java.lang.Object
- htsjdk.samtools.DefaultSAMRecordFactory

All Implemented Interfaces:

SAMRecordFactory
```
public class DefaultSAMRecordFactory
extends Object
implements SAMRecordFactory
```
Default factory for creating SAM and BAM records used by the SamReader classes.

Constructor Summary

Constructors
Constructor Description

DefaultSAMRecordFactory()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Class DefaultSAMRecordFactory

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DefaultSAMRecordFactory

Method Detail

getInstance

createSAMRecord

createBAMRecord