java.lang.Object
- htsjdk.samtools.SAMFileWriterImpl
- - htsjdk.samtools.CRAMFileWriter

All Implemented Interfaces:

SAMFileWriter, Closeable, AutoCloseable
```
public class CRAMFileWriter
extends SAMFileWriterImpl
```

Constructor Summary

Constructors
Constructor	Description
`CRAMFileWriter(OutputStream outputStream, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, String fileName)`	Create a CRAMFileWriter on an output stream.
`CRAMFileWriter(OutputStream outputStream, OutputStream indexOS, boolean presorted, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, String fileName)`	Create a CRAMFileWriter and optional index on output streams.
`CRAMFileWriter(OutputStream outputStream, OutputStream indexOS, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, String fileName)`	Create a CRAMFileWriter and optional index on output streams.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`finish()`	Do any required flushing here.
`Set<String>`	`getCaptureTags()`
`protected String`	`getFilename()`	For producing error messages.
`Set<String>`	`getIgnoreTags()`
`List<PreservationPolicy>`	`getPreservationPolicies()`
`boolean`	`isCaptureAllTags()`
`boolean`	`isPreserveReadNames()`
`void`	`setCaptureAllTags(boolean captureAllTags)`
`void`	`setCaptureTags(Set<String> captureTags)`
`void`	`setIgnoreTags(Set<String> ignoreTags)`
`void`	`setPreserveReadNames(boolean preserveReadNames)`
`protected void`	`writeAlignment(SAMRecord alignment)`	Write an alignment record.
`protected void`	`writeHeader(SAMFileHeader header)`	Write the header to disk.
`protected void`	`writeHeader(String textHeader)`	Write the header to disk.

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl
addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getMaxRecordsInRam, getSortOrder, getTempDirectory, setDefaultMaxRecordsInRam, setHeader, setMaxRecordsInRam, setProgressLogger, setSortOrder, setTempDirectory

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

- Constructor Detail
  - CRAMFileWriter
```
public CRAMFileWriter(OutputStream outputStream,
                      CRAMReferenceSource referenceSource,
                      SAMFileHeader samFileHeader,
                      String fileName)
```
    Create a CRAMFileWriter on an output stream. Requires input records to be presorted to match the sort order defined by the input samFileHeader.
    
    Parameters:
    
    outputStream - where to write the output. Can not be null.
    
    referenceSource - reference source. Can not be null.
    
    samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.
    
    fileName - used for display in error messages
    
    Throws:
    
    IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null
  - CRAMFileWriter
```
public CRAMFileWriter(OutputStream outputStream,
                      OutputStream indexOS,
                      CRAMReferenceSource referenceSource,
                      SAMFileHeader samFileHeader,
                      String fileName)
```
    Create a CRAMFileWriter and optional index on output streams. Requires input records to be presorted to match the sort order defined by the input samFileHeader.
    
    Parameters:
    
    outputStream - where to write the output. Can not be null.
    
    indexOS - where to write the output index. Can be null if no index is required.
    
    referenceSource - reference source
    
    samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.
    
    fileName - used for display in error messages
    
    Throws:
    
    IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null
  - CRAMFileWriter
```
public CRAMFileWriter(OutputStream outputStream,
                      OutputStream indexOS,
                      boolean presorted,
                      CRAMReferenceSource referenceSource,
                      SAMFileHeader samFileHeader,
                      String fileName)
```
    Create a CRAMFileWriter and optional index on output streams.
    
    Parameters:
    
    outputStream - where to write the output. Can not be null.
    
    indexOS - where to write the output index. Can be null if no index is required.
    
    presorted - if true records written to this writer must already be sorted in the order specified by the header
    
    referenceSource - reference source
    
    samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.
    
    fileName - used for display in error message display
    
    Throws:
    
    IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null
- Method Detail
  - writeAlignment
```
protected void writeAlignment(SAMRecord alignment)
```
    Write an alignment record.
    
    Specified by:
    
    writeAlignment in class SAMFileWriterImpl
    
    Parameters:
    
    alignment - must not be null and must have a valid SAMFileHeader.
  - writeHeader
```
protected void writeHeader(String textHeader)
```
    Description copied from class: SAMFileWriterImpl
    
    Write the header to disk. Header object is available via getHeader().
    
    Specified by:
    
    writeHeader in class SAMFileWriterImpl
    
    Parameters:
    
    textHeader - for convenience if the implementation needs it.
  - writeHeader
```
protected void writeHeader(SAMFileHeader header)
```
    Description copied from class: SAMFileWriterImpl
    
    Write the header to disk. Header object is available via getHeader().
    IMPORTANT: this method will be abstract once SAMFileWriterImpl.writeHeader(String) is removed.
    Note: default implementation uses SAMTextHeaderCodec.encode(java.io.Writer, htsjdk.samtools.SAMFileHeader) and calls SAMFileWriterImpl.writeHeader(String).
    
    Overrides:
    
    writeHeader in class SAMFileWriterImpl
    
    Parameters:
    
    header - object to write.
  - finish
```
protected void finish()
```
    Description copied from class: SAMFileWriterImpl
    
    Do any required flushing here.
    
    Specified by:
    
    finish in class SAMFileWriterImpl
  - getFilename
```
protected String getFilename()
```
    Description copied from class: SAMFileWriterImpl
    
    For producing error messages.
    
    Specified by:
    
    getFilename in class SAMFileWriterImpl
    
    Returns:
    
    Output filename, or null if there isn't one.
  - isPreserveReadNames
```
public boolean isPreserveReadNames()
```
  - setPreserveReadNames
```
public void setPreserveReadNames(boolean preserveReadNames)
```
  - getPreservationPolicies
```
public List<PreservationPolicy> getPreservationPolicies()
```
  - isCaptureAllTags
```
public boolean isCaptureAllTags()
```
  - setCaptureAllTags
```
public void setCaptureAllTags(boolean captureAllTags)
```
  - getCaptureTags
```
public Set<String> getCaptureTags()
```
  - setCaptureTags
```
public void setCaptureTags(Set<String> captureTags)
```
  - getIgnoreTags
```
public Set<String> getIgnoreTags()
```
  - setIgnoreTags
```
public void setIgnoreTags(Set<String> ignoreTags)
```

Class CRAMFileWriter

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl

Methods inherited from class java.lang.Object

Constructor Detail

CRAMFileWriter

CRAMFileWriter

CRAMFileWriter

Method Detail

writeAlignment

writeHeader

writeHeader

finish

getFilename

isPreserveReadNames

setPreserveReadNames

getPreservationPolicies

isCaptureAllTags

setCaptureAllTags

getCaptureTags

setCaptureTags

getIgnoreTags

setIgnoreTags