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

All Implemented Interfaces:

SAMFileWriter, Closeable, AutoCloseable
```
public class BAMFileWriter
extends SAMFileWriterImpl
```
Concrete implementation of SAMFileWriter for writing gzipped BAM files.

Constructor Summary

Constructors
Modifier	Constructor	Description
`protected`	`BAMFileWriter(File path)`
`protected`	`BAMFileWriter(File path, int compressionLevel)`
`protected`	`BAMFileWriter(OutputStream os, File file)`
`protected`	`BAMFileWriter(OutputStream os, File file, int compressionLevel)`
`protected`	`BAMFileWriter(OutputStream os, File file, int compressionLevel, DeflaterFactory deflaterFactory)`
`protected`	`BAMFileWriter(OutputStream os, String absoluteFilename, int compressionLevel, DeflaterFactory deflaterFactory)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`finish()`	Do any required flushing here.
`protected String`	`getFilename()`	For producing error messages.
`protected void`	`writeAlignment(SAMRecord alignment)`	Writes the record to disk.
`protected static void`	`writeHeader(BinaryCodec outputBinaryCodec, SAMFileHeader samFileHeader)`	Writes a header to a BAM file.
`protected static void`	`writeHeader(BinaryCodec outputBinaryCodec, SAMFileHeader samFileHeader, String headerText)`	Writes a header to a BAM file.
`static void`	`writeHeader(OutputStream outputStream, SAMFileHeader samFileHeader)`	Write a BAM file header to an output stream in block compressed BAM format.
`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, writeHeader

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

Constructor Detail

BAMFileWriter
```
protected BAMFileWriter(File path)
```

BAMFileWriter

protected BAMFileWriter(File path,
                        int compressionLevel)

BAMFileWriter

protected BAMFileWriter(OutputStream os,
                        File file)

BAMFileWriter

protected BAMFileWriter(OutputStream os,
                        File file,
                        int compressionLevel)

BAMFileWriter

protected BAMFileWriter(OutputStream os,
                        File file,
                        int compressionLevel,
                        DeflaterFactory deflaterFactory)

BAMFileWriter

protected BAMFileWriter(OutputStream os,
                        String absoluteFilename,
                        int compressionLevel,
                        DeflaterFactory deflaterFactory)

Method Detail
- writeAlignment
```
protected void writeAlignment(SAMRecord alignment)
```
  Description copied from class: SAMFileWriterImpl
  
  Writes the record to disk. Sort order has been taken care of by the time this method is called. The record must hava a non-null SAMFileHeader.
  
  Specified by:
  
  writeAlignment in class SAMFileWriterImpl
- 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.
- 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:
  
  absolute path in URI format, or null if this writer does not correspond to a file. To get a Path from this, use: IOUtil.getPath(getFilename())
- writeHeader
```
protected static void writeHeader(BinaryCodec outputBinaryCodec,
                                  SAMFileHeader samFileHeader,
                                  String headerText)
```
  Writes a header to a BAM file. samFileHeader and headerText are redundant - one can be used to regenerate the other but in some instances we already have both so this allows us to save some cycles
- writeHeader
```
protected static void writeHeader(BinaryCodec outputBinaryCodec,
                                  SAMFileHeader samFileHeader)
```
  Writes a header to a BAM file.
- writeHeader
```
public static void writeHeader(OutputStream outputStream,
                               SAMFileHeader samFileHeader)
```
  Write a BAM file header to an output stream in block compressed BAM format.
  
  Parameters:
  
  outputStream - the stream to write the BAM header to
  
  samFileHeader - the header to write

Class BAMFileWriter

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl

Methods inherited from class java.lang.Object

Constructor Detail

BAMFileWriter

BAMFileWriter

BAMFileWriter

BAMFileWriter

BAMFileWriter

BAMFileWriter

Method Detail

writeAlignment

writeHeader

finish

getFilename

writeHeader

writeHeader

writeHeader