htsjdk.samtools

Class BAMFileWriter

java.lang.Object

htsjdk.samtools.SAMFileWriterImpl

htsjdk.samtools.BAMFileWriter

All Implemented Interfaces:

SAMFileWriter, java.io.Closeable, java.lang.AutoCloseable

public class BAMFileWriter
extends SAMFileWriterImpl

Concrete implementation of SAMFileWriter for writing gzipped BAM files.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	BAMFileWriter(java.io.File path)
protected	BAMFileWriter(java.io.File path, int compressionLevel)
protected	BAMFileWriter(java.io.OutputStream os, java.io.File file)
protected	BAMFileWriter(java.io.OutputStream os, java.io.File file, int compressionLevel)
protected	BAMFileWriter(java.io.OutputStream os, java.io.File file, int compressionLevel, DeflaterFactory deflaterFactory)
protected	BAMFileWriter(java.io.OutputStream os, java.lang.String absoluteFilename, int compressionLevel, DeflaterFactory deflaterFactory)

Method Summary

Modifier and Type	Method and Description
protected void	finish() Do any required flushing here.
protected java.lang.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, java.lang.String headerText) Writes a header to a BAM file.
static void	writeHeader(java.io.OutputStream outputStream, SAMFileHeader samFileHeader) Write a BAM file header to an output stream in block compressed BAM format.
protected void	writeHeader(java.lang.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(java.io.File path)

BAMFileWriter

protected BAMFileWriter(java.io.File path,
                        int compressionLevel)

BAMFileWriter

protected BAMFileWriter(java.io.OutputStream os,
                        java.io.File file)

BAMFileWriter

protected BAMFileWriter(java.io.OutputStream os,
                        java.io.File file,
                        int compressionLevel)

BAMFileWriter

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

BAMFileWriter

protected BAMFileWriter(java.io.OutputStream os,
                        java.lang.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(java.lang.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 java.lang.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,
                                  java.lang.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. Might need to regenerate the String version of the header, if one already has both the samFileHeader and the String, use the version of this method which takes both.

writeHeader

public static void writeHeader(java.io.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