SamLocusIterator.LocusInfo (htsjdk 2.6.1 API)

java.lang.Object
- htsjdk.samtools.util.SamLocusIterator.LocusInfo

All Implemented Interfaces:

Locus

Enclosing class:

SamLocusIterator
```
public static final class SamLocusIterator.LocusInfo
extends java.lang.Object
implements Locus
```
The unit of iteration. Holds information about the locus (the SAMSequenceRecord and 1-based position on the reference), plus List of ReadAndOffset objects, one for each read that overlaps the locus; two more List_s_ of ReadAndOffset objects include reads that overlap the locus with insertions and deletions respectively

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(SAMRecord read, int position)` Accumulate info for one read at the locus.
`void`	`addDeleted(SAMRecord read, int previousPosition)` Accumulate info for one read with a deletion
`void`	`addInserted(SAMRecord read, int firstPosition)` Accumulate info for one read with an insertion.
`java.util.List<SamLocusIterator.RecordAndOffset>`	`getDeletedInRecord()`
`java.util.List<SamLocusIterator.RecordAndOffset>`	`getInsertedInRecord()`
`int`	`getPosition()`
`java.util.List<SamLocusIterator.RecordAndOffset>`	`getRecordAndPositions()`
`int`	`getSequenceIndex()`
`int`	`getSequenceLength()`
`java.lang.String`	`getSequenceName()`
`boolean`	`isEmpty()`
`int`	`size()`
`java.lang.String`	`toString()`

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

- Method Detail
  - add
```
public void add(SAMRecord read,
                int position)
```
    Accumulate info for one read at the locus.
  - addDeleted
```
public void addDeleted(SAMRecord read,
                       int previousPosition)
```
    Accumulate info for one read with a deletion
  - addInserted
```
public void addInserted(SAMRecord read,
                        int firstPosition)
```
    Accumulate info for one read with an insertion. For this locus, the reads in the insertion are included also in recordAndOffsets
  - getSequenceIndex
```
public int getSequenceIndex()
```
    Specified by:
    
    getSequenceIndex in interface Locus
  - getPosition
```
public int getPosition()
```
    Specified by:
    
    getPosition in interface Locus
    
    Returns:
    
    1-based reference position
  - getRecordAndPositions
```
public java.util.List<SamLocusIterator.RecordAndOffset> getRecordAndPositions()
```
  - getSequenceName
```
public java.lang.String getSequenceName()
```
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getSequenceLength
```
public int getSequenceLength()
```
  - getDeletedInRecord
```
public java.util.List<SamLocusIterator.RecordAndOffset> getDeletedInRecord()
```
  - getInsertedInRecord
```
public java.util.List<SamLocusIterator.RecordAndOffset> getInsertedInRecord()
```
  - size
```
public int size()
```
    Returns:
    
    the number of records overlapping the position, with deletions included if they are being tracked.
  - isEmpty
```
public boolean isEmpty()
```
    Returns:
    
    true if all the RecordAndOffset lists are empty; false if at least one have records

Class SamLocusIterator.LocusInfo

Method Summary

Methods inherited from class java.lang.Object

Method Detail

add

addDeleted

addInserted

getSequenceIndex

getPosition

getRecordAndPositions

getSequenceName

toString

getSequenceLength

getDeletedInRecord

getInsertedInRecord

size

isEmpty