1 package org.broadinstitute.hellbender.cmdline; 2 3 /** 4 * A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) 5 * is the standard long Option name, and the value of the constant is the standard shortName. 6 */ 7 public final class StandardArgumentDefinitions { 8 StandardArgumentDefinitions()9 private StandardArgumentDefinitions(){} 10 11 public static final String INPUT_LONG_NAME = "input"; 12 public static final String OUTPUT_LONG_NAME = "output"; 13 public static final String REFERENCE_LONG_NAME = "reference"; 14 public static final String VARIANT_LONG_NAME = "variant"; 15 public static final String FEATURE_LONG_NAME = "feature"; 16 public static final String INTERVALS_LONG_NAME = "intervals"; 17 public static final String COMPARISON_LONG_NAME = "comparison"; 18 public static final String RESOURCE_LONG_NAME = "resource"; 19 public static final String READ_INDEX_LONG_NAME = "read-index"; 20 public static final String USE_ORIGINAL_QUALITIES_LONG_NAME = "use-original-qualities"; 21 public static final String LENIENT_LONG_NAME = "lenient"; 22 public static final String VERBOSITY_NAME = "verbosity"; 23 public static final String READ_VALIDATION_STRINGENCY_LONG_NAME = "read-validation-stringency"; 24 public static final String ASSUME_SORTED_LONG_NAME = "assume-sorted"; 25 public static final String DISABLE_TOOL_DEFAULT_ANNOTATIONS = "disable-tool-default-annotations"; 26 public static final String ENABLE_ALL_ANNOTATIONS = "enable-all-annotations"; 27 public static final String CREATE_OUTPUT_BAM_INDEX_LONG_NAME = "create-output-bam-index"; 28 public static final String CREATE_OUTPUT_BAM_MD5_LONG_NAME = "create-output-bam-md5"; 29 public static final String CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME = "create-output-variant-index"; 30 public static final String CREATE_OUTPUT_VARIANT_MD5_LONG_NAME = "create-output-variant-md5"; 31 public static final String METRIC_ACCUMULATION_LEVEL_LONG_NAME = "metric-accumulation-level"; 32 public static final String CLOUD_PREFETCH_BUFFER_LONG_NAME = "cloud-prefetch-buffer"; 33 public static final String CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME = "cloud-index-prefetch-buffer"; 34 public static final String DISABLE_BAM_INDEX_CACHING_LONG_NAME = "disable-bam-index-caching"; 35 public static final String DISABLE_SEQUENCE_DICT_VALIDATION_NAME = "disable-sequence-dictionary-validation"; 36 public static final String ADD_OUTPUT_SAM_PROGRAM_RECORD = "add-output-sam-program-record"; 37 public static final String ADD_OUTPUT_VCF_COMMANDLINE = "add-output-vcf-command-line"; 38 public static final String SEQUENCE_DICTIONARY_NAME = "sequence-dictionary"; 39 public static final String ANNOTATION_LONG_NAME = "annotation"; 40 public static final String ANNOTATION_GROUP_LONG_NAME = "annotation-group"; 41 public static final String ANNOTATIONS_TO_EXCLUDE_LONG_NAME = "annotations-to-exclude"; 42 public static final String SAMPLE_NAME_LONG_NAME = "sample-name"; 43 public static final String PEDIGREE_FILE_LONG_NAME = "pedigree"; 44 public static final String SITES_ONLY_LONG_NAME = "sites-only-vcf-output"; 45 public static final String INVALIDATE_PREVIOUS_FILTERS_LONG_NAME = "invalidate-previous-filters"; 46 public static final String SORT_ORDER_LONG_NAME = "sort-order"; 47 48 49 public static final String INPUT_SHORT_NAME = "I"; 50 public static final String OUTPUT_SHORT_NAME = "O"; 51 public static final String REFERENCE_SHORT_NAME = "R"; 52 public static final String VARIANT_SHORT_NAME = "V"; 53 public static final String FEATURE_SHORT_NAME = "F"; 54 public static final String INTERVALS_SHORT_NAME = "L"; 55 public static final String COMPARISON_SHORT_NAME = "comp"; 56 public static final String READ_INDEX_SHORT_NAME = READ_INDEX_LONG_NAME; 57 public static final String LENIENT_SHORT_NAME = "LE"; 58 public static final String READ_VALIDATION_STRINGENCY_SHORT_NAME = "VS"; 59 public static final String SAMPLE_ALIAS_SHORT_NAME = "ALIAS"; 60 public static final String ASSUME_SORTED_SHORT_NAME = "AS"; 61 public static final String PROGRAM_RECORD_ID_SHORT_NAME = "PG"; 62 public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME = "OQ"; 63 public static final String CREATE_OUTPUT_BAM_INDEX_SHORT_NAME = "OBI"; 64 public static final String CREATE_OUTPUT_BAM_MD5_SHORT_NAME = "OBM"; 65 public static final String CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME = "OVI"; 66 public static final String CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME = "OVM"; 67 public static final String METRIC_ACCUMULATION_LEVEL_SHORT_NAME = "LEVEL"; 68 public static final String CLOUD_PREFETCH_BUFFER_SHORT_NAME = "CPB"; 69 public static final String CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME = "CIPB"; 70 public static final String DISABLE_BAM_INDEX_CACHING_SHORT_NAME = "DBIC"; 71 public static final String ANNOTATION_SHORT_NAME = "A"; 72 public static final String ANNOTATION_GROUP_SHORT_NAME = "G"; 73 public static final String ANNOTATIONS_TO_EXCLUDE_SHORT_NAME = "AX"; 74 public static final String SAMPLE_NAME_SHORT_NAME = "sn"; 75 public static final String PEDIGREE_FILE_SHORT_NAME = "ped"; 76 public static final String SORT_ORDER_SHORT_NAME = "SO"; 77 78 public static final String SPARK_PROPERTY_NAME = "conf"; 79 80 public static final String BQSR_TABLE_SHORT_NAME = "bqsr"; 81 public static final String BQSR_TABLE_LONG_NAME = "bqsr-recal-file"; 82 83 public static final String DUPLICATE_SCORING_STRATEGY_LONG_NAME = "duplicate-scoring-strategy"; 84 public static final String DUPLICATE_SCORING_STRATEGY_SHORT_NAME = "DS"; 85 public static final String METRICS_FILE_LONG_NAME = "metrics-file"; 86 public static final String METRICS_FILE_SHORT_NAME = "M"; 87 88 // Constants for use as companion attributes in WDL WorkflowInput/WorkflowOutput annotations. These values 89 // are used by the WDL generator to emit separate task/workflow input and output arguments for companion files. 90 public static final String INPUT_INDEX_COMPANION = INPUT_LONG_NAME + "Index"; 91 public static final String OUTPUT_INDEX_COMPANION = OUTPUT_LONG_NAME + "Index"; 92 public static final String REFERENCE_INDEX_COMPANION = REFERENCE_LONG_NAME + "Index"; 93 public static final String REFERENCE_DICTIONARY_COMPANION = REFERENCE_LONG_NAME + "Dictionary"; 94 95 /** 96 * The option specifying a main configuration file. 97 * This is used in {@link org.broadinstitute.hellbender.Main} to control which config file is loaded. 98 */ 99 public static final String GATK_CONFIG_FILE_OPTION = "gatk-config-file"; 100 101 public static final String TMP_DIR_NAME = "tmp-dir"; 102 public static final String QUIET_NAME = "QUIET"; 103 public static final String USE_JDK_DEFLATER_LONG_NAME = "use-jdk-deflater"; 104 public static final String USE_JDK_DEFLATER_SHORT_NAME = "jdk-deflater"; 105 public static final String USE_JDK_INFLATER_LONG_NAME = "use-jdk-inflater"; 106 public static final String USE_JDK_INFLATER_SHORT_NAME = "jdk-inflater"; 107 public static final String NIO_MAX_REOPENS_LONG_NAME = "gcs-max-retries"; 108 public static final String NIO_MAX_REOPENS_SHORT_NAME = "gcs-retries"; 109 public static final String NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME = "gcs-project-for-requester-pays"; 110 } 111