Pileup

Summary:
Field
Constructor
Method

| Detail:
Field
Constructor
Method

gngs.Pileup

All Implemented Interfaces and Traits:

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

Field Summary

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

Constructor Summary

Constructors
Constructor and description
`Pileup ()`
`Pileup (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`	`countOf(java.lang.String baseString)`
	`public int`	`countOf(byte base)` Return the count of reads supporting the specified base at the current position.
	`public int[]`	`getSummary()` Returns a summary of the coverage at the location:
	`public java.util.Map<java.lang.String, java.lang.Integer>`	`getSummaryAsMap()` Convenience method to return counts of each base as a map indexed by the base as a string.
	`public boolean`	`hasNext()`
	`public Pileup`	`next()`
	`public void`	`remove()`

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 position
  - public int start
- Constructor Detail
  - public Pileup()
  - public Pileup(htsjdk.samtools.SamReader samFile, java.lang.String chr, int start, int end)
- Method Detail
  - public void close()
  - public int countOf(java.lang.String baseString)
  - public int countOf(byte base)
    
    Return the count of reads supporting the specified base at the current position.
    Parameters:
    base ascii - int code for A,T,C,G,N, etc.
    Returns:
    count of reads supporting base
  - public int[] getSummary()
    
    Returns a summary of the coverage at the location: [ A, T , C, G, Deletion, total ]
    Returns:
  - public java.util.Map<java.lang.String, java.lang.Integer> getSummaryAsMap()
    
    Convenience method to return counts of each base as a map indexed by the base as a string. This is not efficient, but useful in non performance sensitive contexts.
    Returns:
    map of count indexed by base
  - @java.lang.Override public boolean hasNext()
  - public Pileup next()
  - @java.lang.Override public void remove()

Summary:
Field
Constructor
Method

| Detail:
Field
Constructor
Method

Groovy Documentation