htsjdk.samtools

Class BAMStreamWriter

java.lang.Object

htsjdk.samtools.BAMStreamWriter

public class BAMStreamWriter
extends java.lang.Object

Class for writing SAMRecords in BAM format to an output stream.

Constructor Summary

Constructors

Constructor and Description
BAMStreamWriter(java.io.OutputStream outputStream, java.io.OutputStream indexStream, java.io.OutputStream sbiStream, long sbiGranularity, SAMFileHeader header) Create a BAMStreamWriter for writing.

Method Summary

Modifier and Type	Method and Description
void	finish(boolean writeTerminatorBlock) Finish writing and close all the streams.
void	writeAlignment(SAMRecord alignment)
void	writeHeader(SAMFileHeader header)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BAMStreamWriter

public BAMStreamWriter(java.io.OutputStream outputStream,
                       java.io.OutputStream indexStream,
                       java.io.OutputStream sbiStream,
                       long sbiGranularity,
                       SAMFileHeader header)

Create a BAMStreamWriter for writing. All output streams should be uncompressed streams, since this class performs the necessary compression. All output streams are closed by this class after finish(boolean) returns.

Parameters:

outputStream - an output stream for the main BAM output

indexStream - an output stream for the BAI index, or null if no index is required

sbiStream - an output stream for the SBI index, or null if no index is required

sbiGranularity - the granularity of the SBI index (reads per entry)

header - the SAM header

Method Detail

writeHeader

public void writeHeader(SAMFileHeader header)

writeAlignment

public void writeAlignment(SAMRecord alignment)

finish

public void finish(boolean writeTerminatorBlock)

Finish writing and close all the streams.

Parameters:

writeTerminatorBlock - whether to write a BAM terminator block to the main output stream