ReadPileup (gatk 4.0.5.0 API)

java.lang.Object
- org.broadinstitute.hellbender.utils.pileup.ReadPileup

All Implemented Interfaces:

java.lang.Iterable<PileupElement>
```
public class ReadPileup
extends java.lang.Object
implements java.lang.Iterable<PileupElement>
```
Represents a pileup of reads at a given position.

Field Summary

Fields
Modifier and Type	Field and Description
`static java.util.Comparator<PileupElement>`	`baseQualTieBreaker`
`static java.util.Comparator<PileupElement>`	`mapQualTieBreaker`
`static double`	`SAMTOOLS_OVERLAP_LOW_CONFIDENCE` Constant used by samtools to downgrade a quality for overlapping reads that disagrees in their base.

Constructor Summary

Constructors
Constructor and Description
`ReadPileup(htsjdk.samtools.util.Locatable loc)` Create a new pileup without any aligned reads
`ReadPileup(htsjdk.samtools.util.Locatable loc, java.util.List<GATKRead> reads, int offset)` Create a new pileup with the given reads.
`ReadPileup(htsjdk.samtools.util.Locatable loc, java.util.List<GATKRead> reads, java.util.List<java.lang.Integer> offsets)` Create a new pileup with the given reads.
`ReadPileup(htsjdk.samtools.util.Locatable loc, java.util.List<PileupElement> pileup)` Create a new pileup at loc, using the reads and their corresponding offsets.
`ReadPileup(htsjdk.samtools.util.Locatable loc, java.util.Map<java.lang.String,ReadPileup> stratifiedPileup)` Create a new pileup at loc, using an stratified pileup Note: the current implementation of ReadPileup does not efficiently retrieve the stratified pileup

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`fixOverlaps()` Fixes the quality of all the elements that come from an overlapping pair in the same way as samtools does `function in samtools`.
`int[]`	`getBaseCounts()` Get counts of A, C, G, T in order, which returns a int[4] vector with counts according to BaseUtils.simpleBaseToBaseIndex for each base.
`byte[]`	`getBaseQuals()` Returns an array of the quals in this pileup.
`byte[]`	`getBases()` Returns an array of the bases in this pileup.
`htsjdk.samtools.util.Locatable`	`getLocation()`
`int[]`	`getMappingQuals()` Get an array of the mapping qualities.
`int`	`getNumberOfElements(java.util.function.Predicate<PileupElement> peFilter)` Returns the number of elements that satisfy the predicate.
`java.util.List<java.lang.Integer>`	`getOffsets()` Returns a list of the offsets in this pileup.
`ReadPileup`	`getOverlappingFragmentFilteredPileup(boolean discardDiscordant, java.util.Comparator<PileupElement> tieBreaker, htsjdk.samtools.SAMFileHeader header)` Returns a new ReadPileup where only one read from an overlapping read pair is retained.
`ReadPileup`	`getOverlappingFragmentFilteredPileup(htsjdk.samtools.SAMFileHeader header)` Returns a new ReadPileup where only one read from an overlapping read pair is retained.
`ReadPileup`	`getPileupForLane(java.lang.String laneID)` Make a new pileup from elements whose reads have read groups that agree with the given lane ID.
`ReadPileup`	`getPileupForSample(java.lang.String sample, htsjdk.samtools.SAMFileHeader header)` Make a new pileup from elements whose reads belong to the given sample.
`java.lang.String`	`getPileupString(char ref)` Format, assuming a single-sample, in a samtools-like string.
`java.util.Set<java.lang.String>`	`getReadGroupIDs()` Gets a set of the read groups represented in this pileup.
`java.util.List<GATKRead>`	`getReads()` Returns a list of the reads in this pileup.
`java.util.Set<java.lang.String>`	`getSamples(htsjdk.samtools.SAMFileHeader header)` Gets a set of the samples represented in this pileup.
`boolean`	`isEmpty()`
`java.util.Iterator<PileupElement>`	`iterator()` The best way to access PileupElements where you only care about the bases and quals in the pileup.
`static java.util.List<PileupElement>`	`locToReadsPileup(java.util.List<GATKRead> reads, htsjdk.samtools.util.Locatable loc)` Helper routine for converting reads and a single offset to a PileupElement list.
`ReadPileup`	`makeFilteredPileup(java.util.function.Predicate<PileupElement> filter)` Make a new pileup consisting of elements of this pileup that satisfy the predicate.
`int`	`size()` The number of elements in this pileup.
`java.util.Iterator<PileupElement>`	`sortedIterator()` Iterator over sorted by read start PileupElements.
`java.util.Map<java.lang.String,ReadPileup>`	`splitBySample(htsjdk.samtools.SAMFileHeader header, java.lang.String unknownSampleName)` Splits the ReadPileup by sample
`java.lang.String`	`toString()`

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Field Detail
  - SAMTOOLS_OVERLAP_LOW_CONFIDENCE
```
public static final double SAMTOOLS_OVERLAP_LOW_CONFIDENCE
```
    Constant used by samtools to downgrade a quality for overlapping reads that disagrees in their base.
    
    See Also:
    
    Constant Field Values
  - baseQualTieBreaker
```
public static final java.util.Comparator<PileupElement> baseQualTieBreaker
```
  - mapQualTieBreaker
```
public static final java.util.Comparator<PileupElement> mapQualTieBreaker
```
- Constructor Detail
  - ReadPileup
```
public ReadPileup(htsjdk.samtools.util.Locatable loc,
                  java.util.List<PileupElement> pileup)
```
    Create a new pileup at loc, using the reads and their corresponding offsets. Note: This constructor keeps an alias to the given list.
  - ReadPileup
```
public ReadPileup(htsjdk.samtools.util.Locatable loc,
                  java.util.Map<java.lang.String,ReadPileup> stratifiedPileup)
```
    Create a new pileup at loc, using an stratified pileup Note: the current implementation of ReadPileup does not efficiently retrieve the stratified pileup
  - ReadPileup
```
public ReadPileup(htsjdk.samtools.util.Locatable loc)
```
    Create a new pileup without any aligned reads
  - ReadPileup
```
public ReadPileup(htsjdk.samtools.util.Locatable loc,
                  java.util.List<GATKRead> reads,
                  int offset)
```
    Create a new pileup with the given reads.
  - ReadPileup
```
public ReadPileup(htsjdk.samtools.util.Locatable loc,
                  java.util.List<GATKRead> reads,
                  java.util.List<java.lang.Integer> offsets)
```
    Create a new pileup with the given reads.
- Method Detail
  - locToReadsPileup
```
public static java.util.List<PileupElement> locToReadsPileup(java.util.List<GATKRead> reads,
                                                             htsjdk.samtools.util.Locatable loc)
```
    Helper routine for converting reads and a single offset to a PileupElement list.
  - makeFilteredPileup
```
public ReadPileup makeFilteredPileup(java.util.function.Predicate<PileupElement> filter)
```
    Make a new pileup consisting of elements of this pileup that satisfy the predicate. NOTE: the new pileup will not be independent of the old one (no deep copy of the underlying data is performed).
  - getPileupForLane
```
public ReadPileup getPileupForLane(java.lang.String laneID)
```
    Make a new pileup from elements whose reads have read groups that agree with the given lane ID. (if they have a name equal to the ID or starting with ID followed by a period "."). Also, if both laneID and read group ID are null, the read will be included. Returns empty pileup if no suitable elements are found. NOTE: the new pileup will not be independent of the old one (no deep copy of the underlying data is performed).
  - getPileupForSample
```
public ReadPileup getPileupForSample(java.lang.String sample,
                                     htsjdk.samtools.SAMFileHeader header)
```
    Make a new pileup from elements whose reads belong to the given sample. Passing null sample as an argument retrieves reads whose read group or sample name is null NOTE: the new pileup will not be independent of the old one (no deep copy of the underlying data is performed).
  - getReadGroupIDs
```
public java.util.Set<java.lang.String> getReadGroupIDs()
```
    Gets a set of the read groups represented in this pileup. Note: contains null if a read has a null read group
  - getSamples
```
public java.util.Set<java.lang.String> getSamples(htsjdk.samtools.SAMFileHeader header)
```
    Gets a set of the samples represented in this pileup. Note: contains null if a read has a null read group or a null sample name.
  - splitBySample
```
public java.util.Map<java.lang.String,ReadPileup> splitBySample(htsjdk.samtools.SAMFileHeader header,
                                                                java.lang.String unknownSampleName)
```
    Splits the ReadPileup by sample
    
    Parameters:
    
    header - the header to retrieve the samples from
    
    unknownSampleName - the sample name if there is no read group/sample name; null if lack of RG is not expected
    
    Returns:
    
    a Map of sample name to ReadPileup (including empty pileups for a sample)
    
    Throws:
    
    UserException.ReadMissingReadGroup - if unknownSampleName is null and there are reads without RG/sample name
  - iterator
```
public java.util.Iterator<PileupElement> iterator()
```
    The best way to access PileupElements where you only care about the bases and quals in the pileup.
    for (PileupElement p : this) { doSomething(p); }
    Provides efficient iteration of the data.
    
    Specified by:
    
    iterator in interface java.lang.Iterable<PileupElement>
  - sortedIterator
```
public java.util.Iterator<PileupElement> sortedIterator()
```
    Iterator over sorted by read start PileupElements.
  - size
```
public int size()
```
    The number of elements in this pileup.
  - isEmpty
```
public boolean isEmpty()
```
    Returns:
    
    true if there are 0 elements in the pileup, false otherwise
  - getLocation
```
public htsjdk.samtools.util.Locatable getLocation()
```
    Returns:
    
    the location of this pileup.
  - getBaseCounts
```
public int[] getBaseCounts()
```
    Get counts of A, C, G, T in order, which returns a int[4] vector with counts according to BaseUtils.simpleBaseToBaseIndex for each base. Deletions are not counted.
  - fixOverlaps
```
public void fixOverlaps()
```
    Fixes the quality of all the elements that come from an overlapping pair in the same way as samtools does function in samtools.
    Setting the quality of one of the bases to 0 effectively removes the redundant base for calling. In addition, if the bases overlap we have increased confidence if they agree (or reduced if they don't). Thus, the algorithm proceeds as following:
    1. If the bases are the same, the quality of the first element is the sum of both qualities and the quality of the second is reduced to 0. 2. If the bases are different, the base with the highest quality is reduced with a factor of 0.8, and the quality of the lowest is reduced to 0.
    Note: Resulting qualities higher than QualityUtils.MAX_SAM_QUAL_SCORE are capped.
  - getOverlappingFragmentFilteredPileup
```
public ReadPileup getOverlappingFragmentFilteredPileup(htsjdk.samtools.SAMFileHeader header)
```
    Returns a new ReadPileup where only one read from an overlapping read pair is retained. If the two reads in question disagree to their basecall, neither read is retained. If they agree on the base, the read with the higher base quality observation is retained
    
    Returns:
    
    the newly filtered pileup
  - getOverlappingFragmentFilteredPileup
```
public ReadPileup getOverlappingFragmentFilteredPileup(boolean discardDiscordant,
                                                       java.util.Comparator<PileupElement> tieBreaker,
                                                       htsjdk.samtools.SAMFileHeader header)
```
    Returns a new ReadPileup where only one read from an overlapping read pair is retained. If discardDiscordant and the two reads in question disagree to their basecall, neither read is retained. Otherwise, the read with the higher quality (base or mapping, depending on baseQualNotMapQual) observation is retained
    
    Returns:
    
    the newly filtered pileup
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getPileupString
```
public java.lang.String getPileupString(char ref)
```
    Format, assuming a single-sample, in a samtools-like string. Each line represents a genomic position, consisting of chromosome name, coordinate, reference base, read bases and read qualities
    
    Parameters:
    
    ref - the reference base
    
    Returns:
    
    pileup line
  - getReads
```
public java.util.List<GATKRead> getReads()
```
    Returns a list of the reads in this pileup. Note this call costs O(n) and allocates fresh lists each time
  - getNumberOfElements
```
public int getNumberOfElements(java.util.function.Predicate<PileupElement> peFilter)
```
    Returns the number of elements that satisfy the predicate.
  - getOffsets
```
public java.util.List<java.lang.Integer> getOffsets()
```
    Returns a list of the offsets in this pileup. Note: this call costs O(n) and allocates fresh lists each time
  - getBases
```
public byte[] getBases()
```
    Returns an array of the bases in this pileup. Note: this call costs O(n) and allocates fresh array each time
  - getBaseQuals
```
public byte[] getBaseQuals()
```
    Returns an array of the quals in this pileup. Note: this call costs O(n) and allocates fresh array each time
  - getMappingQuals
```
public int[] getMappingQuals()
```
    Get an array of the mapping qualities.

Class ReadPileup

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Field Detail

SAMTOOLS_OVERLAP_LOW_CONFIDENCE

baseQualTieBreaker

mapQualTieBreaker

Constructor Detail

ReadPileup

ReadPileup

ReadPileup

ReadPileup

ReadPileup

Method Detail

locToReadsPileup

makeFilteredPileup

getPileupForLane

getPileupForSample

getReadGroupIDs

getSamples

splitBySample

iterator

sortedIterator

size

isEmpty

getLocation

getBaseCounts

fixOverlaps

getOverlappingFragmentFilteredPileup

getOverlappingFragmentFilteredPileup

toString

getPileupString

getReads

getNumberOfElements

getOffsets

getBases

getBaseQuals

getMappingQuals