def _add_common_chunk_options(p):
# Order matters!
add_debug_option(p)
add_max_nchunks_option(p)
p = _add_chunk_output_dir_option(p)
p = add_output_chunk_json_report_option(p)
return p
def add_options_to_parser(p):
"""
API function for extending main pbreport arg parser (independently of
tool contract interface).
"""
p_wrap = _get_parser_core()
p_wrap.arg_parser.parser = p
p.description = __doc__
add_debug_option(p)
_add_options_to_parser(p_wrap)
return p
def _get_more_options(parser):
"""
Advanced options that won't be exposed via tool contract interface.
"""
parser.add_argument('--outfile',
dest='outfile',
default=None,
help='Use this option to generate all possible output files. Argument here is the root filename of the output files.')
# FIXME: Need to add an extra check for this; it can only be used if --useLDA flag is set.
parser.add_argument('--m5Cgff',
dest='m5Cgff',
default=None,
help='Name of output GFF file containing m5C scores')
# FIXME: Make sure that this is specified if --useLDA flag is set.
parser.add_argument('--m5Cclassifer',
dest='m5Cclassifier',
default=None,
help='Specify csv file containing a 127 x 2 matrix')
parser.add_argument('--csv_h5',
dest='csv_h5',
default=None,
help='Name of csv output to be written in hdf5 format.')
parser.add_argument('--pickle',
dest='pickle',
default=None,
help='Name of output pickle file.')
parser.add_argument('--summary_h5',
dest='summary_h5',
default=None,
help='Name of output summary h5 file.')
parser.add_argument('--ms_csv',
dest='ms_csv',
default=None,
help='Multisite detection CSV file.')
# Calculation options:
parser.add_argument('--control',
dest='control',
default=None,
type=validateNoneOrFile,
help='cmph.h5 file containing a control sample. Tool will perform a case-control analysis')
# Temporary addition to test LDA for Ca5C detection:
parser.add_argument('--useLDA',
action="store_true",
dest='useLDA',
default=False,
help='Set this flag to debug LDA for m5C/Ca5C detection')
# Parameter options:
parser.add_argument('--paramsPath',
dest='paramsPath',
default=_getResourcePath(),
type=validateNoneOrDir,
help='Directory containing in-silico trained model for each chemistry')
parser.add_argument('--minCoverage',
dest='minCoverage',
default=3,
type=int,
help='Minimum coverage required to call a modified base')
parser.add_argument('--maxQueueSize',
dest='maxQueueSize',
default=20,
type=int,
help='Max Queue Size')
parser.add_argument('--maxCoverage',
dest='maxCoverage',
type=int, default=-1,
help='Maximum coverage to use at each site')
parser.add_argument('--mapQvThreshold',
dest='mapQvThreshold',
type=float,
default=-1.0)
parser.add_argument('--ipdModel',
dest='ipdModel',
default=None,
help='Alternate synthetic IPD model HDF5 file')
parser.add_argument('--modelIters',
dest='modelIters',
type=int,
default=-1,
help='[Internal] Number of GBM model iteration to use')
parser.add_argument('--cap_percentile',
dest='cap_percentile',
type=float,
default=99.0,
help='Global IPD percentile to cap IPDs at')
parser.add_argument("--methylMinCov",
type=int,
dest='methylMinCov',
default=10,
help="Do not try to estimate methylFraction unless coverage is at least this.")
parser.add_argument("--identifyMinCov",
type=int,
dest='identifyMinCov',
default=5,
help="Do not try to identify the modification type unless coverage is at least this.")
parser.add_argument("--maxAlignments",
type=int,
dest="maxAlignments",
default=1500,
help="Maximum number of alignments to use for a given window")
# Computation management options:
parser.add_argument("-w", "--referenceWindow", "--referenceWindows",
"--refContigs", # backwards compatibility
type=str,
dest='referenceWindowsAsString',
default=None,
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup[:refStart-refEnd] " + \
"(default: entire reference).")
def slurpWindowFile(fname):
return ",".join(map(str.strip, open(fname).readlines()))
parser.add_argument("--refContigIndex", type=int, dest='refContigIndex', default=-1,
help="For debugging purposes only - rather than enter a reference contig name, simply enter an index" )
parser.add_argument("-W", "--referenceWindowsFile",
"--refContigsFile", # backwards compatibility
type=slurpWindowFile,
dest='referenceWindowsAsString',
default=None,
help="A file containing reference window designations, one per line")
parser.add_argument("--skipUnrecognizedContigs",
type=bool,
default=False,
help="Whether to skip, or abort, unrecognized contigs in the -w/-W flags")
# FIXME shouldn't it always do this?
parser.add_argument("--alignmentSetRefWindows",
action="store_true",
dest="referenceWindowsFromAlignment",
help="Use refWindows in dataset")
# Debugging help options:
parser.add_argument("--threaded", "-T",
action="store_true",
dest="threaded",
default=False,
help="Run threads instead of processes (for debugging purposes only)")
parser.add_argument("--profile",
action="store_true",
dest="doProfiling",
default=False,
help="Enable Python-level profiling (using cProfile).")
add_debug_option(parser)
parser.add_argument("--seed",
action="store",
dest="randomSeed",
type=int,
default=None,
help="Random seed (for development and debugging purposes only)")
parser.add_argument("--referenceStride", action="store", type=int,
default=1000,
help="Size of reference window in internal "+
"parallelization. For testing purposes only.")
return parser
def add_options_to_argument_parser(parser):
def canonicalizedFilePath(path):
return os.path.abspath(os.path.expanduser(path))
basics = parser.add_argument_group("Basic required options")
basics.add_argument(
"inputFilename",
type=canonicalizedFilePath,
help="The input cmp.h5 or BAM alignment file")
basics.add_argument(
"--referenceFilename", "--reference", "-r",
action="store",
dest="referenceFilename",
type=canonicalizedFilePath,
required=True,
help="The filename of the reference FASTA file")
basics.add_argument(
"-o", "--outputFilename",
dest="outputFilenames",
required=True,
type=str,
action="append",
default=[],
help="The output filename(s), as a comma-separated list." + \
"Valid output formats are .fa/.fasta, .fq/.fastq, .gff, .vcf")
parallelism = parser.add_argument_group("Parallelism")
parallelism.add_argument(
"-j", "--numWorkers",
dest="numWorkers",
type=int,
default=1,
help="The number of worker processes to be used")
filtering = parser.add_argument_group("Output filtering")
filtering.add_argument(
"--minConfidence", "-q",
action="store",
dest="minConfidence",
type=int,
default=Constants.DEFAULT_MIN_CONFIDENCE,
help="The minimum confidence for a variant call to be output to variants.{gff,vcf}")
filtering.add_argument(
"--minCoverage", "-x",
action="store",
dest="minCoverage",
default=Constants.DEFAULT_MIN_COVERAGE,
type=int,
help="The minimum site coverage that must be achieved for variant calls and " + \
"consensus to be calculated for a site.")
filtering.add_argument(
"--noEvidenceConsensusCall",
action="store",
choices=["nocall", "reference", "lowercasereference"],
default="lowercasereference",
help="The consensus base that will be output for sites with no effective coverage.")
readSelection = parser.add_argument_group("Read selection/filtering")
readSelection.add_argument(
"--coverage", "-X",
action="store",
dest="coverage",
type=int,
default=Constants.DEFAULT_MAX_COVERAGE,
help="A designation of the maximum coverage level to be used for analysis." + \
" Exact interpretation is algorithm-specific.")
readSelection.add_argument(
"--minMapQV", "-m",
action="store",
dest="minMapQV",
type=float,
default=Constants.DEFAULT_MIN_MAPQV,
help="The minimum MapQV for reads that will be used for analysis.")
# Since the reference isn't loaded at options processing time, we
# can't grok the referenceWindow specified until later. We store
# it as a string (referenceWindowsAsString) and it will later be
# interpreted and stored as a proper window tuple (referenceWindow)
readSelection.add_argument(
"--referenceWindow", "--referenceWindows", "-w",
action="store",
dest="referenceWindowsAsString",
type=str,
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup:refStart-refEnd " + \
"(default: entire reference).",
default=None)
readSelection.add_argument(
"--alignmentSetRefWindows",
action="store_true",
dest="referenceWindowsFromAlignment",
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup:refStart-refEnd " + \
"will be pulled from the alignment file.",
default=False)
def slurpWindowFile(fname):
return ",".join(map(str.strip, open(fname).readlines()))
readSelection.add_argument(
"--referenceWindowsFile", "-W",
action="store",
dest="referenceWindowsAsString",
type=slurpWindowFile,
help="A file containing reference window designations, one per line",
default=None)
readSelection.add_argument(
"--barcode",
type=str,
dest="_barcode",
help="Only process reads with the given barcode name.")
def parseReadStratum(s):
rs = map(int, s.split("/"))
assert len(rs) == 2
assert rs[0] < rs[1]
return rs
readSelection.add_argument(
"--readStratum",
help="A string of the form 'n/N', where n, and N are integers, 0 <= n < N, designating" \
" that the reads are to be deterministically split into N strata of roughly even" \
" size, and stratum n is to be used for variant and consensus calling. This is" \
" mostly useful for Quiver development.",
dest="readStratum",
default=None,
type=parseReadStratum)
readSelection.add_argument(
"--minReadScore",
action="store",
dest="minReadScore",
type=float,
default=Constants.DEFAULT_MIN_READSCORE,
help="The minimum ReadScore for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minSnr",
action="store",
dest="minHqRegionSnr",
type=float,
default=Constants.DEFAULT_MIN_HQREGIONSNR,
help="The minimum acceptable signal-to-noise over all channels for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minZScore",
action="store",
dest="minZScore",
type=float,
default=Constants.DEFAULT_MIN_ZSCORE,
help="The minimum acceptable z-score for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minAccuracy",
action="store",
dest="minAccuracy",
type=float,
default=Constants.DEFAULT_MIN_ACCURACY,
help="The minimum acceptable window-global alignment accuracy for reads that will be used for the analysis (arrow-only).")
algorithm = parser.add_argument_group("Algorithm and parameter settings")
algorithm.add_argument(
"--algorithm",
action="store",
dest="algorithm",
type=str,
choices=Constants.ALGORITHM_CHOICES,
default=Constants.DEFAULT_ALGORITHM)
algorithm.add_argument(
"--parametersFile", "-P",
dest="parametersFile",
type=str,
default=None,
help="Parameter set filename (such as ArrowParameters.json or " + \
"QuiverParameters.ini), or directory D such that either " + \
"D/*/GenomicConsensus/QuiverParameters.ini, " + \
"or D/GenomicConsensus/QuiverParameters.ini, is found. In the " + \
"former case, the lexically largest path is chosen.")
algorithm.add_argument(
"--parametersSpec", "-p",
action="store",
dest="parametersSpec",
type=str,
default="auto",
help="Name of parameter set (chemistry.model) to select from the " + \
"parameters file, or just the name of the chemistry, in which " + \
"case the best available model is chosen. Default is 'auto', " + \
"which selects the best parameter set from the alignment data")
algorithm.add_argument(
"--maskRadius",
dest="maskRadius",
type=int,
default=Constants.DEFAULT_MASK_RADIUS,
help="Radius of window to use when excluding local regions for " + \
"exceeding maskMinErrorRate, where 0 disables any filtering (arrow-only).")
algorithm.add_argument(
"--maskErrorRate",
dest="maskErrorRate",
type=float,
default=Constants.DEFAULT_MASK_ERROR_RATE,
help="Maximum local error rate before the local region defined by " + \
"maskRadius is excluded from polishing (arrow-only).")
debugging = parser.add_argument_group("Verbosity and debugging/profiling")
add_debug_option(debugging)
debugging.add_argument(
"--notrace",
action="store_true",
dest="notrace",
default=False,
help="Suppress stacktrace for exceptions (to simplify testing)")
debugging.add_argument(
"--pdbAtStartup",
action="store_true",
dest="pdbAtStartup",
default=False,
help="Drop into Python debugger at startup (requires ipdb)")
debugging.add_argument(
"--profile",
action="store_true",
dest="doProfiling",
default=False,
help="Enable Python-level profiling (using cProfile).")
debugging.add_argument(
"--annotateGFF",
action="store_true",
help="Augment GFF variant records with additional information")
debugging.add_argument(
"--reportEffectiveCoverage",
action="store_true",
help="Additionally record the *post-filtering* coverage at variant sites")
advanced = parser.add_argument_group("Advanced configuration options")
advanced.add_argument(
"--diploid",
action="store_true",
help="Enable detection of heterozygous variants (experimental)")
advanced.add_argument(
"--queueSize", "-Q",
action="store",
dest="queueSize",
type=int,
default=200)
advanced.add_argument(
"--threaded", "-T",
action="store_true",
dest="threaded",
default=False,
help="Run threads instead of processes (for debugging purposes only)")
advanced.add_argument(
"--referenceChunkSize", "-C",
action="store",
dest="referenceChunkSize",
type=int,
default=500)
advanced.add_argument(
"--fancyChunking",
default=True,
action="store_true",
help="Adaptive reference chunking designed to handle coverage cutouts better")
advanced.add_argument(
"--simpleChunking",
dest="fancyChunking",
action="store_false",
help="Disable adaptive reference chunking")
advanced.add_argument(
"--referenceChunkOverlap",
action="store",
dest="referenceChunkOverlap",
type=int,
default=5)
advanced.add_argument(
"--autoDisableHdf5ChunkCache",
action="store",
type=int,
default=500,
help="Disable the HDF5 chunk cache when the number of datasets in the cmp.h5 " + \
"exceeds the given threshold")
advanced.add_argument(
"--aligner", "-a",
action="store",
choices=["affine", "simple"],
default="affine",
help="The pairwise alignment algorithm that will be used to produce variant calls" \
" from the consensus (Quiver only).")
advanced.add_argument(
"--refineDinucleotideRepeats",
dest="refineDinucleotideRepeats",
action="store_true",
help="Require quiver maximum likelihood search to try one less/more repeat copy in" \
" dinucleotide repeats, which seem to be the most frequent cause of suboptimal" \
" convergence (getting trapped in local optimum) (Quiver only)")
advanced.add_argument(
"--noRefineDinucleotideRepeats",
dest="refineDinucleotideRepeats",
action="store_false",
help="Disable dinucleotide refinement")
advanced.set_defaults(refineDinucleotideRepeats=True)
advanced.add_argument(
"--fast",
dest="fastMode",
action="store_true",
help="Cut some corners to run faster. Unsupported!")
advanced.add_argument(
"--skipUnrecognizedContigs",
action="store_true",
help="Do not abort when told to process a reference window (via -w/--referenceWindow[s]) " \
"that has no aligned coverage. Outputs emptyish files if there are no remaining " \
"non-degenerate windows. Only intended for use by smrtpipe scatter/gather.")
return parser
def constructOptionParser(parser, C=Constants, ccs_mode=False):
"""
Add PBAlignRunner arguments to the parser.
"""
# save reference to PbParser
p = parser
tcp = p.tool_contract_parser
parser = parser.arg_parser.parser
#parser.argument_default = argparse.SUPPRESS
parser.formatter_class = argparse.ArgumentDefaultsHelpFormatter
add_debug_option(parser)
# Optional input.
input_group = parser.add_argument_group("Optional input arguments")
input_group.add_argument("--regionTable",
dest="regionTable",
type=str,
default=None,
action="store",
help="Specify a region table for filtering reads.")
input_group.add_argument("--configFile",
dest="configFile",
default=None,
type=str,
action="store",
help="Specify a set of user-defined argument values.")
helpstr = "When input reads are in fasta format and output is a cmp.h5\n" + \
"this option can specify pls.h5 or bas.h5 or \n" + \
"FOFN files from which pulse metrics can be loaded for Quiver."
input_group.add_argument("--pulseFile",
dest="pulseFile",
default=None,
type=str,
action="store",
help=helpstr)
# Chose an aligner.
align_group = parser.add_argument_group("Alignment options")
helpstr = "Select an aligorithm from {0}.\n".format(ALGORITHM_CANDIDATES)
align_group.add_argument("--algorithm",
dest="algorithm",
type=str,
action="store",
choices=ALGORITHM_CANDIDATES,
default=ALGORITHM_CANDIDATES[0],
help=helpstr)
# Aligner options.
helpstr = "The maximum number of matches of each read to the \n" + \
"reference sequence that will be evaluated."
align_group.add_argument("--maxHits",
dest="maxHits",
type=int,
default=None, # Set as None instead of a real number.
action="store",
help=helpstr)
helpstr = "The minimum anchor size defines the length of the read\n" + \
"that must match against the reference sequence."
align_group.add_argument("--minAnchorSize",
dest="minAnchorSize",
type=int,
default=None, # Set as None to avoid conflicts with
# --algorithmOptions
action="store",
help=helpstr)
# Aligner options: Use ccs or not?
helpstr = "Map the ccsSequence to the genome first, then align\n" + \
"subreads to the interval that the CCS reads mapped to.\n" + \
" useccs: only maps subreads that span the length of\n" + \
" the template.\n" + \
" useccsall: maps all subreads.\n" + \
" useccsdenovo: maps ccs only."
align_group.add_argument("--useccs",
type=str,
choices=["useccs", "useccsall", "useccsdenovo"],
action="store",
default=None,
help=helpstr)
helpstr = "Do not split reads into subreads even if subread \n" + \
"regions are available."
align_group.add_argument("--noSplitSubreads",
dest="noSplitSubreads",
default=DEFAULT_OPTIONS["noSplitSubreads"],
action="store_true",
help=helpstr)
if not ccs_mode:
tcp.add_boolean(C.NO_SPLIT_ID, "noSplitSubreads",
default=DEFAULT_OPTIONS["noSplitSubreads"],
name="Align unsplit polymerase reads",
description=helpstr)
helpstr = "Map subreads of a ZMW to the same genomic location.\n"
align_group.add_argument("--concordant",
dest="concordant",
default=DEFAULT_OPTIONS["concordant"],
action="store_true",
help=helpstr)
if not ccs_mode:
tcp.add_boolean(C.CONCORDANT_ID, "concordant",
default=DEFAULT_OPTIONS["concordant"],
name="Concordant alignment",
description="Map subreads of a ZMW to the same genomic location")
helpstr = "Number of threads."
align_group.add_argument("--nproc",
type=int,
dest="nproc",
default=DEFAULT_OPTIONS["nproc"],
#default=15,
action="store",
help=helpstr)
align_group.add_argument("--algorithmOptions",
type=str,
dest="algorithmOptions",
default=None,
action="append",
help="Pass alignment options through.")
# XXX the arguments used in SMRTpipe 2.3 are different from the defaults
# for the command line tool
tcp.add_str(C.ALGORITHM_OPTIONS_ID, "algorithmOptions",
default=C.ALGORITHM_OPTIONS_DEFAULT,
name="Algorithm options",
description="List of space-separated arguments passed to BLASR")
# Filtering criteria and hit policy.
filter_group = parser.add_argument_group("Filter criteria options")
helpstr = "The maximum allowed percentage divergence of a read \n" + \
"from the reference sequence."
filter_group.add_argument("--maxDivergence",
dest="maxDivergence",
type=float,
default=DEFAULT_OPTIONS["maxDivergence"],
#default=30,
action="store",
help=helpstr)
helpstr = "The minimum concordance of alignments that\n" + \
"will be evaluated."
filter_group.add_argument("--minAccuracy",
dest="minAccuracy",
type=float,
default=DEFAULT_OPTIONS["minAccuracy"],
#default=70,
action="store",
help=helpstr)
tcp.add_float(C.MIN_ACCURACY_ID, "minAccuracy",
default=DEFAULT_OPTIONS["minAccuracy"],
name="Min. concordance",
description="Minimum required alignment concordance")
helpstr = "The minimum aligned read length of alignments that\n" + \
"will be evaluated."
filter_group.add_argument("--minLength",
dest="minLength",
type=int,
default=DEFAULT_OPTIONS["minLength"],
action="store",
help=helpstr)
tcp.add_int(C.MIN_LENGTH_ID, "minLength",
default=DEFAULT_OPTIONS["minLength"],
name="Min. length",
description="Minimum required alignment length")
#helpstr = "Specify a score function for evaluating alignments.\n"
#helpstr += " alignerscore : aligner's score in the SAM tag 'as'.\n"
#helpstr += " editdist : edit distance between read and reference.\n"
#helpstr += " blasrscore : blasr's default score function.\n"
#helpstr += "Default value is {0}.".format(DEFAULT_OPTIONS["scoreFunction"])
#filter_group.add_argument("--scoreFunction",
# dest="scoreFunction",
# type=str,
# choices=SCOREFUNCTION_CANDIDATES,
# default=DEFAULT_OPTIONS["scoreFunction"],
# action="store",
# help=helpstr)
#" userscore : user-defined score matrix (by -scoreMatrix).\n")
#parser.add_argument("--scoreMatrix",
# dest="scoreMatrix",
# type=str,
# default=None,
# help=
# "Specify a user-defined score matrix for "
# "scoring reads.The matrix\n"+\
# "is in the format\n"
# " ACGTN\n"
# " A abcde\n"
# " C fghij\n"
# " G klmno\n"
# " T pqrst\n"
# " N uvwxy\n"
# ". The values a...y should be input as a "
# "quoted space separated\n"
# "string: "a b c ... y". Lower scores are better,"
# "so matches\n"
# "should be less than mismatches e.g. a,g,m,s "
# "= -5 (match),\n"
# "mismatch = 6.\n")
filter_group.add_argument("--scoreCutoff",
dest="scoreCutoff",
type=int,
default=None,
action="store",
help="The worst score to output an alignment.\n")
helpstr = "Specify a policy for how to treat multiple hit\n" + \
" random : selects a random hit.\n" + \
" all : selects all hits.\n" + \
" allbest : selects all the best score hits.\n" + \
" randombest: selects a random hit from all best score hits.\n" + \
" leftmost : selects a hit which has the best score and the\n" + \
" smallest mapping coordinate in any reference.\n"
filter_group.add_argument("--hitPolicy",
dest="hitPolicy",
type=str,
choices=HITPOLICY_CANDIDATES,
default=DEFAULT_OPTIONS["hitPolicy"],
action="store",
help=helpstr)
tcp.add_str(C.HIT_POLICY_ID, "hitPolicy",
default=DEFAULT_OPTIONS["hitPolicy"],
name="Hit policy",
description=helpstr)
helpstr = "If specified, do not report adapter-only hits using\n" + \
"annotations with the reference entry."
filter_group.add_argument("--filterAdapterOnly",
dest="filterAdapterOnly",
default=DEFAULT_OPTIONS["filterAdapterOnly"],
action="store_true",
help=helpstr)
# Output.
# CMP H5 output has been deprecated, let's hide associated options.
cmph5_group = parser.add_argument_group("Options for cmp.h5")
helpstr = "Specify the ReadType attribute in the cmp.h5 output.\n"
cmph5_group.add_argument("--readType",
dest="readType",
type=str,
action="store",
default=DEFAULT_OPTIONS["readType"],
help=argparse.SUPPRESS)
helpstr = "The output cmp.h5 file which will be sorted, loaded\n" + \
"with pulse QV information, and repacked, so that it \n" + \
"can be consumed by quiver directly. This requires\n" + \
"the input file to be in PacBio bas/pls.h5 format,\n" + \
"and --useccs must be None."
cmph5_group.add_argument("--forQuiver",
dest="forQuiver",
action="store_true",
default=DEFAULT_OPTIONS["forQuiver"],
help=argparse.SUPPRESS)
helpstr = "Similar to --forQuiver, the only difference is that \n" + \
"--useccs can be specified."
cmph5_group.add_argument("--loadQVs",
dest="loadQVs",
action="store_true",
default=DEFAULT_OPTIONS["loadQVs"],
help=argparse.SUPPRESS)
helpstr = "Load pulse information using -byread option instead\n" + \
"of -bymetric. Only works when --forQuiver or \n" + \
"--loadQVs are set."
cmph5_group.add_argument("--byread",
dest="byread",
action="store_true",
default=DEFAULT_OPTIONS["byread"],
help=argparse.SUPPRESS)
helpstr = "Load the specified (comma-delimited list of) metrics\n" + \
"instead of the default metrics required by quiver.\n" + \
"This option only works when --forQuiver or \n" + \
"--loadQVs are set."
cmph5_group.add_argument("--metrics",
dest="metrics",
type=str,
action="store",
default=DEFAULT_OPTIONS["metrics"],
help=argparse.SUPPRESS)
# Miscellaneous.
misc_group = parser.add_argument_group("Miscellaneous options")
helpstr = "Output names of unaligned reads to specified file."
misc_group.add_argument("--unaligned",
dest="unaligned",
type=str,
action="store",
default=DEFAULT_OPTIONS["unaligned"],
help=helpstr)
helpstr = "Initialize the random number generator with a none-zero \n" + \
"integer. Zero means that current system time is used.\n"
misc_group.add_argument("--seed",
dest="seed",
type=int,
default=DEFAULT_OPTIONS["seed"],
action="store",
help=helpstr)
helpstr = "Specify a directory for saving temporary files.\n"
misc_group.add_argument("--tmpDir",
dest="tmpDir",
type=str,
action="store",
default=DEFAULT_OPTIONS["tmpDir"],
help=helpstr)
# Keep all temporary & intermediate files.
misc_group.add_argument("--keepTmpFiles",
dest="keepTmpFiles",
action="store_true",
default=False,
help=argparse.SUPPRESS)
return parser
def _f(p):
add_debug_option(p)
f = __gather_options(output_file_msg, input_file_msg, validate_file, chunk_key_func)
return f(p)
def _get_more_options(parser):
"""
Advanced options that won't be exposed via tool contract interface.
"""
parser.add_argument(
'--outfile',
dest='outfile',
default=None,
help=
'Use this option to generate all possible output files. Argument here is the root filename of the output files.'
)
# FIXME: Need to add an extra check for this; it can only be used if --useLDA flag is set.
parser.add_argument('--m5Cgff',
dest='m5Cgff',
default=None,
help='Name of output GFF file containing m5C scores')
# FIXME: Make sure that this is specified if --useLDA flag is set.
parser.add_argument('--m5Cclassifer',
dest='m5Cclassifier',
default=None,
help='Specify csv file containing a 127 x 2 matrix')
parser.add_argument(
'--csv_h5',
dest='csv_h5',
default=None,
help='Name of csv output to be written in hdf5 format.')
parser.add_argument('--pickle',
dest='pickle',
default=None,
help='Name of output pickle file.')
parser.add_argument('--summary_h5',
dest='summary_h5',
default=None,
help='Name of output summary h5 file.')
parser.add_argument('--ms_csv',
dest='ms_csv',
default=None,
help='Multisite detection CSV file.')
# Calculation options:
parser.add_argument(
'--control',
dest='control',
default=None,
type=validateNoneOrFile,
help=
'cmph.h5 file containing a control sample. Tool will perform a case-control analysis'
)
# Temporary addition to test LDA for Ca5C detection:
parser.add_argument(
'--useLDA',
action="store_true",
dest='useLDA',
default=False,
help='Set this flag to debug LDA for m5C/Ca5C detection')
# Parameter options:
defaultParamsPathSpec = _getResourcePathSpec()
parser.add_argument(
'--paramsPath',
dest='paramsPath',
default=defaultParamsPathSpec,
type=validateNoneOrPathSpec,
help=
'List of :-delimited directory paths containing in-silico trained models (default is "%s")'
% defaultParamsPathSpec)
parser.add_argument(
'--minCoverage',
dest='minCoverage',
default=3,
type=int,
help='Minimum coverage required to call a modified base')
parser.add_argument('--maxQueueSize',
dest='maxQueueSize',
default=20,
type=int,
help='Max Queue Size')
parser.add_argument('--maxCoverage',
dest='maxCoverage',
type=int,
default=-1,
help='Maximum coverage to use at each site')
parser.add_argument('--mapQvThreshold',
dest='mapQvThreshold',
type=float,
default=-1.0)
parser.add_argument('--ipdModel',
dest='ipdModel',
default=None,
type=validateNoneOrFile,
help='Alternate synthetic IPD model HDF5 file')
parser.add_argument('--modelIters',
dest='modelIters',
type=int,
default=-1,
help='[Internal] Number of GBM model iteration to use')
parser.add_argument('--cap_percentile',
dest='cap_percentile',
type=float,
default=99.0,
help='Global IPD percentile to cap IPDs at')
parser.add_argument(
"--methylMinCov",
type=int,
dest='methylMinCov',
default=10,
help=
"Do not try to estimate methylFraction unless coverage is at least this."
)
parser.add_argument(
"--identifyMinCov",
type=int,
dest='identifyMinCov',
default=5,
help=
"Do not try to identify the modification type unless coverage is at least this."
)
parser.add_argument(
"--maxAlignments",
type=int,
dest="maxAlignments",
default=1500,
help="Maximum number of alignments to use for a given window")
# Computation management options:
parser.add_argument("-w", "--referenceWindow", "--referenceWindows",
"--refContigs", # backwards compatibility
type=str,
dest='referenceWindowsAsString',
default=None,
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup[:refStart-refEnd] " + \
"(default: entire reference).")
def slurpWindowFile(fname):
return ",".join(map(str.strip, open(fname).readlines()))
parser.add_argument(
"--refContigIndex",
type=int,
dest='refContigIndex',
default=-1,
help=
"For debugging purposes only - rather than enter a reference contig name, simply enter an index"
)
parser.add_argument(
"-W",
"--referenceWindowsFile",
"--refContigsFile", # backwards compatibility
type=slurpWindowFile,
dest='referenceWindowsAsString',
default=None,
help="A file containing reference window designations, one per line")
parser.add_argument(
"--skipUnrecognizedContigs",
type=bool,
default=False,
help=
"Whether to skip, or abort, unrecognized contigs in the -w/-W flags")
# FIXME shouldn't it always do this?
parser.add_argument("--alignmentSetRefWindows",
action="store_true",
dest="referenceWindowsFromAlignment",
help="Use refWindows in dataset")
# Debugging help options:
parser.add_argument(
"--threaded",
"-T",
action="store_true",
dest="threaded",
default=False,
help="Run threads instead of processes (for debugging purposes only)")
parser.add_argument("--profile",
action="store_true",
dest="doProfiling",
default=False,
help="Enable Python-level profiling (using cProfile).")
add_debug_option(parser)
parser.add_argument(
"--seed",
action="store",
dest="randomSeed",
type=int,
default=None,
help="Random seed (for development and debugging purposes only)")
parser.add_argument("--referenceStride",
action="store",
type=int,
default=1000,
help="Size of reference window in internal " +
"parallelization. For testing purposes only.")
return parser
def constructOptionParser(parser, C=Constants, ccs_mode=False):
"""
Add PBAlignRunner arguments to the parser.
"""
# save reference to PbParser
p = parser
tcp = p.tool_contract_parser
parser = parser.arg_parser.parser
#parser.argument_default = argparse.SUPPRESS
parser.formatter_class = argparse.ArgumentDefaultsHelpFormatter
add_debug_option(parser)
# Optional input.
input_group = parser.add_argument_group("Optional input arguments")
input_group.add_argument(
"--regionTable",
dest="regionTable",
type=str,
default=None,
action="store",
help="Specify a region table for filtering reads.")
input_group.add_argument(
"--configFile",
dest="configFile",
default=None,
type=str,
action="store",
help="Specify a set of user-defined argument values.")
helpstr = "When input reads are in fasta format and output is a cmp.h5\n" + \
"this option can specify pls.h5 or bas.h5 or \n" + \
"FOFN files from which pulse metrics can be loaded for Quiver."
input_group.add_argument("--pulseFile",
dest="pulseFile",
default=None,
type=str,
action="store",
help=helpstr)
# Chose an aligner.
align_group = parser.add_argument_group("Alignment options")
helpstr = "Select an aligorithm from {0}.\n".format(ALGORITHM_CANDIDATES)
align_group.add_argument("--algorithm",
dest="algorithm",
type=str,
action="store",
choices=ALGORITHM_CANDIDATES,
default=ALGORITHM_CANDIDATES[0],
help=helpstr)
# Aligner options.
helpstr = "The maximum number of matches of each read to the \n" + \
"reference sequence that will be evaluated."
align_group.add_argument(
"--maxHits",
dest="maxHits",
type=int,
default=None, # Set as None instead of a real number.
action="store",
help=helpstr)
helpstr = "The minimum anchor size defines the length of the read\n" + \
"that must match against the reference sequence."
align_group.add_argument(
"--minAnchorSize",
dest="minAnchorSize",
type=int,
default=None, # Set as None to avoid conflicts with
# --algorithmOptions
action="store",
help=helpstr)
# Aligner options: Use ccs or not?
helpstr = "Map the ccsSequence to the genome first, then align\n" + \
"subreads to the interval that the CCS reads mapped to.\n" + \
" useccs: only maps subreads that span the length of\n" + \
" the template.\n" + \
" useccsall: maps all subreads.\n" + \
" useccsdenovo: maps ccs only."
align_group.add_argument("--useccs",
type=str,
choices=["useccs", "useccsall", "useccsdenovo"],
action="store",
default=None,
help=helpstr)
helpstr = "Do not split reads into subreads even if subread \n" + \
"regions are available."
align_group.add_argument("--noSplitSubreads",
dest="noSplitSubreads",
default=DEFAULT_OPTIONS["noSplitSubreads"],
action="store_true",
help=helpstr)
if not ccs_mode:
tcp.add_boolean(C.NO_SPLIT_ID,
"noSplitSubreads",
default=DEFAULT_OPTIONS["noSplitSubreads"],
name="Align unsplit polymerase reads",
description=helpstr)
helpstr = "Map subreads of a ZMW to the same genomic location.\n"
align_group.add_argument("--concordant",
dest="concordant",
default=DEFAULT_OPTIONS["concordant"],
action="store_true",
help=helpstr)
if not ccs_mode:
tcp.add_boolean(
C.CONCORDANT_ID,
"concordant",
default=DEFAULT_OPTIONS["concordant"],
name="Concordant alignment",
description="Map subreads of a ZMW to the same genomic location")
helpstr = "Number of threads."
align_group.add_argument(
"--nproc",
type=int,
dest="nproc",
default=DEFAULT_OPTIONS["nproc"],
#default=15,
action="store",
help=helpstr)
align_group.add_argument("--algorithmOptions",
type=str,
dest="algorithmOptions",
default=None,
action="append",
help="Pass alignment options through.")
# XXX the arguments used in SMRTpipe 2.3 are different from the defaults
# for the command line tool
tcp.add_str(
C.ALGORITHM_OPTIONS_ID,
"algorithmOptions",
default=C.ALGORITHM_OPTIONS_DEFAULT,
name="Algorithm options",
description="List of space-separated arguments passed to BLASR")
# Filtering criteria and hit policy.
filter_group = parser.add_argument_group("Filter criteria options")
helpstr = "The maximum allowed percentage divergence of a read \n" + \
"from the reference sequence."
filter_group.add_argument(
"--maxDivergence",
dest="maxDivergence",
type=float,
default=DEFAULT_OPTIONS["maxDivergence"],
#default=30,
action="store",
help=helpstr)
helpstr = "The minimum concordance of alignments that\n" + \
"will be evaluated."
filter_group.add_argument(
"--minAccuracy",
dest="minAccuracy",
type=float,
default=DEFAULT_OPTIONS["minAccuracy"],
#default=70,
action="store",
help=helpstr)
tcp.add_float(C.MIN_ACCURACY_ID,
"minAccuracy",
default=DEFAULT_OPTIONS["minAccuracy"],
name="Min. concordance",
description="Minimum required alignment concordance")
helpstr = "The minimum aligned read length of alignments that\n" + \
"will be evaluated."
filter_group.add_argument("--minLength",
dest="minLength",
type=int,
default=DEFAULT_OPTIONS["minLength"],
action="store",
help=helpstr)
tcp.add_int(C.MIN_LENGTH_ID,
"minLength",
default=DEFAULT_OPTIONS["minLength"],
name="Min. length",
description="Minimum required alignment length")
#helpstr = "Specify a score function for evaluating alignments.\n"
#helpstr += " alignerscore : aligner's score in the SAM tag 'as'.\n"
#helpstr += " editdist : edit distance between read and reference.\n"
#helpstr += " blasrscore : blasr's default score function.\n"
#helpstr += "Default value is {0}.".format(DEFAULT_OPTIONS["scoreFunction"])
#filter_group.add_argument("--scoreFunction",
# dest="scoreFunction",
# type=str,
# choices=SCOREFUNCTION_CANDIDATES,
# default=DEFAULT_OPTIONS["scoreFunction"],
# action="store",
# help=helpstr)
#" userscore : user-defined score matrix (by -scoreMatrix).\n")
#parser.add_argument("--scoreMatrix",
# dest="scoreMatrix",
# type=str,
# default=None,
# help=
# "Specify a user-defined score matrix for "
# "scoring reads.The matrix\n"+\
# "is in the format\n"
# " ACGTN\n"
# " A abcde\n"
# " C fghij\n"
# " G klmno\n"
# " T pqrst\n"
# " N uvwxy\n"
# ". The values a...y should be input as a "
# "quoted space separated\n"
# "string: "a b c ... y". Lower scores are better,"
# "so matches\n"
# "should be less than mismatches e.g. a,g,m,s "
# "= -5 (match),\n"
# "mismatch = 6.\n")
filter_group.add_argument("--scoreCutoff",
dest="scoreCutoff",
type=int,
default=None,
action="store",
help="The worst score to output an alignment.\n")
helpstr = "Specify a policy for how to treat multiple hit\n" + \
" random : selects a random hit.\n" + \
" all : selects all hits.\n" + \
" allbest : selects all the best score hits.\n" + \
" randombest: selects a random hit from all best score hits.\n" + \
" leftmost : selects a hit which has the best score and the\n" + \
" smallest mapping coordinate in any reference.\n"
filter_group.add_argument("--hitPolicy",
dest="hitPolicy",
type=str,
choices=HITPOLICY_CANDIDATES,
default=DEFAULT_OPTIONS["hitPolicy"],
action="store",
help=helpstr)
tcp.add_str(C.HIT_POLICY_ID,
"hitPolicy",
default=DEFAULT_OPTIONS["hitPolicy"],
name="Hit policy",
description=helpstr)
helpstr = "If specified, do not report adapter-only hits using\n" + \
"annotations with the reference entry."
filter_group.add_argument("--filterAdapterOnly",
dest="filterAdapterOnly",
default=DEFAULT_OPTIONS["filterAdapterOnly"],
action="store_true",
help=helpstr)
# Output.
# CMP H5 output has been deprecated, let's hide associated options.
cmph5_group = parser.add_argument_group("Options for cmp.h5")
helpstr = "Specify the ReadType attribute in the cmp.h5 output.\n"
cmph5_group.add_argument("--readType",
dest="readType",
type=str,
action="store",
default=DEFAULT_OPTIONS["readType"],
help=argparse.SUPPRESS)
helpstr = "The output cmp.h5 file which will be sorted, loaded\n" + \
"with pulse QV information, and repacked, so that it \n" + \
"can be consumed by quiver directly. This requires\n" + \
"the input file to be in PacBio bas/pls.h5 format,\n" + \
"and --useccs must be None."
cmph5_group.add_argument("--forQuiver",
dest="forQuiver",
action="store_true",
default=DEFAULT_OPTIONS["forQuiver"],
help=argparse.SUPPRESS)
helpstr = "Similar to --forQuiver, the only difference is that \n" + \
"--useccs can be specified."
cmph5_group.add_argument("--loadQVs",
dest="loadQVs",
action="store_true",
default=DEFAULT_OPTIONS["loadQVs"],
help=argparse.SUPPRESS)
helpstr = "Load pulse information using -byread option instead\n" + \
"of -bymetric. Only works when --forQuiver or \n" + \
"--loadQVs are set."
cmph5_group.add_argument("--byread",
dest="byread",
action="store_true",
default=DEFAULT_OPTIONS["byread"],
help=argparse.SUPPRESS)
helpstr = "Load the specified (comma-delimited list of) metrics\n" + \
"instead of the default metrics required by quiver.\n" + \
"This option only works when --forQuiver or \n" + \
"--loadQVs are set."
cmph5_group.add_argument("--metrics",
dest="metrics",
type=str,
action="store",
default=DEFAULT_OPTIONS["metrics"],
help=argparse.SUPPRESS)
# Miscellaneous.
misc_group = parser.add_argument_group("Miscellaneous options")
helpstr = "Output names of unaligned reads to specified file."
misc_group.add_argument("--unaligned",
dest="unaligned",
type=str,
action="store",
default=DEFAULT_OPTIONS["unaligned"],
help=helpstr)
helpstr = "Initialize the random number generator with a none-zero \n" + \
"integer. Zero means that current system time is used.\n"
misc_group.add_argument("--seed",
dest="seed",
type=int,
default=DEFAULT_OPTIONS["seed"],
action="store",
help=helpstr)
helpstr = "Specify a directory for saving temporary files.\n"
misc_group.add_argument("--tmpDir",
dest="tmpDir",
type=str,
action="store",
default=DEFAULT_OPTIONS["tmpDir"],
help=helpstr)
# Keep all temporary & intermediate files.
misc_group.add_argument("--keepTmpFiles",
dest="keepTmpFiles",
action="store_true",
default=False,
help=argparse.SUPPRESS)
return parser
def _f(p):
add_debug_option(p)
f = __gather_options(output_file_msg, input_file_msg, validate_file,
chunk_key_func)
return f(p)
def add_options_to_argument_parser(parser):
def canonicalizedFilePath(path):
return os.path.abspath(os.path.expanduser(path))
basics = parser.add_argument_group("Basic required options")
basics.add_argument(
"inputFilename",
type=canonicalizedFilePath,
help="The input cmp.h5 or BAM alignment file")
basics.add_argument(
"--referenceFilename", "--reference", "-r",
action="store",
dest="referenceFilename",
type=canonicalizedFilePath,
required=True,
help="The filename of the reference FASTA file")
basics.add_argument(
"-o", "--outputFilename",
dest="outputFilenames",
required=True,
type=str,
action="append",
default=[],
help="The output filename(s), as a comma-separated list." + \
"Valid output formats are .fa/.fasta, .fq/.fastq, .gff, .vcf")
parallelism = parser.add_argument_group("Parallelism")
parallelism.add_argument(
"-j", "--numWorkers",
dest="numWorkers",
type=int,
default=1,
help="The number of worker processes to be used")
filtering = parser.add_argument_group("Output filtering")
filtering.add_argument(
"--minConfidence", "-q",
action="store",
dest="minConfidence",
type=int,
default=Constants.DEFAULT_MIN_CONFIDENCE,
help="The minimum confidence for a variant call to be output to variants.{gff,vcf}")
filtering.add_argument(
"--minCoverage", "-x",
action="store",
dest="minCoverage",
default=Constants.DEFAULT_MIN_COVERAGE,
type=int,
help="The minimum site coverage that must be achieved for variant calls and " + \
"consensus to be calculated for a site.")
filtering.add_argument(
"--noEvidenceConsensusCall",
action="store",
choices=["nocall", "reference", "lowercasereference"],
default="lowercasereference",
help="The consensus base that will be output for sites with no effective coverage.")
readSelection = parser.add_argument_group("Read selection/filtering")
readSelection.add_argument(
"--coverage", "-X",
action="store",
dest="coverage",
type=int,
default=Constants.DEFAULT_MAX_COVERAGE,
help="A designation of the maximum coverage level to be used for analysis." + \
" Exact interpretation is algorithm-specific.")
readSelection.add_argument(
"--minMapQV", "-m",
action="store",
dest="minMapQV",
type=float,
default=Constants.DEFAULT_MIN_MAPQV,
help="The minimum MapQV for reads that will be used for analysis.")
# Since the reference isn't loaded at options processing time, we
# can't grok the referenceWindow specified until later. We store
# it as a string (referenceWindowsAsString) and it will later be
# interpreted and stored as a proper window tuple (referenceWindow)
readSelection.add_argument(
"--referenceWindow", "--referenceWindows", "-w",
action="store",
dest="referenceWindowsAsString",
type=str,
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup:refStart-refEnd " + \
"(default: entire reference).",
default=None)
readSelection.add_argument(
"--alignmentSetRefWindows",
action="store_true",
dest="referenceWindowsFromAlignment",
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup:refStart-refEnd " + \
"will be pulled from the alignment file.",
default=False)
def slurpWindowFile(fname):
return ",".join(map(str.strip, open(fname).readlines()))
readSelection.add_argument(
"--referenceWindowsFile", "-W",
action="store",
dest="referenceWindowsAsString",
type=slurpWindowFile,
help="A file containing reference window designations, one per line",
default=None)
readSelection.add_argument(
"--barcode",
type=str,
dest="_barcode",
help="Only process reads with the given barcode name.")
def parseReadStratum(s):
rs = map(int, s.split("/"))
assert len(rs) == 2
assert rs[0] < rs[1]
return rs
readSelection.add_argument(
"--readStratum",
help="A string of the form 'n/N', where n, and N are integers, 0 <= n < N, designating" \
" that the reads are to be deterministically split into N strata of roughly even" \
" size, and stratum n is to be used for variant and consensus calling. This is" \
" mostly useful for Quiver development.",
dest="readStratum",
default=None,
type=parseReadStratum)
readSelection.add_argument(
"--minReadScore",
action="store",
dest="minReadScore",
type=float,
default=Constants.DEFAULT_MIN_READSCORE,
help="The minimum ReadScore for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minSnr",
action="store",
dest="minHqRegionSnr",
type=float,
default=Constants.DEFAULT_MIN_HQREGIONSNR,
help="The minimum acceptable signal-to-noise over all channels for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minZScore",
action="store",
dest="minZScore",
type=float,
default=Constants.DEFAULT_MIN_ZSCORE,
help="The minimum acceptable z-score for reads that will be used for analysis (arrow-only).")
readSelection.add_argument(
"--minAccuracy",
action="store",
dest="minAccuracy",
type=float,
default=Constants.DEFAULT_MIN_ACCURACY,
help="The minimum acceptable window-global alignment accuracy for reads that will be used for the analysis (arrow-only).")
algorithm = parser.add_argument_group("Algorithm and parameter settings")
algorithm.add_argument(
"--algorithm",
action="store",
dest="algorithm",
type=str,
choices=Constants.ALGORITHM_CHOICES,
default=Constants.DEFAULT_ALGORITHM)
algorithm.add_argument(
"--parametersFile", "-P",
dest="parametersFile",
type=str,
default=None,
help="Parameter set filename (such as ArrowParameters.json or " + \
"QuiverParameters.ini), or directory D such that either " + \
"D/*/GenomicConsensus/QuiverParameters.ini, " + \
"or D/GenomicConsensus/QuiverParameters.ini, is found. In the " + \
"former case, the lexically largest path is chosen.")
algorithm.add_argument(
"--parametersSpec", "-p",
action="store",
dest="parametersSpec",
type=str,
default="auto",
help="Name of parameter set (chemistry.model) to select from the " + \
"parameters file, or just the name of the chemistry, in which " + \
"case the best available model is chosen. Default is 'auto', " + \
"which selects the best parameter set from the alignment data")
algorithm.add_argument(
"--maskRadius",
dest="maskRadius",
type=int,
default=Constants.DEFAULT_MASK_RADIUS,
help="Radius of window to use when excluding local regions for " + \
"exceeding maskMinErrorRate, where 0 disables any filtering (arrow-only).")
algorithm.add_argument(
"--maskErrorRate",
dest="maskErrorRate",
type=float,
default=Constants.DEFAULT_MASK_ERROR_RATE,
help="Maximum local error rate before the local region defined by " + \
"maskRadius is excluded from polishing (arrow-only).")
debugging = parser.add_argument_group("Verbosity and debugging/profiling")
add_debug_option(debugging)
debugging.add_argument(
"--notrace",
action="store_true",
dest="notrace",
default=False,
help="Suppress stacktrace for exceptions (to simplify testing)")
debugging.add_argument(
"--pdbAtStartup",
action="store_true",
dest="pdbAtStartup",
default=False,
help="Drop into Python debugger at startup (requires ipdb)")
debugging.add_argument(
"--profile",
action="store_true",
dest="doProfiling",
default=False,
help="Enable Python-level profiling (using cProfile).")
debugging.add_argument(
"--dumpEvidence", "-d",
dest="dumpEvidence",
nargs="?",
default=None,
const="variants",
choices=["variants", "all", "outliers"])
debugging.add_argument(
"--evidenceDirectory",
default="evidence_dump")
debugging.add_argument(
"--annotateGFF",
action="store_true",
help="Augment GFF variant records with additional information")
debugging.add_argument(
"--reportEffectiveCoverage",
action="store_true",
help="Additionally record the *post-filtering* coverage at variant sites")
advanced = parser.add_argument_group("Advanced configuration options")
advanced.add_argument(
"--diploid",
action="store_true",
help="Enable detection of heterozygous variants (experimental)")
advanced.add_argument(
"--queueSize", "-Q",
action="store",
dest="queueSize",
type=int,
default=200)
advanced.add_argument(
"--threaded", "-T",
action="store_true",
dest="threaded",
default=False,
help="Run threads instead of processes (for debugging purposes only)")
advanced.add_argument(
"--referenceChunkSize", "-C",
action="store",
dest="referenceChunkSize",
type=int,
default=500)
advanced.add_argument(
"--fancyChunking",
default=True,
action="store_true",
help="Adaptive reference chunking designed to handle coverage cutouts better")
advanced.add_argument(
"--simpleChunking",
dest="fancyChunking",
action="store_false",
help="Disable adaptive reference chunking")
advanced.add_argument(
"--referenceChunkOverlap",
action="store",
dest="referenceChunkOverlap",
type=int,
default=5)
advanced.add_argument(
"--autoDisableHdf5ChunkCache",
action="store",
type=int,
default=500,
help="Disable the HDF5 chunk cache when the number of datasets in the cmp.h5 " + \
"exceeds the given threshold")
advanced.add_argument(
"--aligner", "-a",
action="store",
choices=["affine", "simple"],
default="affine",
help="The pairwise alignment algorithm that will be used to produce variant calls" \
" from the consensus (Quiver only).")
advanced.add_argument(
"--refineDinucleotideRepeats",
dest="refineDinucleotideRepeats",
action="store_true",
help="Require quiver maximum likelihood search to try one less/more repeat copy in" \
" dinucleotide repeats, which seem to be the most frequent cause of suboptimal" \
" convergence (getting trapped in local optimum) (Quiver only)")
advanced.add_argument(
"--noRefineDinucleotideRepeats",
dest="refineDinucleotideRepeats",
action="store_false",
help="Disable dinucleotide refinement")
advanced.set_defaults(refineDinucleotideRepeats=True)
advanced.add_argument(
"--fast",
dest="fastMode",
action="store_true",
help="Cut some corners to run faster. Unsupported!")
advanced.add_argument(
"--skipUnrecognizedContigs",
action="store_true",
help="Do not abort when told to process a reference window (via -w/--referenceWindow[s]) " \
"that has no aligned coverage. Outputs emptyish files if there are no remaining " \
"non-degenerate windows. Only intended for use by smrtpipe scatter/gather.")
return parser
def _example_parser():
p = get_default_argparser("1.0.0", "Example Mock Parser")
p = CU.add_debug_option(p)
p.add_argument('example_file', type=str, help="No testing of existence")
return p
def add_args_run_diagnstic(p):
_add_required_preset_xml_option(p)
add_debug_option(p)
_add_output_dir_option(p)
_add_simple_mode_option(p)
return p
