Package picard.sam.markduplicates

Class SimpleMarkDuplicatesWithMateCigar

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

picard.sam.markduplicates.MarkDuplicates

picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar

All Implemented Interfaces:

MarkDuplicatesHelper

Direct Known Subclasses:

UmiAwareMarkDuplicatesWithMateCigar

@DocumentedFeature
@ExperimentalFeature
public class SimpleMarkDuplicatesWithMateCigar
extends MarkDuplicates

This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator. Users should continue to use MarkDuplicates in general. The main motivation of this tool was the fact that MarkDuplicates has many, many, many useful test cases, but few unit tests for validating individual duplicate sets. To test the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator, the most expedient method was to write this tool and make sure it behaves similarly to MarkDuplicates. Not the best, I know, but good enough. NH 06/25/2015. See MarkDuplicates for more details.

Nested Class Summary

Nested classes/interfaces inherited from class picard.sam.markduplicates.MarkDuplicates

MarkDuplicates.DuplicateTaggingPolicy, MarkDuplicates.DuplicateType

Nested classes/interfaces inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator

Field Summary

Fields inherited from class picard.sam.markduplicates.MarkDuplicates

BARCODE_TAG, CLEAR_DT, DUPLEX_UMI, DUPLICATE_SET_INDEX_TAG, DUPLICATE_SET_SIZE_TAG, DUPLICATE_TYPE_LIBRARY, DUPLICATE_TYPE_SEQUENCING, DUPLICATE_TYPE_TAG, duplicateIndexes, flowBasedArguments, fragSort, libraryIdGenerator, MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP, MOLECULAR_IDENTIFIER_TAG, opticalDuplicateIndexes, pairSort, READ_ONE_BARCODE_TAG, READ_TWO_BARCODE_TAG, REMOVE_SEQUENCING_DUPLICATES, representativeReadIndicesForDuplicates, SORTING_COLLECTION_SIZE_RATIO, TAG_DUPLICATE_SET_MEMBERS, TAGGING_POLICY

Fields inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

ASSUME_SORT_ORDER, ASSUME_SORTED, COMMENT, DUPLICATE_SCORING_STRATEGY, INPUT, METRICS_FILE, OUTPUT, pgIdsSeen, pgTagArgumentCollection, PROGRAM_GROUP_COMMAND_LINE, PROGRAM_GROUP_NAME, PROGRAM_GROUP_VERSION, PROGRAM_RECORD_ID, 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, 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

Constructor Summary

Constructors

Constructor	Description
SimpleMarkDuplicatesWithMateCigar()

Method Summary

Modifier and Type	Method	Description
protected int	doWork()	Main work method.
protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet>	getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator, htsjdk.samtools.SAMRecordDuplicateComparator comparator)

Methods inherited from class picard.sam.markduplicates.MarkDuplicates

areComparableForDuplicates, buildReadEnds, generateDuplicateIndexes, getReadDuplicateScore, handleChunk, markDuplicateFragments

Methods inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

addReadToLibraryMetrics, addSingletonToCount, finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates

Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

customCommandLineValidation, setupOpticalDuplicateFinder

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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

Constructor Details

SimpleMarkDuplicatesWithMateCigar

public SimpleMarkDuplicatesWithMateCigar()

Method Details

doWork

protected int doWork()

Main work method.

Overrides:

doWork in class MarkDuplicates

Returns:

program exit status.

getDuplicateSetIterator

protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet> getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator,
 htsjdk.samtools.SAMRecordDuplicateComparator comparator)