SamRecordTrackingBuffer (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.util.SamRecordTrackingBuffer<T>

```
public class SamRecordTrackingBuffer<T extends SamRecordWithOrdinal>
extends Object
```
This class stores SAMRecords for return. The purpose of this class is to buffer records that need to be modified or processed in some fashion, and only return (or emit) them when they have been recorded as being fully examined. If we have too many records in RAM, we can spill over to disk. The order in which they are given (via SamRecordWithOrdinal) determines their order of being returned. It is the responsibility of the user of this class to make sure all records have unique index and are added in order. When a record is examined, we also store a result state. This is currently a boolean to reduce on memory and disk footprint. We store groups of records in blocks and the size of these blocks can be controlled. If we have too many records in RAM, we start spilling blocks to disk. Users should check isEmpty() to see if any records are still being tracked. If so, they should check canEmit() to see if the next record can be returned. If so, they can call next() to get that record. When users are done with this structure, call close().

Constructor Summary

Constructors
Constructor	Description
`SamRecordTrackingBuffer(int maxRecordsInRam, int blockSize, List<File> tmpDirs, SAMFileHeader header, Class<T> clazz)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(SamRecordWithOrdinal samRecordWithOrdinal)`	Add the given SAMRecordIndex to the buffer.
`boolean`	`canEmit()`	Returns true if we can return the next record (it has been examined).
`void`	`close()`	Close IO resources associated with each underlying BufferBlock
`boolean`	`contains(SamRecordWithOrdinal samRecordWithOrdinal)`	Returns true if this buffer contains the record at the given index, false otherwise
`boolean`	`isEmpty()`	Returns true if we are tracking no records, false otherwise
`SamRecordWithOrdinal`	`next()`	Returns the next element in the iteration.
`void`	`remove()`	Removes the next record from this buffer
`void`	`setResultState(SamRecordWithOrdinal samRecordWithOrdinal, boolean resultState)`	Mark the current samRecordWithOrdinal as having been examined.
`long`	`size()`	Return the total number of elements in the queue, both in memory and on disk

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

- Constructor Detail
  - SamRecordTrackingBuffer
```
public SamRecordTrackingBuffer(int maxRecordsInRam,
                               int blockSize,
                               List<File> tmpDirs,
                               SAMFileHeader header,
                               Class<T> clazz)
```
    Parameters:
    
    maxRecordsInRam - how many records to buffer before spilling to disk
    
    blockSize - the number of records in a given block
    
    tmpDirs - the temporary directories to use when spilling to disk
    
    header - the header
    
    clazz - the class that extends SamRecordWithOrdinal
- Method Detail
  - isEmpty
```
public boolean isEmpty()
```
    Returns true if we are tracking no records, false otherwise
  - canEmit
```
public boolean canEmit()
```
    Returns true if we can return the next record (it has been examined).
  - add
```
public void add(SamRecordWithOrdinal samRecordWithOrdinal)
```
    Add the given SAMRecordIndex to the buffer. The records must be added in order.
    
    Parameters:
    
    samRecordWithOrdinal - The samRecordWithOrdinal to be added
  - next
```
public SamRecordWithOrdinal next()
```
    Returns the next element in the iteration.
    
    Returns:
    
    The next element in the iteration.
    
    Throws:
    
    NoSuchElementException - if the buffer is empty.
    
    SAMException - if the buffer is not competent to emit (canEmit returns false)
  - remove
```
public void remove()
```
    Removes the next record from this buffer
  - size
```
public long size()
```
    Return the total number of elements in the queue, both in memory and on disk
  - contains
```
public boolean contains(SamRecordWithOrdinal samRecordWithOrdinal)
```
    Returns true if this buffer contains the record at the given index, false otherwise
  - setResultState
```
public void setResultState(SamRecordWithOrdinal samRecordWithOrdinal,
                           boolean resultState)
```
    Mark the current samRecordWithOrdinal as having been examined.
    
    Parameters:
    
    samRecordWithOrdinal - The samRecordWithOrdinal to be marked
    
    resultState - Boolean flag indicating the result of the examination of this record.
    
    Throws:
    
    SAMException - if the provided recordIndex is not found within the SamRecordTrackingBuffer
  - close
```
public void close()
```
    Close IO resources associated with each underlying BufferBlock

Class SamRecordTrackingBuffer<T extends SamRecordWithOrdinal>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SamRecordTrackingBuffer

Method Detail

isEmpty

canEmit

add

next

remove

size

contains

setResultState

close