org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions Maven / Gradle / Ivy
package org.broadinstitute.hellbender.cmdline;
/**
* 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.
*/
public final class StandardArgumentDefinitions {
private StandardArgumentDefinitions(){}
public static final String INPUT_LONG_NAME = "input";
public static final String OUTPUT_LONG_NAME = "output";
public static final String REFERENCE_LONG_NAME = "reference";
public static final String VARIANT_LONG_NAME = "variant";
public static final String FEATURE_LONG_NAME = "feature";
public static final String INTERVALS_LONG_NAME = "intervals";
public static final String COMPARISON_LONG_NAME = "comparison";
public static final String RESOURCE_LONG_NAME = "resource";
public static final String READ_INDEX_LONG_NAME = "read-index";
public static final String USE_ORIGINAL_QUALITIES_LONG_NAME = "use-original-qualities";
public static final String LENIENT_LONG_NAME = "lenient";
public static final String VERBOSITY_NAME = "verbosity";
public static final String READ_VALIDATION_STRINGENCY_LONG_NAME = "read-validation-stringency";
public static final String ASSUME_SORTED_LONG_NAME = "assume-sorted";
public static final String DISABLE_TOOL_DEFAULT_ANNOTATIONS = "disable-tool-default-annotations";
public static final String ENABLE_ALL_ANNOTATIONS = "enable-all-annotations";
public static final String CREATE_OUTPUT_BAM_INDEX_LONG_NAME = "create-output-bam-index";
public static final String CREATE_OUTPUT_BAM_MD5_LONG_NAME = "create-output-bam-md5";
public static final String CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME = "create-output-variant-index";
public static final String CREATE_OUTPUT_VARIANT_MD5_LONG_NAME = "create-output-variant-md5";
public static final String METRIC_ACCUMULATION_LEVEL_LONG_NAME = "metric-accumulation-level";
public static final String CLOUD_PREFETCH_BUFFER_LONG_NAME = "cloud-prefetch-buffer";
public static final String CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME = "cloud-index-prefetch-buffer";
public static final String DISABLE_BAM_INDEX_CACHING_LONG_NAME = "disable-bam-index-caching";
public static final String DISABLE_SEQUENCE_DICT_VALIDATION_NAME = "disable-sequence-dictionary-validation";
public static final String ADD_OUTPUT_SAM_PROGRAM_RECORD = "add-output-sam-program-record";
public static final String ADD_OUTPUT_VCF_COMMANDLINE = "add-output-vcf-command-line";
public static final String SEQUENCE_DICTIONARY_NAME = "sequence-dictionary";
public static final String ANNOTATION_LONG_NAME = "annotation";
public static final String ANNOTATION_GROUP_LONG_NAME = "annotation-group";
public static final String ANNOTATIONS_TO_EXCLUDE_LONG_NAME = "annotations-to-exclude";
public static final String SAMPLE_NAME_LONG_NAME = "sample-name";
public static final String PEDIGREE_FILE_LONG_NAME = "pedigree";
public static final String SITES_ONLY_LONG_NAME = "sites-only-vcf-output";
public static final String INVALIDATE_PREVIOUS_FILTERS_LONG_NAME = "invalidate-previous-filters";
public static final String SORT_ORDER_LONG_NAME = "sort-order";
public static final String INPUT_SHORT_NAME = "I";
public static final String OUTPUT_SHORT_NAME = "O";
public static final String REFERENCE_SHORT_NAME = "R";
public static final String VARIANT_SHORT_NAME = "V";
public static final String FEATURE_SHORT_NAME = "F";
public static final String INTERVALS_SHORT_NAME = "L";
public static final String COMPARISON_SHORT_NAME = "comp";
public static final String READ_INDEX_SHORT_NAME = READ_INDEX_LONG_NAME;
public static final String LENIENT_SHORT_NAME = "LE";
public static final String READ_VALIDATION_STRINGENCY_SHORT_NAME = "VS";
public static final String SAMPLE_ALIAS_SHORT_NAME = "ALIAS";
public static final String ASSUME_SORTED_SHORT_NAME = "AS";
public static final String PROGRAM_RECORD_ID_SHORT_NAME = "PG";
public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME = "OQ";
public static final String CREATE_OUTPUT_BAM_INDEX_SHORT_NAME = "OBI";
public static final String CREATE_OUTPUT_BAM_MD5_SHORT_NAME = "OBM";
public static final String CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME = "OVI";
public static final String CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME = "OVM";
public static final String METRIC_ACCUMULATION_LEVEL_SHORT_NAME = "LEVEL";
public static final String CLOUD_PREFETCH_BUFFER_SHORT_NAME = "CPB";
public static final String CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME = "CIPB";
public static final String DISABLE_BAM_INDEX_CACHING_SHORT_NAME = "DBIC";
public static final String ANNOTATION_SHORT_NAME = "A";
public static final String ANNOTATION_GROUP_SHORT_NAME = "G";
public static final String ANNOTATIONS_TO_EXCLUDE_SHORT_NAME = "AX";
public static final String SAMPLE_NAME_SHORT_NAME = "sn";
public static final String PEDIGREE_FILE_SHORT_NAME = "ped";
public static final String SORT_ORDER_SHORT_NAME = "SO";
public static final String SPARK_PROPERTY_NAME = "conf";
public static final String BQSR_TABLE_SHORT_NAME = "bqsr";
public static final String BQSR_TABLE_LONG_NAME = "bqsr-recal-file";
public static final String DUPLICATE_SCORING_STRATEGY_LONG_NAME = "duplicate-scoring-strategy";
public static final String DUPLICATE_SCORING_STRATEGY_SHORT_NAME = "DS";
public static final String METRICS_FILE_LONG_NAME = "metrics-file";
public static final String METRICS_FILE_SHORT_NAME = "M";
/**
* The option specifying a main configuration file.
* This is used in {@link org.broadinstitute.hellbender.Main} to control which config file is loaded.
*/
public static final String GATK_CONFIG_FILE_OPTION = "gatk-config-file";
public static final String TMP_DIR_NAME = "tmp-dir";
public static final String QUIET_NAME = "QUIET";
public static final String USE_JDK_DEFLATER_LONG_NAME = "use-jdk-deflater";
public static final String USE_JDK_DEFLATER_SHORT_NAME = "jdk-deflater";
public static final String USE_JDK_INFLATER_LONG_NAME = "use-jdk-inflater";
public static final String USE_JDK_INFLATER_SHORT_NAME = "jdk-inflater";
public static final String NIO_MAX_REOPENS_LONG_NAME = "gcs-max-retries";
public static final String NIO_MAX_REOPENS_SHORT_NAME = "gcs-retries";
public static final String NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME = "gcs-project-for-requester-pays";
}