org.broadinstitute.hellbender.cmdline.argumentcollections

Class MarkDuplicatesSparkArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection

All Implemented Interfaces:

java.io.Serializable

public final class MarkDuplicatesSparkArgumentCollection
extends java.lang.Object
implements java.io.Serializable

An argument collection for use with tools that mark optical duplicates.

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Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DO_NOT_MARK_UNMAPPED_MATES_LONG_NAME
boolean	dontMarkUnmappedMates
static java.lang.String	DUPLICATE_TAGGING_POLICY_LONG_NAME
MarkDuplicatesScoringStrategy	duplicatesScoringStrategy
static java.lang.String	REMOVE_ALL_DUPLICATE_READS
static java.lang.String	REMOVE_SEQUENCING_DUPLICATE_READS
boolean	removeAllDuplicates
boolean	removeSequencingDuplicates
MarkDuplicates.DuplicateTaggingPolicy	taggingPolicy

Constructor Summary

Constructors

Constructor and Description
MarkDuplicatesSparkArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

DO_NOT_MARK_UNMAPPED_MATES_LONG_NAME

public static final java.lang.String DO_NOT_MARK_UNMAPPED_MATES_LONG_NAME

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Constant Field Values

DUPLICATE_TAGGING_POLICY_LONG_NAME

public static final java.lang.String DUPLICATE_TAGGING_POLICY_LONG_NAME

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Constant Field Values

REMOVE_ALL_DUPLICATE_READS

public static final java.lang.String REMOVE_ALL_DUPLICATE_READS

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Constant Field Values

REMOVE_SEQUENCING_DUPLICATE_READS

public static final java.lang.String REMOVE_SEQUENCING_DUPLICATE_READS

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Constant Field Values

duplicatesScoringStrategy

@Argument(shortName="DS",
          fullName="duplicate-scoring-strategy",
          doc="The scoring strategy for choosing the non-duplicate among candidates.")
public MarkDuplicatesScoringStrategy duplicatesScoringStrategy

dontMarkUnmappedMates

@Argument(fullName="do-not-mark-unmapped-mates",
          doc="Enabling this option will mean unmapped mates of duplicate marked reads will not be marked as duplicates.")
public boolean dontMarkUnmappedMates

taggingPolicy

@Argument(fullName="duplicate-tagging-policy",
          doc="Determines how duplicate types are recorded in the DT optional attribute.",
          optional=true,
          mutex={"remove-all-duplicates","remove-sequencing-duplicates"})
public MarkDuplicates.DuplicateTaggingPolicy taggingPolicy

removeAllDuplicates

@Argument(fullName="remove-all-duplicates",
          doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.",
          mutex={"duplicate-tagging-policy","remove-sequencing-duplicates"},
          optional=true)
public boolean removeAllDuplicates

removeSequencingDuplicates

@Argument(fullName="remove-sequencing-duplicates",
          doc="If true do not write optical/sequencing duplicates to the output file instead of writing them with appropriate flags set.",
          mutex={"duplicate-tagging-policy","remove-all-duplicates"},
          optional=true)
public boolean removeSequencingDuplicates

Constructor Detail

MarkDuplicatesSparkArgumentCollection

public MarkDuplicatesSparkArgumentCollection()