org.seqdoop.hadoop_bam

Class LazyBAMRecordFactory

java.lang.Object

org.seqdoop.hadoop_bam.LazyBAMRecordFactory

All Implemented Interfaces:

htsjdk.samtools.SAMRecordFactory

public class LazyBAMRecordFactory
extends Object
implements htsjdk.samtools.SAMRecordFactory

A factory for the kind of lazy BAMRecord used internally.

Constructor Summary

Constructors

Constructor and Description
LazyBAMRecordFactory()

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.BAMRecord	createBAMRecord(htsjdk.samtools.SAMFileHeader hdr, int referenceSequenceIndex, int alignmentStart, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceSequenceIndex, int mateAlignmentStart, int insertSize, byte[] variableLengthBlock)
htsjdk.samtools.SAMRecord	createSAMRecord(htsjdk.samtools.SAMFileHeader hdr)

Methods inherited from class java.lang.Object

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

Constructor Detail

LazyBAMRecordFactory

public LazyBAMRecordFactory()

Method Detail

createSAMRecord

public htsjdk.samtools.SAMRecord createSAMRecord(htsjdk.samtools.SAMFileHeader hdr)

Specified by:

createSAMRecord in interface htsjdk.samtools.SAMRecordFactory

createBAMRecord

public htsjdk.samtools.BAMRecord createBAMRecord(htsjdk.samtools.SAMFileHeader hdr,
                                                 int referenceSequenceIndex,
                                                 int alignmentStart,
                                                 short readNameLength,
                                                 short mappingQuality,
                                                 int indexingBin,
                                                 int cigarLen,
                                                 int flags,
                                                 int readLen,
                                                 int mateReferenceSequenceIndex,
                                                 int mateAlignmentStart,
                                                 int insertSize,
                                                 byte[] variableLengthBlock)

Specified by:

createBAMRecord in interface htsjdk.samtools.SAMRecordFactory