79 lines
3.7 KiB
Java
79 lines
3.7 KiB
Java
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broad.tribble.vcf;
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public final class VCFConstants {
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// standard INFO/FORMAT field keys
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public static final String ANCESTRAL_ALLELE_KEY = "AA";
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public static final String ALLELE_COUNT_KEY = "AC";
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public static final String ALLELE_FREQUENCY_KEY = "AF";
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public static final String ALLELE_NUMBER_KEY = "AN";
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public static final String RMS_BASE_QUALITY_KEY = "BQ";
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public static final String CIGAR_KEY = "CIGAR";
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public static final String DBSNP_KEY = "DB";
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public static final String DEPTH_KEY = "DP";
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public static final String END_KEY = "END";
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public static final String GENOTYPE_FILTER_KEY = "FT";
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public static final String GENOTYPE_KEY = "GT";
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public static final String GENOTYPE_LIKELIHOODS_KEY = "GL";
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public static final String GENOTYPE_QUALITY_KEY = "GQ";
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public static final String HAPMAP2_KEY = "H2";
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public static final String HAPMAP3_KEY = "H3";
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public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
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public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
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public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0";
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public static final String SAMPLE_NUMBER_KEY = "NS";
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public static final String OLD_DEPTH_KEY = "RD";
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public static final String STRAND_BIAS_KEY = "SB";
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public static final String SOMATIC_KEY = "SOMATIC";
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public static final String VALIDATED_KEY = "VALIDATED";
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// separators
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public static final String FORMAT_FIELD_SEPARATOR = ":";
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public static final String GENOTYPE_FIELD_SEPARATOR = ":";
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public static final String FIELD_SEPARATOR = "\t";
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public static final String FILTER_CODE_SEPARATOR = ";";
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public static final String INFO_FIELD_SEPARATOR = ";";
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// missing/default values
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public static final String UNFILTERED = ".";
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public static final String PASSES_FILTERS_v3 = "0";
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public static final String PASSES_FILTERS_v4 = "PASS";
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public static final String EMPTY_ID_FIELD = ".";
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public static final String EMPTY_INFO_FIELD = ".";
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public static final String EMPTY_ALTERNATE_ALLELE_FIELD = ".";
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public static final String MISSING_VALUE_v4 = ".";
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public static final String MISSING_QUALITY_v3 = "-1";
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public static final String MISSING_GENOTYPE_QUALITY_v3 = "-1";
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public static final String MISSING_HAPLOTYPE_QUALITY_v3 = "-1";
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public static final String MISSING_DEPTH_v3 = "-1";
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public static final String EMPTY_ALLELE = ".";
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public static final String EMPTY_GENOTYPE = "./.";
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public static final double MAX_GENOTYPE_QUAL = 99.0;
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public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
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}
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