PileupState

Summary:
Field
Method

| Detail:
Field
Method

gngs.PileupState

```
public class PileupState
extends java.lang.Object
```
Additional state about a read that is part of a pileup
Authors:
simon.sadedin@mcri.edu.au

Field Summary

Fields
Modifiers	Name	Description
`byte`	`base`
`htsjdk.samtools.CigarOperator`	`cigar`
`htsjdk.samtools.CigarElement`	`cigarElement`
`java.util.Iterator<htsjdk.samtools.CigarElement>`	`cigarIterator`
`int`	`cigarPos`	Offset within the current cigar element
`int`	`nextReadPos`	Offset from start of read for the next
`byte`	`qual`
`htsjdk.samtools.SAMRecord`	`read`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`public boolean`	`next()` Move forward one reference position.

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 byte base
  - public htsjdk.samtools.CigarOperator cigar
  - public htsjdk.samtools.CigarElement cigarElement
  - public java.util.Iterator<htsjdk.samtools.CigarElement> cigarIterator
  - public int cigarPos
    
    Offset within the current cigar element
  - public int nextReadPos
    
    Offset from start of read for the next
  - public byte qual
  - public htsjdk.samtools.SAMRecord read
- Method Detail
  - public boolean next()
    
    Move forward one reference position. If the position covers a deletion, this does not alter the read position. If the position covers an insertion, it will jump forward over the insertion in the read.

Summary:
Field
Method

| Detail:
Field
Method

Groovy Documentation