Package picard.analysis
Class CollectRrbsMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CollectRrbsMetrics
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well
as CpG sites across all reads in the input BAM/SAM file.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
int
static final String
double
int
int
static final String
static final String
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, 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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected String[]
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.protected ReferenceArgumentCollection
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
@Argument(doc="The SAM/BAM/CRAM file containing aligned reads. Must be coordinate sorted", shortName="I") public File INPUT -
METRICS_FILE_PREFIX
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MINIMUM_READ_LENGTH
@Argument(doc="Minimum read length") public int MINIMUM_READ_LENGTH -
C_QUALITY_THRESHOLD
@Argument(doc="Threshold for base quality of a C base before it is considered") public int C_QUALITY_THRESHOLD -
NEXT_BASE_QUALITY_THRESHOLD
@Argument(doc="Threshold for quality of a base next to a C before the C base is considered") public int NEXT_BASE_QUALITY_THRESHOLD -
MAX_MISMATCH_RATE
@Argument(doc="Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1") public double MAX_MISMATCH_RATE -
SEQUENCE_NAMES
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ASSUME_SORTED
@Argument(shortName="AS", doc="If true, assume that the input file is coordinate sorted even if the header says otherwise.") public boolean ASSUME_SORTED -
METRIC_ACCUMULATION_LEVEL
@Argument(shortName="LEVEL", doc="The level(s) at which to accumulate metrics. ") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL -
DETAIL_FILE_EXTENSION
- See Also:
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SUMMARY_FILE_EXTENSION
- See Also:
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PDF_FILE_EXTENSION
- See Also:
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Constructor Details
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CollectRrbsMetrics
public CollectRrbsMetrics()
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Method Details
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makeReferenceArgumentCollection
- Overrides:
makeReferenceArgumentCollection
in classCommandLineProgram
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doWork
protected 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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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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