htsjdk.samtools

Class DefaultSAMRecordFactory

java.lang.Object

htsjdk.samtools.DefaultSAMRecordFactory

All Implemented Interfaces:

SAMRecordFactory

public class DefaultSAMRecordFactory
extends java.lang.Object
implements SAMRecordFactory

Default factory for creating SAM and BAM records used by the SamReader classes.

Constructor Summary

Constructors

Constructor and Description
DefaultSAMRecordFactory()

Method Summary

Modifier and Type	Method and Description
BAMRecord	createBAMRecord(SAMFileHeader header, int referenceSequenceIndex, int alignmentStart, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceSequenceIndex, int mateAlignmentStart, int insertSize, byte[] variableLengthBlock) Create a new BAM Record.
SAMRecord	createSAMRecord(SAMFileHeader header) Create a new SAMRecord to be filled in
static DefaultSAMRecordFactory	getInstance()

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultSAMRecordFactory

public DefaultSAMRecordFactory()

Method Detail

getInstance

public static DefaultSAMRecordFactory getInstance()

createSAMRecord

public SAMRecord createSAMRecord(SAMFileHeader header)

Create a new SAMRecord to be filled in

Specified by:

createSAMRecord in interface SAMRecordFactory

createBAMRecord

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

Create a new BAM Record. If the reference sequence index or mate reference sequence index are any value other than NO_ALIGNMENT_REFERENCE_INDEX, the values must be resolvable against the sequence dictionary in the header argument.

Specified by:

createBAMRecord in interface SAMRecordFactory