AbstractRecordAndOffset (htsjdk 2.18.2 API)

java.lang.Object
- htsjdk.samtools.util.AbstractRecordAndOffset

Direct Known Subclasses:

EdgingRecordAndOffset, SamLocusIterator.RecordAndOffset
```
public class AbstractRecordAndOffset
extends Object
```
Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing AbstractLocusInfo. One object represents one base for SamLocusIterator.RecordAndOffset implementation or one alignment block of SAMRecord for TypedRecordAndOffset implementation.

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`offset`	Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
`protected SAMRecord`	`record`	A SAMRecord aligned to reference position

Constructor Summary

Constructors
Constructor Description

AbstractRecordAndOffset(SAMRecord record, int offset)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`byte[]`	`getBaseQualities()`
`byte`	`getBaseQuality()`
`int`	`getLength()`
`int`	`getOffset()`
`byte`	`getReadBase()`
`String`	`getReadName()`
`SAMRecord`	`getRecord()`
`protected void`	`validateOffset(int offset, byte[] array)`

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

- Field Detail
  - record
```
protected final SAMRecord record
```
    A SAMRecord aligned to reference position
  - offset
```
protected final int offset
```
    Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
- Constructor Detail
  - AbstractRecordAndOffset
```
public AbstractRecordAndOffset(SAMRecord record,
                               int offset)
```
    Parameters:
    
    record - inner SAMRecord
    
    offset - from the start of the read
- Method Detail
  - getOffset
```
public int getOffset()
```
    Returns:
    
    offset of aligned read base from the start of the read.
  - getRecord
```
public SAMRecord getRecord()
```
    Returns:
    
    inner SAMRecord object.
  - getReadBase
```
public byte getReadBase()
```
    Returns:
    
    the read base according to offset.
  - getLength
```
public int getLength()
```
    Returns:
    
    the length of alignment block represented by the object.
  - getReadName
```
public String getReadName()
```
    Returns:
    
    read name of inner SAMRecord.
  - getBaseQualities
```
public byte[] getBaseQualities()
```
    Returns:
    
    array of base qualities of inner SAMRecord.
  - getBaseQuality
```
public byte getBaseQuality()
```
    Returns:
    
    the base quality according to offset.
  - validateOffset
```
protected void validateOffset(int offset,
                              byte[] array)
```