org.seqdoop.hadoop_bam.util

Class SAMOutputPreparer

java.lang.Object

org.seqdoop.hadoop_bam.util.SAMOutputPreparer

public class SAMOutputPreparer
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static byte[]	BAM_MAGIC

Constructor Summary

Constructors

Constructor and Description
SAMOutputPreparer()

Method Summary

Modifier and Type	Method and Description
OutputStream	prepareForRecords(OutputStream out, SAMFormat format, htsjdk.samtools.SAMFileHeader header) Prepares the given output stream for writing of SAMRecords in the given format.

Methods inherited from class java.lang.Object

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

Field Detail

BAM_MAGIC

public static final byte[] BAM_MAGIC

Constructor Detail

SAMOutputPreparer

public SAMOutputPreparer()

Method Detail

prepareForRecords

public OutputStream prepareForRecords(OutputStream out,
                                      SAMFormat format,
                                      htsjdk.samtools.SAMFileHeader header)
                               throws IOException

Prepares the given output stream for writing of SAMRecords in the given format. This includes writing the given SAM header and, in the case of BAM or CRAM, writing some further metadata as well as compressing everything written. Returns a new stream to replace the original: it will do the appropriate compression for BAM/CRAM files.

Throws:

IOException