CRAMIterator (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.CRAMIterator

All Implemented Interfaces:

SAMRecordIterator, CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>
```
public class CRAMIterator
extends Object
implements SAMRecordIterator
```

Field Summary

Fields
Modifier and Type Field and Description

Container container

Fields
Modifier and Type	Field and Description
`Container`	`container`

Constructor Summary

Constructors
Constructor and Description
`CRAMIterator(InputStream inputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)`
`CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates)` Deprecated.
`CRAMIterator(SeekableStream seekableStream, CRAMReferenceSource referenceSource, long[] coordinates, ValidationStringency validationStringency)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`advanceToAlignmentInContainer(int refIndex, int pos)` Skip cached records until given alignment start position.
`SAMRecordIterator`	`assertSorted(SAMFileHeader.SortOrder sortOrder)` Establishes that records returned by this iterator are expected to be in the specified sort order.
`void`	`close()` Should be implemented to close/release any underlying resources.
`CramHeader`	`getCramHeader()`
`SamReader`	`getFileSource()`
`SAMFileHeader`	`getSAMFileHeader()`
`ValidationStringency`	`getValidationStringency()`
`boolean`	`hasNext()`
`SAMRecord`	`next()`
`void`	`remove()`
`void`	`setFileSource(SamReader mReader)`
`void`	`setValidationStringency(ValidationStringency validationStringency)`

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.util.Iterator
forEachRemaining

- Field Detail
  - container
```
public Container container
```
- Constructor Detail
  - CRAMIterator
```
public CRAMIterator(InputStream inputStream,
                    CRAMReferenceSource referenceSource,
                    ValidationStringency validationStringency)
             throws IOException
```
    Throws:
    
    IOException
  - CRAMIterator
```
public CRAMIterator(SeekableStream seekableStream,
                    CRAMReferenceSource referenceSource,
                    long[] coordinates,
                    ValidationStringency validationStringency)
             throws IOException
```
    Throws:
    
    IOException
  - CRAMIterator
```
@Deprecated
public CRAMIterator(SeekableStream seekableStream,
                                CRAMReferenceSource referenceSource,
                                long[] coordinates)
                         throws IOException
```
    Deprecated.
    
    Throws:
    
    IOException
- Method Detail
  - getValidationStringency
```
public ValidationStringency getValidationStringency()
```
  - setValidationStringency
```
public void setValidationStringency(ValidationStringency validationStringency)
```
  - getCramHeader
```
public CramHeader getCramHeader()
```
  - advanceToAlignmentInContainer
```
public boolean advanceToAlignmentInContainer(int refIndex,
                                             int pos)
```
    Skip cached records until given alignment start position.
    
    Parameters:
    
    refIndex - reference sequence index
    
    pos - alignment start to skip to
  - hasNext
```
public boolean hasNext()
```
    Specified by:
    
    hasNext in interface Iterator<SAMRecord>
  - next
```
public SAMRecord next()
```
    Specified by:
    
    next in interface Iterator<SAMRecord>
  - remove
```
public void remove()
```
    Specified by:
    
    remove in interface Iterator<SAMRecord>
  - close
```
public void close()
```
    Description copied from interface: CloseableIterator
    
    Should be implemented to close/release any underlying resources.
    
    Specified by:
    
    close in interface CloseableIterator<SAMRecord>
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
  - assertSorted
```
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
```
    Description copied from interface: SAMRecordIterator
    
    Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.
    
    Specified by:
    
    assertSorted in interface SAMRecordIterator
    
    Parameters:
    
    sortOrder - The order in which records are expected to be returned
    
    Returns:
    
    This SAMRecordIterator
  - getFileSource
```
public SamReader getFileSource()
```
  - setFileSource
```
public void setFileSource(SamReader mReader)
```
  - getSAMFileHeader
```
public SAMFileHeader getSAMFileHeader()
```

Class CRAMIterator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Field Detail

container

Constructor Detail

CRAMIterator

CRAMIterator

CRAMIterator

Method Detail

getValidationStringency

setValidationStringency

getCramHeader

advanceToAlignmentInContainer

hasNext

next

remove

close

assertSorted

getFileSource

setFileSource

getSAMFileHeader