Package picard.sam.markduplicates.util
Class AbstractMarkDuplicatesCommandLineProgram
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- Direct Known Subclasses:
MarkDuplicates
,MarkDuplicatesWithMateCigar
public abstract class AbstractMarkDuplicatesCommandLineProgram
extends AbstractOpticalDuplicateFinderCommandLineProgram
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM/CRAM files.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic final class
Little class used to package up a header and an iterable/iterator. -
Field Summary
FieldsModifier and TypeFieldDescriptionhtsjdk.samtools.SAMFileHeader.SortOrder
boolean
Deprecated.htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
The program groups that have been seen during the course of examining the input records.protected final PGTagArgumentCollection
boolean
Fields inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
LOG, MAX_OPTICAL_DUPLICATE_SET_SIZE, OPTICAL_DUPLICATE_PIXEL_DISTANCE, opticalDuplicateFinder, READ_NAME_REGEX
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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic DuplicationMetrics
addReadToLibraryMetrics
(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.SAMFileHeader header, LibraryIdGenerator libraryIdGenerator, boolean flowMetrics) static void
addSingletonToCount
(LibraryIdGenerator libraryIdGenerator) static void
finalizeAndWriteMetrics
(LibraryIdGenerator libraryIdGenerator, htsjdk.samtools.metrics.MetricsFile<DuplicationMetrics, Double> metricsFile, File outputFile) Writes the metrics given by the libraryIdGenerator to the outputFile.getChainedPgIds
(htsjdk.samtools.SAMFileHeader outputHeader) We have to re-chain the program groups based on this algorithm.openInputs
(boolean eagerlyDecode) Since this may read its inputs more than once this method does all the opening and checking of the inputs.static void
trackOpticalDuplicates
(List<? extends ReadEnds> ends, ReadEnds keeper, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator) Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation, setupOpticalDuplicateFinder
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, doWork, 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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pgTagArgumentCollection
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INPUT
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OUTPUT
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METRICS_FILE
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REMOVE_DUPLICATES
@Argument(doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.") public boolean REMOVE_DUPLICATES -
ASSUME_SORTED
@Deprecated @Argument(shortName="AS", doc="If true, assume that the input file is coordinate sorted even if the header says otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead.", mutex="ASSUME_SORT_ORDER") public boolean ASSUME_SORTEDDeprecated. -
ASSUME_SORT_ORDER
@Argument(shortName="ASO", doc="If not null, assume that the input file has this order even if the header says otherwise.", optional=true, mutex="ASSUME_SORTED") public htsjdk.samtools.SAMFileHeader.SortOrder ASSUME_SORT_ORDER -
DUPLICATE_SCORING_STRATEGY
@Argument(shortName="DS", doc="The scoring strategy for choosing the non-duplicate among candidates.") public htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy DUPLICATE_SCORING_STRATEGY -
PROGRAM_RECORD_ID
@Argument(shortName="PG", doc="The program record ID for the @PG record(s) created by this program. Set to null to disable PG record creation. This string may have a suffix appended to avoid collision with other program record IDs.", optional=true) public String PROGRAM_RECORD_ID -
PROGRAM_GROUP_VERSION
@Argument(shortName="PG_VERSION", doc="Value of VN tag of PG record to be created. If not specified, the version will be detected automatically.", optional=true) public String PROGRAM_GROUP_VERSION -
PROGRAM_GROUP_COMMAND_LINE
@Argument(shortName="PG_COMMAND", doc="Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically.", optional=true) public String PROGRAM_GROUP_COMMAND_LINE -
PROGRAM_GROUP_NAME
@Argument(shortName="PG_NAME", doc="Value of PN tag of PG record to be created.") public String PROGRAM_GROUP_NAME -
COMMENT
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pgIdsSeen
The program groups that have been seen during the course of examining the input records.
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Constructor Details
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AbstractMarkDuplicatesCommandLineProgram
public AbstractMarkDuplicatesCommandLineProgram()
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Method Details
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getChainedPgIds
We have to re-chain the program groups based on this algorithm. This returns the map from existing program group ID to new program group ID. -
finalizeAndWriteMetrics
public static void finalizeAndWriteMetrics(LibraryIdGenerator libraryIdGenerator, htsjdk.samtools.metrics.MetricsFile<DuplicationMetrics, Double> metricsFile, File outputFile) Writes the metrics given by the libraryIdGenerator to the outputFile.- Parameters:
libraryIdGenerator
- ALibraryIdGenerator
object that contains the map from library toDuplicationMetrics
for that librarymetricsFile
- An emptyMetricsFile
object that will be filled, with "finalized" metrics and written out. It needs to be generated from a non-static context so that various commandline information is added to the header whenCommandLineProgram.getMetricsFile()
is called.outputFile
- The file to write the metrics to
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addReadToLibraryMetrics
public static DuplicationMetrics addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.SAMFileHeader header, LibraryIdGenerator libraryIdGenerator, boolean flowMetrics) -
openInputs
protected AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator openInputs(boolean eagerlyDecode) Since this may read its inputs more than once this method does all the opening and checking of the inputs. -
trackOpticalDuplicates
public static void trackOpticalDuplicates(List<? extends ReadEnds> ends, ReadEnds keeper, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator) Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram. Additionally sets the transient isOpticalDuplicate flag on each read end that is identified as an optical duplicate. -
addSingletonToCount
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