org.broadinstitute.hellbender.cmdline

Class StandardArgumentDefinitions

java.lang.Object

org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions

public final class StandardArgumentDefinitions
extends java.lang.Object

A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ADD_OUTPUT_SAM_PROGRAM_RECORD
static java.lang.String	ADD_OUTPUT_VCF_COMMANDLINE
static java.lang.String	ANNOTATION_GROUP_LONG_NAME
static java.lang.String	ANNOTATION_GROUP_SHORT_NAME
static java.lang.String	ANNOTATION_LONG_NAME
static java.lang.String	ANNOTATION_SHORT_NAME
static java.lang.String	ANNOTATIONS_TO_EXCLUDE_LONG_NAME
static java.lang.String	ANNOTATIONS_TO_EXCLUDE_SHORT_NAME
static java.lang.String	ASSUME_SORTED_LONG_NAME
static java.lang.String	ASSUME_SORTED_SHORT_NAME
static java.lang.String	BQSR_TABLE_LONG_NAME
static java.lang.String	BQSR_TABLE_SHORT_NAME
static java.lang.String	CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME
static java.lang.String	CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME
static java.lang.String	CLOUD_PREFETCH_BUFFER_LONG_NAME
static java.lang.String	CLOUD_PREFETCH_BUFFER_SHORT_NAME
static java.lang.String	COMPARISON_LONG_NAME
static java.lang.String	COMPARISON_SHORT_NAME
static java.lang.String	CREATE_OUTPUT_BAM_INDEX_LONG_NAME
static java.lang.String	CREATE_OUTPUT_BAM_INDEX_SHORT_NAME
static java.lang.String	CREATE_OUTPUT_BAM_MD5_LONG_NAME
static java.lang.String	CREATE_OUTPUT_BAM_MD5_SHORT_NAME
static java.lang.String	CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME
static java.lang.String	CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME
static java.lang.String	CREATE_OUTPUT_VARIANT_MD5_LONG_NAME
static java.lang.String	CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME
static java.lang.String	DISABLE_BAM_INDEX_CACHING_LONG_NAME
static java.lang.String	DISABLE_BAM_INDEX_CACHING_SHORT_NAME
static java.lang.String	DISABLE_SEQUENCE_DICT_VALIDATION_NAME
static java.lang.String	DISABLE_TOOL_DEFAULT_ANNOTATIONS
static java.lang.String	DUPLICATE_SCORING_STRATEGY_LONG_NAME
static java.lang.String	DUPLICATE_SCORING_STRATEGY_SHORT_NAME
static java.lang.String	ENABLE_ALL_ANNOTATIONS
static java.lang.String	FEATURE_LONG_NAME
static java.lang.String	FEATURE_SHORT_NAME
static java.lang.String	GATK_CONFIG_FILE_OPTION The option specifying a main configuration file.
static java.lang.String	INPUT_INDEX_COMPANION
static java.lang.String	INPUT_LONG_NAME
static java.lang.String	INPUT_SHORT_NAME
static java.lang.String	INTERVALS_LONG_NAME
static java.lang.String	INTERVALS_SHORT_NAME
static java.lang.String	INVALIDATE_PREVIOUS_FILTERS_LONG_NAME
static java.lang.String	LENIENT_LONG_NAME
static java.lang.String	LENIENT_SHORT_NAME
static java.lang.String	METRIC_ACCUMULATION_LEVEL_LONG_NAME
static java.lang.String	METRIC_ACCUMULATION_LEVEL_SHORT_NAME
static java.lang.String	METRICS_FILE_LONG_NAME
static java.lang.String	METRICS_FILE_SHORT_NAME
static java.lang.String	NIO_MAX_REOPENS_LONG_NAME
static java.lang.String	NIO_MAX_REOPENS_SHORT_NAME
static java.lang.String	NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME
static java.lang.String	OUTPUT_INDEX_COMPANION
static java.lang.String	OUTPUT_LONG_NAME
static java.lang.String	OUTPUT_SHORT_NAME
static java.lang.String	PEDIGREE_FILE_LONG_NAME
static java.lang.String	PEDIGREE_FILE_SHORT_NAME
static java.lang.String	PROGRAM_RECORD_ID_SHORT_NAME
static java.lang.String	QUIET_NAME
static java.lang.String	READ_INDEX_LONG_NAME
static java.lang.String	READ_INDEX_SHORT_NAME
static java.lang.String	READ_VALIDATION_STRINGENCY_LONG_NAME
static java.lang.String	READ_VALIDATION_STRINGENCY_SHORT_NAME
static java.lang.String	REFERENCE_DICTIONARY_COMPANION
static java.lang.String	REFERENCE_INDEX_COMPANION
static java.lang.String	REFERENCE_LONG_NAME
static java.lang.String	REFERENCE_SHORT_NAME
static java.lang.String	RESOURCE_LONG_NAME
static java.lang.String	SAMPLE_ALIAS_SHORT_NAME
static java.lang.String	SAMPLE_NAME_LONG_NAME
static java.lang.String	SAMPLE_NAME_SHORT_NAME
static java.lang.String	SEQUENCE_DICTIONARY_NAME
static java.lang.String	SITES_ONLY_LONG_NAME
static java.lang.String	SORT_ORDER_LONG_NAME
static java.lang.String	SORT_ORDER_SHORT_NAME
static java.lang.String	SPARK_PROPERTY_NAME
static java.lang.String	TMP_DIR_NAME
static java.lang.String	USE_JDK_DEFLATER_LONG_NAME
static java.lang.String	USE_JDK_DEFLATER_SHORT_NAME
static java.lang.String	USE_JDK_INFLATER_LONG_NAME
static java.lang.String	USE_JDK_INFLATER_SHORT_NAME
static java.lang.String	USE_ORIGINAL_QUALITIES_LONG_NAME
static java.lang.String	USE_ORIGINAL_QUALITIES_SHORT_NAME
static java.lang.String	VARIANT_LONG_NAME
static java.lang.String	VARIANT_SHORT_NAME
static java.lang.String	VERBOSITY_NAME

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

INPUT_LONG_NAME

public static final java.lang.String INPUT_LONG_NAME

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Constant Field Values

OUTPUT_LONG_NAME

public static final java.lang.String OUTPUT_LONG_NAME

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Constant Field Values

REFERENCE_LONG_NAME

public static final java.lang.String REFERENCE_LONG_NAME

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Constant Field Values

VARIANT_LONG_NAME

public static final java.lang.String VARIANT_LONG_NAME

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Constant Field Values

FEATURE_LONG_NAME

public static final java.lang.String FEATURE_LONG_NAME

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Constant Field Values

INTERVALS_LONG_NAME

public static final java.lang.String INTERVALS_LONG_NAME

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Constant Field Values

COMPARISON_LONG_NAME

public static final java.lang.String COMPARISON_LONG_NAME

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Constant Field Values

RESOURCE_LONG_NAME

public static final java.lang.String RESOURCE_LONG_NAME

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Constant Field Values

READ_INDEX_LONG_NAME

public static final java.lang.String READ_INDEX_LONG_NAME

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Constant Field Values

USE_ORIGINAL_QUALITIES_LONG_NAME

public static final java.lang.String USE_ORIGINAL_QUALITIES_LONG_NAME

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Constant Field Values

LENIENT_LONG_NAME

public static final java.lang.String LENIENT_LONG_NAME

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Constant Field Values

VERBOSITY_NAME

public static final java.lang.String VERBOSITY_NAME

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Constant Field Values

READ_VALIDATION_STRINGENCY_LONG_NAME

public static final java.lang.String READ_VALIDATION_STRINGENCY_LONG_NAME

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Constant Field Values

ASSUME_SORTED_LONG_NAME

public static final java.lang.String ASSUME_SORTED_LONG_NAME

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Constant Field Values

DISABLE_TOOL_DEFAULT_ANNOTATIONS

public static final java.lang.String DISABLE_TOOL_DEFAULT_ANNOTATIONS

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Constant Field Values

ENABLE_ALL_ANNOTATIONS

public static final java.lang.String ENABLE_ALL_ANNOTATIONS

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Constant Field Values

CREATE_OUTPUT_BAM_INDEX_LONG_NAME

public static final java.lang.String CREATE_OUTPUT_BAM_INDEX_LONG_NAME

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Constant Field Values

CREATE_OUTPUT_BAM_MD5_LONG_NAME

public static final java.lang.String CREATE_OUTPUT_BAM_MD5_LONG_NAME

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Constant Field Values

CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME

public static final java.lang.String CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME

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Constant Field Values

CREATE_OUTPUT_VARIANT_MD5_LONG_NAME

public static final java.lang.String CREATE_OUTPUT_VARIANT_MD5_LONG_NAME

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Constant Field Values

METRIC_ACCUMULATION_LEVEL_LONG_NAME

public static final java.lang.String METRIC_ACCUMULATION_LEVEL_LONG_NAME

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Constant Field Values

CLOUD_PREFETCH_BUFFER_LONG_NAME

public static final java.lang.String CLOUD_PREFETCH_BUFFER_LONG_NAME

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Constant Field Values

CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME

public static final java.lang.String CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME

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Constant Field Values

DISABLE_BAM_INDEX_CACHING_LONG_NAME

public static final java.lang.String DISABLE_BAM_INDEX_CACHING_LONG_NAME

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Constant Field Values

DISABLE_SEQUENCE_DICT_VALIDATION_NAME

public static final java.lang.String DISABLE_SEQUENCE_DICT_VALIDATION_NAME

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Constant Field Values

ADD_OUTPUT_SAM_PROGRAM_RECORD

public static final java.lang.String ADD_OUTPUT_SAM_PROGRAM_RECORD

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Constant Field Values

ADD_OUTPUT_VCF_COMMANDLINE

public static final java.lang.String ADD_OUTPUT_VCF_COMMANDLINE

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Constant Field Values

SEQUENCE_DICTIONARY_NAME

public static final java.lang.String SEQUENCE_DICTIONARY_NAME

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Constant Field Values

ANNOTATION_LONG_NAME

public static final java.lang.String ANNOTATION_LONG_NAME

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Constant Field Values

ANNOTATION_GROUP_LONG_NAME

public static final java.lang.String ANNOTATION_GROUP_LONG_NAME

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Constant Field Values

ANNOTATIONS_TO_EXCLUDE_LONG_NAME

public static final java.lang.String ANNOTATIONS_TO_EXCLUDE_LONG_NAME

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Constant Field Values

SAMPLE_NAME_LONG_NAME

public static final java.lang.String SAMPLE_NAME_LONG_NAME

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Constant Field Values

PEDIGREE_FILE_LONG_NAME

public static final java.lang.String PEDIGREE_FILE_LONG_NAME

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Constant Field Values

SITES_ONLY_LONG_NAME

public static final java.lang.String SITES_ONLY_LONG_NAME

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Constant Field Values

INVALIDATE_PREVIOUS_FILTERS_LONG_NAME

public static final java.lang.String INVALIDATE_PREVIOUS_FILTERS_LONG_NAME

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Constant Field Values

SORT_ORDER_LONG_NAME

public static final java.lang.String SORT_ORDER_LONG_NAME

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Constant Field Values

INPUT_SHORT_NAME

public static final java.lang.String INPUT_SHORT_NAME

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Constant Field Values

OUTPUT_SHORT_NAME

public static final java.lang.String OUTPUT_SHORT_NAME

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Constant Field Values

REFERENCE_SHORT_NAME

public static final java.lang.String REFERENCE_SHORT_NAME

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Constant Field Values

VARIANT_SHORT_NAME

public static final java.lang.String VARIANT_SHORT_NAME

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Constant Field Values

FEATURE_SHORT_NAME

public static final java.lang.String FEATURE_SHORT_NAME

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Constant Field Values

INTERVALS_SHORT_NAME

public static final java.lang.String INTERVALS_SHORT_NAME

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Constant Field Values

COMPARISON_SHORT_NAME

public static final java.lang.String COMPARISON_SHORT_NAME

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Constant Field Values

READ_INDEX_SHORT_NAME

public static final java.lang.String READ_INDEX_SHORT_NAME

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Constant Field Values

LENIENT_SHORT_NAME

public static final java.lang.String LENIENT_SHORT_NAME

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Constant Field Values

READ_VALIDATION_STRINGENCY_SHORT_NAME

public static final java.lang.String READ_VALIDATION_STRINGENCY_SHORT_NAME

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Constant Field Values

SAMPLE_ALIAS_SHORT_NAME

public static final java.lang.String SAMPLE_ALIAS_SHORT_NAME

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Constant Field Values

ASSUME_SORTED_SHORT_NAME

public static final java.lang.String ASSUME_SORTED_SHORT_NAME

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Constant Field Values

PROGRAM_RECORD_ID_SHORT_NAME

public static final java.lang.String PROGRAM_RECORD_ID_SHORT_NAME

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Constant Field Values

USE_ORIGINAL_QUALITIES_SHORT_NAME

public static final java.lang.String USE_ORIGINAL_QUALITIES_SHORT_NAME

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Constant Field Values

CREATE_OUTPUT_BAM_INDEX_SHORT_NAME

public static final java.lang.String CREATE_OUTPUT_BAM_INDEX_SHORT_NAME

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Constant Field Values

CREATE_OUTPUT_BAM_MD5_SHORT_NAME

public static final java.lang.String CREATE_OUTPUT_BAM_MD5_SHORT_NAME

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Constant Field Values

CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME

public static final java.lang.String CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME

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Constant Field Values

CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME

public static final java.lang.String CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME

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Constant Field Values

METRIC_ACCUMULATION_LEVEL_SHORT_NAME

public static final java.lang.String METRIC_ACCUMULATION_LEVEL_SHORT_NAME

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Constant Field Values

CLOUD_PREFETCH_BUFFER_SHORT_NAME

public static final java.lang.String CLOUD_PREFETCH_BUFFER_SHORT_NAME

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Constant Field Values

CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME

public static final java.lang.String CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME

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Constant Field Values

DISABLE_BAM_INDEX_CACHING_SHORT_NAME

public static final java.lang.String DISABLE_BAM_INDEX_CACHING_SHORT_NAME

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Constant Field Values

ANNOTATION_SHORT_NAME

public static final java.lang.String ANNOTATION_SHORT_NAME

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Constant Field Values

ANNOTATION_GROUP_SHORT_NAME

public static final java.lang.String ANNOTATION_GROUP_SHORT_NAME

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Constant Field Values

ANNOTATIONS_TO_EXCLUDE_SHORT_NAME

public static final java.lang.String ANNOTATIONS_TO_EXCLUDE_SHORT_NAME

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Constant Field Values

SAMPLE_NAME_SHORT_NAME

public static final java.lang.String SAMPLE_NAME_SHORT_NAME

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Constant Field Values

PEDIGREE_FILE_SHORT_NAME

public static final java.lang.String PEDIGREE_FILE_SHORT_NAME

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Constant Field Values

SORT_ORDER_SHORT_NAME

public static final java.lang.String SORT_ORDER_SHORT_NAME

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Constant Field Values

SPARK_PROPERTY_NAME

public static final java.lang.String SPARK_PROPERTY_NAME

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Constant Field Values

BQSR_TABLE_SHORT_NAME

public static final java.lang.String BQSR_TABLE_SHORT_NAME

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Constant Field Values

BQSR_TABLE_LONG_NAME

public static final java.lang.String BQSR_TABLE_LONG_NAME

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Constant Field Values

DUPLICATE_SCORING_STRATEGY_LONG_NAME

public static final java.lang.String DUPLICATE_SCORING_STRATEGY_LONG_NAME

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Constant Field Values

DUPLICATE_SCORING_STRATEGY_SHORT_NAME

public static final java.lang.String DUPLICATE_SCORING_STRATEGY_SHORT_NAME

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Constant Field Values

METRICS_FILE_LONG_NAME

public static final java.lang.String METRICS_FILE_LONG_NAME

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Constant Field Values

METRICS_FILE_SHORT_NAME

public static final java.lang.String METRICS_FILE_SHORT_NAME

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Constant Field Values

INPUT_INDEX_COMPANION

public static final java.lang.String INPUT_INDEX_COMPANION

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Constant Field Values

OUTPUT_INDEX_COMPANION

public static final java.lang.String OUTPUT_INDEX_COMPANION

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Constant Field Values

REFERENCE_INDEX_COMPANION

public static final java.lang.String REFERENCE_INDEX_COMPANION

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Constant Field Values

REFERENCE_DICTIONARY_COMPANION

public static final java.lang.String REFERENCE_DICTIONARY_COMPANION

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Constant Field Values

GATK_CONFIG_FILE_OPTION

public static final java.lang.String GATK_CONFIG_FILE_OPTION

The option specifying a main configuration file. This is used in Main to control which config file is loaded.

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Constant Field Values

TMP_DIR_NAME

public static final java.lang.String TMP_DIR_NAME

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Constant Field Values

QUIET_NAME

public static final java.lang.String QUIET_NAME

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Constant Field Values

USE_JDK_DEFLATER_LONG_NAME

public static final java.lang.String USE_JDK_DEFLATER_LONG_NAME

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Constant Field Values

USE_JDK_DEFLATER_SHORT_NAME

public static final java.lang.String USE_JDK_DEFLATER_SHORT_NAME

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Constant Field Values

USE_JDK_INFLATER_LONG_NAME

public static final java.lang.String USE_JDK_INFLATER_LONG_NAME

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Constant Field Values

USE_JDK_INFLATER_SHORT_NAME

public static final java.lang.String USE_JDK_INFLATER_SHORT_NAME

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Constant Field Values

NIO_MAX_REOPENS_LONG_NAME

public static final java.lang.String NIO_MAX_REOPENS_LONG_NAME

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Constant Field Values

NIO_MAX_REOPENS_SHORT_NAME

public static final java.lang.String NIO_MAX_REOPENS_SHORT_NAME

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Constant Field Values

NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME

public static final java.lang.String NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME

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Constant Field Values