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 files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator Little class used to package up a header and an iterable/iterator.

Field Summary

Fields

Modifier and Type	Field and Description
htsjdk.samtools.SAMFileHeader.SortOrder	ASSUME_SORT_ORDER
boolean	ASSUME_SORTED Deprecated.
java.util.List<java.lang.String>	COMMENT
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy	DUPLICATE_SCORING_STRATEGY
java.util.List<java.lang.String>	INPUT
java.io.File	METRICS_FILE
java.io.File	OUTPUT
protected java.util.Set<java.lang.String>	pgIdsSeen The program groups that have been seen during the course of examining the input records.
protected PGTagArgumentCollection	pgTagArgumentCollection
java.lang.String	PROGRAM_GROUP_COMMAND_LINE
java.lang.String	PROGRAM_GROUP_NAME
java.lang.String	PROGRAM_GROUP_VERSION
java.lang.String	PROGRAM_RECORD_ID
boolean	REMOVE_DUPLICATES

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, 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

Constructor Summary

Constructors

Constructor and Description
AbstractMarkDuplicatesCommandLineProgram()

Method Summary

Modifier and Type	Method and Description
static void	addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec, DuplicationMetrics metrics)
static DuplicationMetrics	addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.SAMFileHeader header, LibraryIdGenerator libraryIdGenerator)
static void	addSingletonToCount(LibraryIdGenerator libraryIdGenerator)
static void	finalizeAndWriteMetrics(LibraryIdGenerator libraryIdGenerator, htsjdk.samtools.metrics.MetricsFile<DuplicationMetrics,java.lang.Double> metricsFile, java.io.File outputFile) Writes the metrics given by the libraryIdGenerator to the outputFile.
protected java.util.Map<java.lang.String,java.lang.String>	getChainedPgIds(htsjdk.samtools.SAMFileHeader outputHeader) We have to re-chain the program groups based on this algorithm.
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.
static void	trackOpticalDuplicates(java.util.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

doWork, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

pgTagArgumentCollection

@ArgumentCollection
protected final PGTagArgumentCollection pgTagArgumentCollection

INPUT

@Argument(shortName="I",
          doc="One or more input SAM or BAM files to analyze. Must be coordinate sorted.")
public java.util.List<java.lang.String> INPUT

OUTPUT

@Argument(shortName="O",
          doc="The output file to write marked records to")
public java.io.File OUTPUT

METRICS_FILE

@Argument(shortName="M",
          doc="File to write duplication metrics to")
public java.io.File METRICS_FILE

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_SORTED

Deprecated.

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 java.lang.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 java.lang.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 java.lang.String PROGRAM_GROUP_COMMAND_LINE

PROGRAM_GROUP_NAME

@Argument(shortName="PG_NAME",
          doc="Value of PN tag of PG record to be created.")
public java.lang.String PROGRAM_GROUP_NAME

COMMENT

@Argument(shortName="CO",
          doc="Comment(s) to include in the output file\'s header.",
          optional=true)
public java.util.List<java.lang.String> COMMENT

pgIdsSeen

protected final java.util.Set<java.lang.String> pgIdsSeen

The program groups that have been seen during the course of examining the input records.

Constructor Detail

AbstractMarkDuplicatesCommandLineProgram

public AbstractMarkDuplicatesCommandLineProgram()

Method Detail

getChainedPgIds

protected java.util.Map<java.lang.String,java.lang.String> getChainedPgIds(htsjdk.samtools.SAMFileHeader outputHeader)

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,java.lang.Double> metricsFile,
                                           java.io.File outputFile)

Writes the metrics given by the libraryIdGenerator to the outputFile.

Parameters:

libraryIdGenerator - A LibraryIdGenerator object that contains the map from library to DuplicationMetrics for that library

metricsFile - An empty MetricsFile 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 when CommandLineProgram.getMetricsFile() is called.

outputFile - The file to write the metrics to

addReadToLibraryMetrics

public static DuplicationMetrics addReadToLibraryMetrics(htsjdk.samtools.SAMRecord rec,
                                                         htsjdk.samtools.SAMFileHeader header,
                                                         LibraryIdGenerator libraryIdGenerator)

addDuplicateReadToMetrics

public static void addDuplicateReadToMetrics(htsjdk.samtools.SAMRecord rec,
                                             DuplicationMetrics metrics)

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(java.util.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

public static void addSingletonToCount(LibraryIdGenerator libraryIdGenerator)