Package picard.sam.markduplicates
Class SimpleMarkDuplicatesWithMateCigar
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
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- picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
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- picard.sam.markduplicates.MarkDuplicates
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- picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
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- 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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.sam.markduplicates.MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy, MarkDuplicates.DuplicateType
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Nested classes/interfaces inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
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Field Summary
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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
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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
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Fields inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
LOG, MAX_OPTICAL_DUPLICATE_SET_SIZE, OPTICAL_DUPLICATE_PIXEL_DISTANCE, opticalDuplicateFinder, READ_NAME_REGEX
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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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description SimpleMarkDuplicatesWithMateCigar()
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Methods inherited from class picard.sam.markduplicates.MarkDuplicates
areComparableForDuplicates, buildReadEnds, generateDuplicateIndexes, getReadDuplicateScore, handleChunk, markDuplicateFragments
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Methods inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
addReadToLibraryMetrics, addSingletonToCount, finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates
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Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation, setupOpticalDuplicateFinder
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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
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Method Detail
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doWork
protected int doWork()
Main work method.- Overrides:
doWork
in classMarkDuplicates
- Returns:
- program exit status.
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getDuplicateSetIterator
protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet> getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator, htsjdk.samtools.SAMRecordDuplicateComparator comparator)
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