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

Class CMPH5Constants

java.lang.Object

com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants

public class CMPH5Constants
extends java.lang.Object

Constants used in PacBio cmp.h5 files

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CMPH5_VERSION_1_1_MARKER
static java.lang.String	CMPH5_VERSION_1_2_MARKER
static java.lang.String	CMPH5_VERSION_1_3_MARKER
static java.lang.String	CMPH5_VERSION_2_0_MARKER
static java.lang.String	HDF_ATTRIBUTE_COL_NAME
static java.lang.String	HDF_ATTRIBUTE_LAST_ROW
static java.lang.String	HDF_ATTRIBUTE_READ_GROUP_FULL_SEQUENCE_NAME
static java.lang.String	HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_LENGTH
static java.lang.String	HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_MD5
static java.lang.String	HDF_ATTRIBUTE_READTYPE
static java.lang.String	HDF_ATTRIBUTE_VERSION
static java.lang.String	HDF_DATASET_ALIGNMENT_INDEX
static java.lang.String	HDF_DATASET_ALN_GROUP
static java.lang.String	HDF_DATASET_ALN_INDEX
static java.lang.String	HDF_DATASET_ALN_INFO
static java.lang.String	HDF_DATASET_MOVIE_FRAMERATE
static java.lang.String	HDF_DATASET_MOVIE_ID
static java.lang.String	HDF_DATASET_MOVIE_INFO
static java.lang.String	HDF_DATASET_MOVIE_NAME
static java.lang.String	HDF_DATASET_MOVIE_NAME_V1
static java.lang.String	HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_1
static java.lang.String	HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_2
static java.lang.String	HDF_DATASET_READ_GROUP_CONSENSUS_CALLS
static java.lang.String	HDF_DATASET_READ_GROUP_CONSENSUS_CONFIDENCE
static java.lang.String	HDF_DATASET_READ_GROUP_KINETICS_IPDRATIO
static java.lang.String	HDF_DATASET_READ_GROUP_NORM_IPD
static java.lang.String	HDF_DATASET_READ_GROUP_PATH
static java.lang.String	HDF_DATASET_READ_GROUP_PATH_ID
static java.lang.String	HDF_DATASET_READ_GROUP_PKMID
static java.lang.String	HDF_DATASET_READ_GROUP_PULSE_WIDTH
static java.lang.String	HDF_DATASET_READ_GROUP_QUALITY_VALUE
static java.lang.String	HDF_DATASET_READ_GROUP_RAW_IPD
static java.lang.String	HDF_DATASET_REF_GROUP
static java.lang.String	HDF_DATASET_REF_ID
static java.lang.String	HDF_DATASET_REF_INFO
static java.lang.String	HDF_DATASET_REF_INFO_FULL_NAME
static java.lang.String	HDF_DATASET_REF_INFO_ID
static java.lang.String	HDF_DATASET_REF_PATH
static java.lang.String	HDF_DATASET_REF_SEQ_ID
static java.lang.String	HDF_DATASET_REF_SEQ_NAME
static java.lang.String	HDF_DATASET_SORTED_INDEX_TABLE
static java.lang.String	HDF_DATASET_SORTED_REF_INDEX
static java.lang.String	HDF_GROUP_CONSENSUS
static java.lang.String	HDF_GROUP_KINETICS
static java.lang.String	HDF_PATH_SEPARATOR
static java.lang.String	HDF_READTYPE_CDNA
static java.lang.String	HDF_READTYPE_CSS
static java.lang.String	HDF_READTYPE_STANDARD
static java.lang.String	HDF_READTYPE_STROBE

Constructor Summary

Constructors

Constructor and Description
CMPH5Constants()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

CMPH5_VERSION_1_1_MARKER

public static final java.lang.String CMPH5_VERSION_1_1_MARKER

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Constant Field Values

CMPH5_VERSION_1_2_MARKER

public static final java.lang.String CMPH5_VERSION_1_2_MARKER

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Constant Field Values

CMPH5_VERSION_1_3_MARKER

public static final java.lang.String CMPH5_VERSION_1_3_MARKER

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Constant Field Values

CMPH5_VERSION_2_0_MARKER

public static final java.lang.String CMPH5_VERSION_2_0_MARKER

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Constant Field Values

HDF_DATASET_ALIGNMENT_INDEX

public static final java.lang.String HDF_DATASET_ALIGNMENT_INDEX

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Constant Field Values

HDF_DATASET_MOVIE_ID

public static final java.lang.String HDF_DATASET_MOVIE_ID

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Constant Field Values

HDF_DATASET_READ_GROUP_PATH_ID

public static final java.lang.String HDF_DATASET_READ_GROUP_PATH_ID

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Constant Field Values

HDF_DATASET_REF_SEQ_ID

public static final java.lang.String HDF_DATASET_REF_SEQ_ID

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Constant Field Values

HDF_DATASET_MOVIE_NAME_V1

public static final java.lang.String HDF_DATASET_MOVIE_NAME_V1

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Constant Field Values

HDF_DATASET_REF_SEQ_NAME

public static final java.lang.String HDF_DATASET_REF_SEQ_NAME

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Constant Field Values

HDF_DATASET_READ_GROUP_PATH

public static final java.lang.String HDF_DATASET_READ_GROUP_PATH

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Constant Field Values

HDF_DATASET_SORTED_INDEX_TABLE

public static final java.lang.String HDF_DATASET_SORTED_INDEX_TABLE

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Constant Field Values

HDF_DATASET_REF_GROUP

public static final java.lang.String HDF_DATASET_REF_GROUP

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Constant Field Values

HDF_DATASET_REF_ID

public static final java.lang.String HDF_DATASET_REF_ID

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Constant Field Values

HDF_DATASET_REF_PATH

public static final java.lang.String HDF_DATASET_REF_PATH

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Constant Field Values

HDF_DATASET_REF_INFO_ID

public static final java.lang.String HDF_DATASET_REF_INFO_ID

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Constant Field Values

HDF_DATASET_SORTED_REF_INDEX

public static final java.lang.String HDF_DATASET_SORTED_REF_INDEX

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Constant Field Values

HDF_DATASET_REF_INFO

public static final java.lang.String HDF_DATASET_REF_INFO

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Constant Field Values

HDF_DATASET_REF_INFO_FULL_NAME

public static final java.lang.String HDF_DATASET_REF_INFO_FULL_NAME

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Constant Field Values

HDF_DATASET_ALN_INFO

public static final java.lang.String HDF_DATASET_ALN_INFO

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Constant Field Values

HDF_DATASET_ALN_INDEX

public static final java.lang.String HDF_DATASET_ALN_INDEX

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Constant Field Values

HDF_DATASET_ALN_GROUP

public static final java.lang.String HDF_DATASET_ALN_GROUP

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Constant Field Values

HDF_DATASET_MOVIE_INFO

public static final java.lang.String HDF_DATASET_MOVIE_INFO

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Constant Field Values

HDF_DATASET_MOVIE_NAME

public static final java.lang.String HDF_DATASET_MOVIE_NAME

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Constant Field Values

HDF_DATASET_MOVIE_FRAMERATE

public static final java.lang.String HDF_DATASET_MOVIE_FRAMERATE

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Constant Field Values

HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_1

public static final java.lang.String HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_1

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Constant Field Values

HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_2

public static final java.lang.String HDF_DATASET_READ_GROUP_ALIGNMENT_ARRAY_V1_2

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Constant Field Values

HDF_DATASET_READ_GROUP_RAW_IPD

public static final java.lang.String HDF_DATASET_READ_GROUP_RAW_IPD

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Constant Field Values

HDF_DATASET_READ_GROUP_NORM_IPD

public static final java.lang.String HDF_DATASET_READ_GROUP_NORM_IPD

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Constant Field Values

HDF_DATASET_READ_GROUP_PULSE_WIDTH

public static final java.lang.String HDF_DATASET_READ_GROUP_PULSE_WIDTH

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Constant Field Values

HDF_DATASET_READ_GROUP_QUALITY_VALUE

public static final java.lang.String HDF_DATASET_READ_GROUP_QUALITY_VALUE

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Constant Field Values

HDF_DATASET_READ_GROUP_PKMID

public static final java.lang.String HDF_DATASET_READ_GROUP_PKMID

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Constant Field Values

HDF_GROUP_CONSENSUS

public static final java.lang.String HDF_GROUP_CONSENSUS

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Constant Field Values

HDF_DATASET_READ_GROUP_CONSENSUS_CALLS

public static final java.lang.String HDF_DATASET_READ_GROUP_CONSENSUS_CALLS

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Constant Field Values

HDF_DATASET_READ_GROUP_CONSENSUS_CONFIDENCE

public static final java.lang.String HDF_DATASET_READ_GROUP_CONSENSUS_CONFIDENCE

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Constant Field Values

HDF_GROUP_KINETICS

public static final java.lang.String HDF_GROUP_KINETICS

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Constant Field Values

HDF_DATASET_READ_GROUP_KINETICS_IPDRATIO

public static final java.lang.String HDF_DATASET_READ_GROUP_KINETICS_IPDRATIO

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Constant Field Values

HDF_ATTRIBUTE_LAST_ROW

public static final java.lang.String HDF_ATTRIBUTE_LAST_ROW

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Constant Field Values

HDF_ATTRIBUTE_VERSION

public static final java.lang.String HDF_ATTRIBUTE_VERSION

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Constant Field Values

HDF_ATTRIBUTE_READTYPE

public static final java.lang.String HDF_ATTRIBUTE_READTYPE

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Constant Field Values

HDF_READTYPE_STANDARD

public static final java.lang.String HDF_READTYPE_STANDARD

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Constant Field Values

HDF_READTYPE_STROBE

public static final java.lang.String HDF_READTYPE_STROBE

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Constant Field Values

HDF_READTYPE_CDNA

public static final java.lang.String HDF_READTYPE_CDNA

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Constant Field Values

HDF_READTYPE_CSS

public static final java.lang.String HDF_READTYPE_CSS

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Constant Field Values

HDF_ATTRIBUTE_READ_GROUP_FULL_SEQUENCE_NAME

public static final java.lang.String HDF_ATTRIBUTE_READ_GROUP_FULL_SEQUENCE_NAME

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Constant Field Values

HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_MD5

public static final java.lang.String HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_MD5

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Constant Field Values

HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_LENGTH

public static final java.lang.String HDF_ATTRIBUTE_READ_GROUP_SEQUENCE_LENGTH

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Constant Field Values

HDF_ATTRIBUTE_COL_NAME

public static final java.lang.String HDF_ATTRIBUTE_COL_NAME

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Constant Field Values

HDF_PATH_SEPARATOR

public static final java.lang.String HDF_PATH_SEPARATOR

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Constant Field Values

Constructor Detail

CMPH5Constants

public CMPH5Constants()