile):
logging.info("Loading reference")
reference.loadFromFile(options.referenceFilename, alnFile)
# Grok the referenceWindow spec, if any.
if options.referenceWindowsAsString is None:
options.referenceWindows = ()
elif options.skipUnrecognizedContigs:
# This is a workaround for smrtpipe scatter/gather.
options.referenceWindows = []
for s in options.referenceWindowsAsString.split(","):
try:
win = reference.stringToWindow(s)
options.referenceWindows.append(win)
except Exception:
msg = traceback.format_exc()
logging.debug(msg)
pass
else:
options.referenceWindows = map(
reference.stringToWindow,
options.referenceWindowsAsString.split(","))
if options.referenceWindowsFromAlignment:
options.referenceWindows = alnFile.refWindows