Package picard.analysis
Class CollectRrbsMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.CollectRrbsMetrics
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@DocumentedFeature public class CollectRrbsMetrics extends CommandLineProgram
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 Classes Modifier and Type Class Description static class
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
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Field Summary
Fields Modifier and Type Field Description boolean
ASSUME_SORTED
int
C_QUALITY_THRESHOLD
static String
DETAIL_FILE_EXTENSION
File
INPUT
double
MAX_MISMATCH_RATE
Set<MetricAccumulationLevel>
METRIC_ACCUMULATION_LEVEL
String
METRICS_FILE_PREFIX
int
MINIMUM_READ_LENGTH
int
NEXT_BASE_QUALITY_THRESHOLD
static String
PDF_FILE_EXTENSION
Set<String>
SEQUENCE_NAMES
static String
SUMMARY_FILE_EXTENSION
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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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectRrbsMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
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
makeReferenceArgumentCollection()
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="The BAM or SAM file containing aligned reads. Must be coordinate sorted", shortName="I") public File INPUT
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METRICS_FILE_PREFIX
@Argument(doc="Base name for output files", shortName="M") public String METRICS_FILE_PREFIX
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MINIMUM_READ_LENGTH
@Argument(doc="Minimum read length") public int MINIMUM_READ_LENGTH
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C_QUALITY_THRESHOLD
@Argument(doc="Threshold for base quality of a C base before it is considered") public int C_QUALITY_THRESHOLD
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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
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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
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SEQUENCE_NAMES
@Argument(doc="Set of sequence names to consider, if not specified all sequences will be used", optional=true) public Set<String> 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
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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
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DETAIL_FILE_EXTENSION
public static final String DETAIL_FILE_EXTENSION
- See Also:
- Constant Field Values
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SUMMARY_FILE_EXTENSION
public static final String SUMMARY_FILE_EXTENSION
- See Also:
- Constant Field Values
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PDF_FILE_EXTENSION
public static final String PDF_FILE_EXTENSION
- See Also:
- Constant Field Values
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Method Detail
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makeReferenceArgumentCollection
protected ReferenceArgumentCollection 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
protected String[] 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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