def configure(options, cmpH5):
if cmpH5.readType != "standard":
raise U.IncompatibleDataException(
"The Quiver algorithm requires a cmp.h5 file containing standard (non-CCS) reads." )
if options.parametersSpec == "auto":
if options.diploid:
logging.info("Diploid analysis--resorting to unknown.NoQVsModel until other " +
"parameter sets can be recalibrated.")
params = M.loadParameterSets(options.parametersFile, spec="unknown.NoQVsModel")
else:
params = M.loadParameterSets(options.parametersFile, cmpH5=cmpH5)
if not M.allQVsLoaded(cmpH5):
logging.warn(
"This .cmp.h5 file lacks some of the QV data tracks that are required " +
"for optimal performance of the Quiver algorithm. For optimal results" +
" use the ResequencingQVs workflow in SMRTPortal with bas.h5 files " +
"from an instrument using software version 1.3.1 or later.")
else:
params = M.loadParameterSets(options.parametersFile,
spec=options.parametersSpec,
cmpH5=cmpH5)
if not all(ps.model.isCompatibleWithCmpH5(cmpH5) for ps in params.values()):
raise U.IncompatibleDataException(
"Selected Quiver parameter set is incompatible with this cmp.h5 file " +
"due to missing data tracks.")
logging.info("Using Quiver parameter set(s): %s" % (", ".join(ps.name for ps in params.values())))
return M.QuiverConfig(minMapQV=options.minMapQV,
noEvidenceConsensus=options.noEvidenceConsensusCall,
refineDinucleotideRepeats=(not options.fastMode) and options.refineDinucleotideRepeats,
computeConfidence=(not options.fastMode),
parameterSets=params)
def configure(options, cmpH5):
if options.verbosity > 1:
cc.Logging.EnableDiagnosticLogging()
if cmpH5.readType != "standard":
raise U.IncompatibleDataException(
"The Quiver algorithm requires an alignment file containing standard (non-CCS) reads."
)
if options.parametersSpec == "auto":
# Reject Sequel chemistries explicitly---there are no Quiver
# trainings for Sequel. Arrow should be used.
# (Not that power-users can bypass this requirement using an explicit parameter set)
for chem in cmpH5.sequencingChemistry:
if chem.startswith("S/"):
raise U.IncompatibleDataException(
"The Quiver algorithm is not trained for Sequel data. " +
"Please use the Arrow algorithm instead.")
if options.diploid:
logging.info(
"Diploid analysis--resorting to unknown.NoQVsModel until other "
+ "parameter sets can be recalibrated.")
params = M.loadParameterSets(options.parametersFile,
spec="unknown.NoQVsModel")
else:
params = M.loadParameterSets(options.parametersFile, cmpH5=cmpH5)
qvMsg = "This alignment file file lacks some of the QV data tracks that are required " + \
"for optimal performance of the Quiver algorithm. For optimal results" + \
" use the ResequencingQVs workflow in SMRTPortal with bas.h5 files " + \
"from an instrument using software version 1.3.1 or later, or the " + \
"--forQuiver option to pbalign."
if not M.enoughQVsLoaded(cmpH5):
raise U.IncompatibleDataException(qvMsg)
elif not M.allQVsLoaded(cmpH5):
logging.warn(qvMsg)
else:
params = M.loadParameterSets(options.parametersFile,
spec=options.parametersSpec,
cmpH5=cmpH5)
if not all(
ps.model.isCompatibleWithCmpH5(cmpH5)
for ps in params.values()):
raise U.IncompatibleDataException(
"Selected Quiver parameter set is incompatible with this alignment file "
+ "due to missing data tracks.")
logging.info("Using Quiver parameter set(s): %s" %
(", ".join(ps.name for ps in params.values())))
return M.QuiverConfig(minMapQV=options.minMapQV,
noEvidenceConsensus=options.noEvidenceConsensusCall,
refineDinucleotideRepeats=(not options.fastMode)
and options.refineDinucleotideRepeats,
computeConfidence=(not options.fastMode),
parameterSets=params)
def configure(options, cmpH5):
if options.verbosity > 1:
cc.Logging.EnableDiagnosticLogging()
if cmpH5.readType != "standard":
raise U.IncompatibleDataException(
"The Quiver algorithm requires an alignment file containing standard (non-CCS) reads." )
if options.parametersSpec == "auto":
# Reject Sequel chemistries explicitly---there are no Quiver
# trainings for Sequel. Arrow should be used.
# (Not that power-users can bypass this requirement using an explicit parameter set)
for chem in cmpH5.sequencingChemistry:
if chem.startswith("S/"):
raise U.IncompatibleDataException(
"The Quiver algorithm is not trained for Sequel data. " +
"Please use the Arrow algorithm instead.")
if options.diploid:
logging.info("Diploid analysis--resorting to unknown.NoQVsModel until other " +
"parameter sets can be recalibrated.")
params = M.loadParameterSets(options.parametersFile, spec="unknown.NoQVsModel")
else:
params = M.loadParameterSets(options.parametersFile, cmpH5=cmpH5)
qvMsg = "This alignment file file lacks some of the QV data tracks that are required " + \
"for optimal performance of the Quiver algorithm. For optimal results" + \
" use the ResequencingQVs workflow in SMRTPortal with bas.h5 files " + \
"from an instrument using software version 1.3.1 or later, or the " + \
"--forQuiver option to pbalign."
if not M.enoughQVsLoaded(cmpH5):
raise U.IncompatibleDataException(qvMsg)
elif not M.allQVsLoaded(cmpH5):
logging.warn(qvMsg)
else:
params = M.loadParameterSets(options.parametersFile,
spec=options.parametersSpec,
cmpH5=cmpH5)
if not all(ps.model.isCompatibleWithCmpH5(cmpH5) for ps in params.values()):
raise U.IncompatibleDataException(
"Selected Quiver parameter set is incompatible with this alignment file " +
"due to missing data tracks.")
logging.info("Using Quiver parameter set(s): %s" % (", ".join(ps.name for ps in params.values())))
return M.QuiverConfig(minMapQV=options.minMapQV,
noEvidenceConsensus=options.noEvidenceConsensusCall,
refineDinucleotideRepeats=(not options.fastMode) and options.refineDinucleotideRepeats,
computeConfidence=(not options.fastMode),
parameterSets=params)