def configure(options, alnFile):
if alnFile.readType != "standard":
raise U.IncompatibleDataException(
"The Arrow algorithm requires a BAM file containing standard (non-CCS) reads."
)
if options.diploid:
logging.warn("Diploid analysis not yet supported under Arrow model.")
# load parameters from file
if options.parametersFile:
logging.info("Loading model parameters from: ({0})".format(
options.parametersFile))
if not cc.LoadModels(options.parametersFile):
die("Arrow: unable to load parameters from: ({0})".format(
options.parametersFile))
# test available chemistries
supp = set(cc.SupportedChemistries())
logging.info("Found consensus models for: ({0})".format(", ".join(
sorted(supp))))
used = set([])
if options.parametersSpec != "auto":
logging.info("Overriding model selection with: ({0})".format(
options.parametersSpec))
if not cc.OverrideModel(options.parametersSpec):
die("Arrow: unable to override model with: ({0})".format(
options.parametersSpec))
used.add(options.parametersSpec)
else:
used.update(alnFile.sequencingChemistry)
unsupp = used - supp
if used - supp:
die("Arrow: unsupported chemistries found: ({0})".format(", ".join(
sorted(unsupp))))
# All arrow models require PW except P6 and the first S/P1-C1
for readGroup in alnFile.readGroupTable:
if set([readGroup["SequencingChemistry"]]) - set(
["P6-C4", "S/P1-C1/beta"]):
if ("Ipd" not in readGroup["BaseFeatures"]
or "PulseWidth" not in readGroup["BaseFeatures"]):
die("Arrow model requires missing base feature: IPD or PulseWidth"
)
logging.info("Using consensus models for: ({0})".format(", ".join(
sorted(used))))
return M.ArrowConfig(minMapQV=options.minMapQV,
noEvidenceConsensus=options.noEvidenceConsensusCall,
computeConfidence=(not options.fastMode),
minReadScore=options.minReadScore,
minHqRegionSnr=options.minHqRegionSnr,
minZScore=options.minZScore,
minAccuracy=options.minAccuracy)
def configure(options, alnFile):
if alnFile.readType != "standard":
raise U.IncompatibleDataException(
"The Arrow algorithm requires a BAM file containing standard (non-CCS) reads."
)
if options.diploid:
logging.warn("Diploid analysis not yet supported under Arrow model.")
return M.ArrowConfig(minMapQV=options.minMapQV,
noEvidenceConsensus=options.noEvidenceConsensusCall,
computeConfidence=(not options.fastMode))