com.pacbio.secondary.vis.io.hdf.constants

Class AlignmentConstants

java.lang.Object

com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants

public class AlignmentConstants
extends java.lang.Object

Constants used by aligned data pairs

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
static int	ANNOTATED_READS_WITH_BASES
static int	ANNOTATED_READS_WITH_PW
static int	ANNOTATED_READS_WITH_QV
static int	ANNOTATED_READS_WITH_RAW_IPD
static int	CMPH5_FWD_IPD_OFFSET
static int	CMPH5_REV_IPD_OFFSET
static int	RESULTS_METRICS_BITMASK
static char[]	TRANSLATE_READ_4BITS Translates a 4-bit compressed base into a letter
static char[]	TRANSLATE_REVERSE_READ_4BITS Translates a 4-bit compressed complemented base into a letter

Constructor Summary

Constructors

Constructor and Description
AlignmentConstants()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

TRANSLATE_READ_4BITS

public static final char[] TRANSLATE_READ_4BITS

Translates a 4-bit compressed base into a letter

TRANSLATE_REVERSE_READ_4BITS

public static final char[] TRANSLATE_REVERSE_READ_4BITS

Translates a 4-bit compressed complemented base into a letter

RESULTS_METRICS_BITMASK

public static final int RESULTS_METRICS_BITMASK

See Also:

Constant Field Values

ANNOTATED_READS_WITH_BASES

public static final int ANNOTATED_READS_WITH_BASES

See Also:

Constant Field Values

ANNOTATED_READS_WITH_QV

public static final int ANNOTATED_READS_WITH_QV

See Also:

Constant Field Values

ANNOTATED_READS_WITH_RAW_IPD

public static final int ANNOTATED_READS_WITH_RAW_IPD

See Also:

Constant Field Values

ANNOTATED_READS_WITH_PW

public static final int ANNOTATED_READS_WITH_PW

See Also:

Constant Field Values

CMPH5_FWD_IPD_OFFSET

public static final int CMPH5_FWD_IPD_OFFSET

See Also:

Constant Field Values

CMPH5_REV_IPD_OFFSET

public static final int CMPH5_REV_IPD_OFFSET

See Also:

Constant Field Values

Constructor Detail

AlignmentConstants

public AlignmentConstants()