Package picard.analysis
Class CollectMultipleMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CollectMultipleMetrics
Class that is designed to instantiate and execute multiple metrics programs that extend
SinglePassSamProgram while making only a single pass through the SAM file and supplying
each program with the records as it goes.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
static interface
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
boolean
int
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected String[]
Put any custom command-line validation in an override of this method.int
doWork()
Do the work after command line has been parsed.void
setProgramsToRun
(Collection<CollectMultipleMetrics.ProgramInterface> programsToRun) Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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ASSUME_SORTED
@Argument(shortName="AS", doc="If true (default), then the sort order in the header file will be ignored.") public boolean ASSUME_SORTED -
STOP_AFTER
@Argument(doc="Stop after processing N reads, mainly for debugging.") public int STOP_AFTER -
OUTPUT
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METRIC_ACCUMULATION_LEVEL
@Argument(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL -
FILE_EXTENSION
@Argument(shortName="EXT", doc="Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null", optional=true) public String FILE_EXTENSION -
PROGRAM
@Argument(doc="Set of metrics programs to apply during the pass through the SAM file.") public Set<CollectMultipleMetrics.Program> PROGRAM -
INTERVALS
@Argument(doc="An optional list of intervals to restrict analysis to. Only pertains to some of the PROGRAMs. Programs whose stand-alone CLP does not have an INTERVALS argument will silently ignore this argument.", optional=true) public File INTERVALS -
DB_SNP
@Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis by some PROGRAMs; PROGRAMs whose CLP doesn\'t allow for this argument will quietly ignore it.", optional=true) public File DB_SNP -
REF_FLAT
@Argument(doc="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat", optional=true) public File REF_FLAT -
IGNORE_SEQUENCE
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INCLUDE_UNPAIRED
@Argument(shortName="UNPAIRED", doc="Include unpaired reads in CollectSequencingArtifactMetrics. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored in CollectSequencingArtifactMetrics.") public boolean INCLUDE_UNPAIRED -
EXTRA_ARGUMENT
@Argument(doc="extra arguments to the various tools can be specified using the following format:<PROGRAM>::<ARGUMENT_AND_VALUE> where <PROGRAM> is one of the programs specified in PROGRAM, and <ARGUMENT_AND_VALUE> are the argument and value that you\'d like to specify as you would on the command line. For example, to change the HISTOGRAM_WIDTH in CollectInsertSizeMetrics to 200, use:\n \"EXTRA_ARGUMENT=CollectInsertSizeMetrics::HISTOGRAM_WIDTH=200\"\n or, in the new parser:--EXTRA_ARGUMENT \"CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 200\"\n (Quotes are required to avoid the shell from separating this into two arguments.) Note that the following arguments cannot be modified on a per-program level: INPUT, REFERENCE_SEQUENCE, ASSUME_SORTED, and STOP_AFTER. Providing them in an EXTRA_ARGUMENT will _not_ result in an error, but they will be silently ignored. ", optional=true) public List<String> EXTRA_ARGUMENT
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Constructor Details
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CollectMultipleMetrics
public CollectMultipleMetrics()
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Method Details
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customCommandLineValidation
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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setProgramsToRun
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum. This must be called before doWork(). -
doWork
public int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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