htsjdk.samtools.cram.mask

Class FastaByteArrayMaskFactory

java.lang.Object

htsjdk.samtools.cram.mask.FastaByteArrayMaskFactory

All Implemented Interfaces:

ReadMaskFactory<java.lang.String>

public class FastaByteArrayMaskFactory
extends java.lang.Object
implements ReadMaskFactory<java.lang.String>

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BUFFER_SIZE
static byte	DEFAULT_MASK_BYTE
static byte	DEFAULT_NON_MASK_BYTE

Constructor Summary

Constructors

Constructor and Description
FastaByteArrayMaskFactory()
FastaByteArrayMaskFactory(byte maskByte)
FastaByteArrayMaskFactory(byte maskByte, int bufSize)

Method Summary

Methods

Modifier and Type	Method and Description
PositionMask	createMask(java.lang.String line)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MASK_BYTE

public static final byte DEFAULT_MASK_BYTE

See Also:

Constant Field Values

DEFAULT_NON_MASK_BYTE

public static final byte DEFAULT_NON_MASK_BYTE

See Also:

Constant Field Values

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

Constructor Detail

FastaByteArrayMaskFactory

public FastaByteArrayMaskFactory(byte maskByte,
                         int bufSize)

FastaByteArrayMaskFactory

public FastaByteArrayMaskFactory(byte maskByte)

FastaByteArrayMaskFactory

public FastaByteArrayMaskFactory()

Method Detail

createMask

public PositionMask createMask(java.lang.String line)
                        throws ReadMaskFormatException

Specified by:

createMask in interface ReadMaskFactory<java.lang.String>

Throws:

ReadMaskFormatException