ReadBaseStratification (gatk 4.1.7.0 API)

java.lang.Object
- picard.sam.SamErrorMetric.ReadBaseStratification

```
public class ReadBaseStratification
extends java.lang.Object
```
Classes, methods, and enums that deal with the stratification of read bases and reference information.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`ReadBaseStratification.BinnedReadCycleStratifier` Stratifies into quintiles of read cycle.
`static class`	`ReadBaseStratification.CigarOperatorsInReadStratifier` Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
`static class`	`ReadBaseStratification.CollectionStratifier` A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
`static class`	`ReadBaseStratification.Consensus` Types of consensus reads as determined by the number of duplicates used from first and second strands.
`static class`	`ReadBaseStratification.ConsensusStratifier` Stratify by tags used during duplex and single index consensus calling.
`static class`	`ReadBaseStratification.CycleBin` An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
`static class`	`ReadBaseStratification.FlowCellTileStratifier` Stratifies base into their read's tile which is parsed from the read-name.
`static class`	`ReadBaseStratification.GCContentStratifier` A stratifier that uses GC (of the read) to stratify.
`static class`	`ReadBaseStratification.IndelLengthStratifier` Stratifies according to the length of an insertion or deletion.
`static class`	`ReadBaseStratification.IndelsInReadStratifier` Stratifies according to the number of indel bases (from CIGAR string) that the read has.
`static class`	`ReadBaseStratification.LongShortHomopolymer`
`static class`	`ReadBaseStratification.LongShortHomopolymerStratifier` Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
`static class`	`ReadBaseStratification.MismatchesInReadStratifier` Stratifies according to the overall mismatches (from `SAMTag.NM`) that the read has against the reference, NOT including the current base.
`static class`	`ReadBaseStratification.NsInReadStratifier` Stratify by the number of Ns found in the read.
`static class`	`ReadBaseStratification.PairOrientation` An enum for holding a reads read-pair's Orientation (i.e.
`static class`	`ReadBaseStratification.PairStratifier<T extends java.lang.Comparable<T>,R extends java.lang.Comparable<R>>` A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
`static class`	`ReadBaseStratification.ProperPaired` An enum to hold information about the "properness" of a read pair
`static class`	`ReadBaseStratification.ReadDirection` An enum for holding the direction for a read (positive strand or negative strand
`static class`	`ReadBaseStratification.ReadOrdinality` An enum to hold the ordinality of a read
`static interface`	`ReadBaseStratification.RecordAndOffsetStratifier<T extends java.lang.Comparable<T>>` The main interface for a stratifier.

Field Summary

Fields
Modifier and Type	Field and Description
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>`	`baseCycleStratifier` Get the one-based cycle number of the base, taking the direction of the read into account
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Byte>`	`baseQualityStratifier` Stratifies into the base-quality of the base under consideration
`static htsjdk.samtools.util.Lazy<ReadBaseStratification.PairStratifier<ReadBaseStratification.LongShortHomopolymer,Pair<java.lang.Character,java.lang.Character>>>`	`binnedHomopolymerStratifier` Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.
`static ReadBaseStratification.BinnedReadCycleStratifier`	`binnedReadCycleStratifier` Stratifies into quintiles of read cycle.
`static ReadBaseStratification.ConsensusStratifier`	`consensusStratifier` Stratify by tags used during duplex and single index consensus calling.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character>`	`currentReadBaseStratifier` Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
`static ReadBaseStratification.CigarOperatorsInReadStratifier`	`deletionsInReadStratifier` Stratify by Deletions in the read cigars.
`static ReadBaseStratification.FlowCellTileStratifier`	`flowCellTileStratifier` Stratifies base into their read's tile which is parsed from the read-name.
`static ReadBaseStratification.GCContentStratifier`	`gcContentStratifier` A stratifier that uses GC (of the read) to stratify.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>`	`homoPolymerLengthStratifier` Stratifies a base onto the length of the homopolymer preceding it (in the read direction).
`static ReadBaseStratification.PairStratifier<java.lang.Integer,Pair<java.lang.Character,java.lang.Character>>`	`homopolymerStratifier` Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.
`static ReadBaseStratification.IndelLengthStratifier`	`indelLengthStratifier` Stratifies into the number of bases in an insertion
`static ReadBaseStratification.IndelsInReadStratifier`	`indelsInReadStratifier` Stratify by Indels in the read cigars.
`static ReadBaseStratification.CigarOperatorsInReadStratifier`	`insertionsInReadStratifier` Stratify by Insertions in the read cigars.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>`	`insertLengthStratifier` Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>`	`mappingQualityStratifier` Stratifies into the mapping-quality of the read under consideration
`static ReadBaseStratification.MismatchesInReadStratifier`	`mismatchesInReadStratifier` Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character>`	`nextReadBaseStratifier` Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.
`static picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<java.lang.String>`	`nonStratifier` A constant stratifier which places all the reads into a single stratum.
`static int`	`NOT_ALIGNED_ERROR`
`static ReadBaseStratification.NsInReadStratifier`	`nsInReadStratifier` Stratify by the number of Ns found in the read.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.String>`	`oneBasePaddedContextStratifier` Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
`static ReadBaseStratification.PairStratifier<java.lang.Character,java.lang.Character>`	`postDiNucleotideStratifier` Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
`static ReadBaseStratification.PairStratifier<java.lang.Character,java.lang.Character>`	`preDiNucleotideStratifier` Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character>`	`previousReadBaseStratifier` Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
`static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadDirection>`	`readDirectionStratifier` Stratifies bases into their read's Direction (i.e.
`static picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<java.lang.String>`	`readgroupStratifier` Stratifies to the readgroup id of the read.
`static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadOrdinality>`	`readOrdinalityStratifier` Stratifies bases into their read's Ordinality (i.e.
`static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.PairOrientation>`	`readOrientationStratifier` Stratifies bases into their read-pair's Orientation (i.e.
`static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ProperPaired>`	`readPairednessStratifier` Stratifies bases into their read's Proper-pairedness
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character>`	`referenceBaseStratifier` Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>`	`softClipsLengthStratifier` Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
`static ReadBaseStratification.RecordAndOffsetStratifier<java.lang.String>`	`twoBasePaddedContextStratifier` Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer

Constructor Summary

Constructors
Constructor and Description

ReadBaseStratification()

Constructors
Constructor and Description
`ReadBaseStratification()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static htsjdk.samtools.CigarElement`	`getIndelElement(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset)`
`static <T extends java.lang.Comparable<T>,S extends java.lang.Comparable<S>> ReadBaseStratification.PairStratifier<T,S>`	`PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T> leftStratifier, ReadBaseStratification.RecordAndOffsetStratifier<S> rightStratifier, java.lang.String suffix)` A factory for generating "pair" stratifier instances from two stratifiers and a string
`static void`	`setGcCacheSize(int gcCacheSize)`
`static void`	`setLongHomopolymer(int longHomopolymer)` defaults to 6

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

- Field Detail
  - currentReadBaseStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character> currentReadBaseStratifier
```
    Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
  - previousReadBaseStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character> previousReadBaseStratifier
```
    Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
  - nextReadBaseStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character> nextReadBaseStratifier
```
    Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
  - referenceBaseStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Character> referenceBaseStratifier
```
    Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
  - postDiNucleotideStratifier
```
public static final ReadBaseStratification.PairStratifier<java.lang.Character,java.lang.Character> postDiNucleotideStratifier
```
    Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
  - preDiNucleotideStratifier
```
public static final ReadBaseStratification.PairStratifier<java.lang.Character,java.lang.Character> preDiNucleotideStratifier
```
    Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
  - homoPolymerLengthStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer> homoPolymerLengthStratifier
```
    Stratifies a base onto the length of the homopolymer preceding it (in the read direction). Read direction and only the preceding bases are taken into account (i.e. ignoring reference and current base).
  - homopolymerStratifier
```
public static final ReadBaseStratification.PairStratifier<java.lang.Integer,Pair<java.lang.Character,java.lang.Character>> homopolymerStratifier
```
    Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came. Read direction and only the preceding bases are taken into account.
  - binnedHomopolymerStratifier
```
public static final htsjdk.samtools.util.Lazy<ReadBaseStratification.PairStratifier<ReadBaseStratification.LongShortHomopolymer,Pair<java.lang.Character,java.lang.Character>>> binnedHomopolymerStratifier
```
    Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came. Read direction and only the preceding bases are taken into account.
    This is done with a Lazy wrapper since it requires access to LONG_HOMOPOLYMER which can be set with setLongHomopolymer(int).
  - oneBasePaddedContextStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.String> oneBasePaddedContextStratifier
```
    Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
  - twoBasePaddedContextStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.String> twoBasePaddedContextStratifier
```
    Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
  - nonStratifier
```
public static final picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<java.lang.String> nonStratifier
```
    A constant stratifier which places all the reads into a single stratum.
  - gcContentStratifier
```
public static final ReadBaseStratification.GCContentStratifier gcContentStratifier
```
    A stratifier that uses GC (of the read) to stratify. Since the reads are expected to be seen over and over again, the GC is cached
    Stratification happens into (integer) percents.
  - flowCellTileStratifier
```
public static final ReadBaseStratification.FlowCellTileStratifier flowCellTileStratifier
```
    Stratifies base into their read's tile which is parsed from the read-name.
  - readgroupStratifier
```
public static final picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<java.lang.String> readgroupStratifier
```
    Stratifies to the readgroup id of the read.
  - readOrdinalityStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadOrdinality> readOrdinalityStratifier
```
    Stratifies bases into their read's Ordinality (i.e. First or Second)
  - readPairednessStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ProperPaired> readPairednessStratifier
```
    Stratifies bases into their read's Proper-pairedness
  - readDirectionStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadDirection> readDirectionStratifier
```
    Stratifies bases into their read's Direction (i.e. forward or reverse)
  - readOrientationStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.PairOrientation> readOrientationStratifier
```
    Stratifies bases into their read-pair's Orientation (i.e. F1R2, F2R1, F1F2 or R1R2)
  - binnedReadCycleStratifier
```
public static final ReadBaseStratification.BinnedReadCycleStratifier binnedReadCycleStratifier
```
    Stratifies into quintiles of read cycle.
  - baseCycleStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer> baseCycleStratifier
```
    Get the one-based cycle number of the base, taking the direction of the read into account
  - insertLengthStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer> insertLengthStratifier
```
    Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
  - softClipsLengthStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer> softClipsLengthStratifier
```
    Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
  - baseQualityStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Byte> baseQualityStratifier
```
    Stratifies into the base-quality of the base under consideration
  - mappingQualityStratifier
```
public static final ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer> mappingQualityStratifier
```
    Stratifies into the mapping-quality of the read under consideration
  - mismatchesInReadStratifier
```
public static final ReadBaseStratification.MismatchesInReadStratifier mismatchesInReadStratifier
```
    Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
  - consensusStratifier
```
public static final ReadBaseStratification.ConsensusStratifier consensusStratifier
```
    Stratify by tags used during duplex and single index consensus calling.
  - nsInReadStratifier
```
public static final ReadBaseStratification.NsInReadStratifier nsInReadStratifier
```
    Stratify by the number of Ns found in the read. This is particularly useful for data that has been consensus-called (a process that can add 'N' bases when there is no consensus)
  - insertionsInReadStratifier
```
public static final ReadBaseStratification.CigarOperatorsInReadStratifier insertionsInReadStratifier
```
    Stratify by Insertions in the read cigars.
  - deletionsInReadStratifier
```
public static final ReadBaseStratification.CigarOperatorsInReadStratifier deletionsInReadStratifier
```
    Stratify by Deletions in the read cigars.
  - indelsInReadStratifier
```
public static final ReadBaseStratification.IndelsInReadStratifier indelsInReadStratifier
```
    Stratify by Indels in the read cigars.
  - indelLengthStratifier
```
public static final ReadBaseStratification.IndelLengthStratifier indelLengthStratifier
```
    Stratifies into the number of bases in an insertion
  - NOT_ALIGNED_ERROR
```
public static final int NOT_ALIGNED_ERROR
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - ReadBaseStratification
```
public ReadBaseStratification()
```
- Method Detail
  - setGcCacheSize
```
public static void setGcCacheSize(int gcCacheSize)
```
  - setLongHomopolymer
```
public static void setLongHomopolymer(int longHomopolymer)
```
    defaults to 6
  - PairStratifierFactory
```
public static <T extends java.lang.Comparable<T>,S extends java.lang.Comparable<S>> ReadBaseStratification.PairStratifier<T,S> PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T> leftStratifier,
                                                                                                                                                     ReadBaseStratification.RecordAndOffsetStratifier<S> rightStratifier,
                                                                                                                                                     java.lang.String suffix)
```
    A factory for generating "pair" stratifier instances from two stratifiers and a string
    
    Type Parameters:
    
    T - the type of the left Stratifier
    
    S - the type of the right Stratifier
    
    Parameters:
    
    leftStratifier - a RecordAndOffsetStratifier to use
    
    rightStratifier - a RecordAndOffsetStratifier ~~to use~~
    
    suffix - the suffix to use for the new stratifier
    
    Returns:
    
    an instance of PairStratifier> that will stratify according to both leftStratifier and rightStratifier
  getIndelElement
  
  public static htsjdk.samtools.CigarElement getIndelElement(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset)

Class ReadBaseStratification

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

currentReadBaseStratifier

previousReadBaseStratifier

nextReadBaseStratifier

referenceBaseStratifier

postDiNucleotideStratifier

preDiNucleotideStratifier

homoPolymerLengthStratifier

homopolymerStratifier

binnedHomopolymerStratifier

oneBasePaddedContextStratifier

twoBasePaddedContextStratifier

nonStratifier

gcContentStratifier

flowCellTileStratifier

readgroupStratifier

readOrdinalityStratifier

readPairednessStratifier

readDirectionStratifier

readOrientationStratifier

binnedReadCycleStratifier

baseCycleStratifier

insertLengthStratifier

softClipsLengthStratifier

baseQualityStratifier

mappingQualityStratifier

mismatchesInReadStratifier

consensusStratifier

nsInReadStratifier

insertionsInReadStratifier

deletionsInReadStratifier

indelsInReadStratifier

indelLengthStratifier

NOT_ALIGNED_ERROR

Constructor Detail

ReadBaseStratification

Method Detail

setGcCacheSize

setLongHomopolymer

PairStratifierFactory

getIndelElement