PileupIterator

| Detail:
Field
Constructor
Method

gngs.PileupIterator

All Implemented Interfaces and Traits:

java.util.Iterator
```
public class PileupIterator
extends java.lang.Object
implements java.util.Iterator
```
Overall class containing pileup state
Authors:
simon.sadedin@mcri.edu.au

Nested Class Summary

Nested classes
Modifiers	Name	Description
`class`	`PileupIterator.Pileup`	Inner class that captures pileup state at a specific position

Field Summary

Fields
Modifiers	Name	Description
`java.util.List<PileupState>`	`alignments`
`java.lang.String`	`chr`
`int`	`end`
`int`	`iteratorPosition`
`int`	`start`

Constructor Summary

Constructors
Constructor and description
`PileupIterator ()`
`PileupIterator (htsjdk.samtools.SamReader samFile, java.lang.String chr, int start, int end)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`public void`	`close()`
	`public int`	`getMinMappingQuality()`
	`public htsjdk.samtools.SAMRecordIterator`	`getReadIterator()`
	`public boolean`	`hasNext()`
	`public Pileup`	`next()` Move the iterator to the next base position within the requested pileup range and return a Pileup object for that position.
	`public void`	`remove()`
	`public void`	`setMinMappingQuality(int minMappingQuality)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Field Detail
  - public java.util.List<PileupState> alignments
  - public java.lang.String chr
  - public int end
  - public int iteratorPosition
  - public int start
- Constructor Detail
  - public PileupIterator()
  - public PileupIterator(htsjdk.samtools.SamReader samFile, java.lang.String chr, int start, int end)
- Method Detail
  - public void close()
  - public int getMinMappingQuality()
  - public htsjdk.samtools.SAMRecordIterator getReadIterator()
  - @java.lang.Override public boolean hasNext()
  - public Pileup next()
    
    Move the iterator to the next base position within the requested pileup range and return a Pileup object for that position.
    The logic here is as follows:
  - consume reads until we have found a read that is past the current coordinate of the pileup
  - keep reads in a list that is ordered by their start position
  - drop any reads from the list that end prior to the (new) start position
    This creates an efficient store of all the reads overlapping the current pileup position.
    Each read is not stored directly but in an object that captures its state within the current pileup (PileupState).
  - @java.lang.Override public void remove()
  - public void setMinMappingQuality(int minMappingQuality)

| Detail:
Field
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Groovy Documentation