UmiAwareMarkDuplicatesWithMateCigar (picard 2.7.1 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
  - - picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
    - - picard.sam.markduplicates.MarkDuplicates
      - picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
        
        picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar

```
public class UmiAwareMarkDuplicatesWithMateCigar
extends SimpleMarkDuplicatesWithMateCigar
```
This is a simple tool to mark duplicates making use of UMIs in the reads. It makes use of the fact that duplicate sets with UMIs can be broken up into subsets based on information contained in the UMI. Since UMIs may contain sequencing errors, this tool allows for UMIs that are different but within a given edit distance to be considered to be part of the same duplicate set. Users should continue to use MarkDuplicates in general, the main motivation for this tool is to provide a way to mark duplicates using information from UMIs.

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
Modifier and Type Field and Description

boolean ALLOW_MISSING_UMIS

String ASSIGNED_UMI_TAG

int MAX_EDIT_DISTANCE_TO_JOIN

String UMI_TAG_NAME
- Fields inherited from class picard.sam.markduplicates.MarkDuplicates
  BARCODE_TAG, DUPLICATE_TYPE_LIBRARY, DUPLICATE_TYPE_SEQUENCING, DUPLICATE_TYPE_TAG, libraryIdGenerator, MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP, READ_ONE_BARCODE_TAG, READ_TWO_BARCODE_TAG, REMOVE_SEQUENCING_DUPLICATES, SORTING_COLLECTION_SIZE_RATIO, 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, 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, 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_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field and Description
`boolean`	`ALLOW_MISSING_UMIS`
`String`	`ASSIGNED_UMI_TAG`
`int`	`MAX_EDIT_DISTANCE_TO_JOIN`
`String`	`UMI_TAG_NAME`

Constructor Summary

Constructors
Constructor and Description

UmiAwareMarkDuplicatesWithMateCigar()

Constructors
Constructor and Description
`UmiAwareMarkDuplicatesWithMateCigar()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet>`	`getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator, htsjdk.samtools.SAMRecordDuplicateComparator comparator)`

Methods inherited from class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
doWork, main

Methods inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates

Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
customCommandLineValidation, setupOpticalDuplicateFinder

Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_EDIT_DISTANCE_TO_JOIN

@Option(shortName="MAX_EDIT_DISTANCE_TO_JOIN",
        doc="Largest edit distance that UMIs must have in order to be considered as coming from distinct source molecules.",
        optional=true)
public int MAX_EDIT_DISTANCE_TO_JOIN

UMI_TAG_NAME

@Option(shortName="UMI_TAG_NAME",
        doc="Tag name to use for UMI",
        optional=true)
public String UMI_TAG_NAME

ASSIGNED_UMI_TAG

@Option(shortName="ASSIGNED_UMI_TAG",
        doc="Tag name to use for assigned UMI",
        optional=true)
public String ASSIGNED_UMI_TAG

ALLOW_MISSING_UMIS

@Option(doc="Allow for missing UMIs if data doesn\'t have UMIs.  This option is intended to be used only for testing the code.  Use SimpleMarkDuplicatesWithMateCigar if data has missing UMIs.",
        optional=true)
public boolean ALLOW_MISSING_UMIS

Constructor Detail
- UmiAwareMarkDuplicatesWithMateCigar
```
public UmiAwareMarkDuplicatesWithMateCigar()
```

Method Detail

getDuplicateSetIterator

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

Overrides:: getDuplicateSetIterator in class SimpleMarkDuplicatesWithMateCigar

Class UmiAwareMarkDuplicatesWithMateCigar

Nested Class Summary

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

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

Field Summary

Fields inherited from class picard.sam.markduplicates.MarkDuplicates

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

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

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar

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

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

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

MAX_EDIT_DISTANCE_TO_JOIN

UMI_TAG_NAME

ASSIGNED_UMI_TAG

ALLOW_MISSING_UMIS

Constructor Detail

UmiAwareMarkDuplicatesWithMateCigar

Method Detail

getDuplicateSetIterator