/*
* Copyright (c) 2012 The Broad Institute
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
* 
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* 
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package htsjdk.variant.vcf;

import java.util.Locale;

public final class VCFConstants {
    public static final Locale VCF_LOCALE = Locale.US;

    // reserved INFO/FORMAT field keys
    public static final String ANCESTRAL_ALLELE_KEY = "AA";
    public static final String ALLELE_COUNT_KEY = "AC";
    public static final String ALLELE_FREQUENCY_KEY = "AF";
    public static final String ALLELE_NUMBER_KEY = "AN";
    public static final String RMS_BASE_QUALITY_KEY = "BQ";
    public static final String CIGAR_KEY = "CIGAR";
    public static final String DBSNP_KEY = "DB";
    public static final String DEPTH_KEY = "DP";
    public static final String END_KEY = "END";

    public static final String GENOTYPE_FILTER_KEY = "FT";
    public static final String GENOTYPE_KEY = "GT";
    public static final String GENOTYPE_POSTERIORS_KEY = "GP";
    public static final String GENOTYPE_QUALITY_KEY = "GQ";
    public static final String GENOTYPE_ALLELE_DEPTHS = "AD"; //AD isn't reserved, but is specifically handled by VariantContext
    public static final String GENOTYPE_PL_KEY = "PL";   // phred-scaled genotype likelihoods
    public static final String EXPECTED_ALLELE_COUNT_KEY = "EC";
    @Deprecated public static final String GENOTYPE_LIKELIHOODS_KEY = "GL";         // log10 scaled genotype likelihoods

    public static final String HAPMAP2_KEY = "H2";
    public static final String HAPMAP3_KEY = "H3";
    public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
    public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
    public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0";
    public static final String SAMPLE_NUMBER_KEY = "NS";
    public static final String PHASE_QUALITY_KEY = "PQ";
    public static final String PHASE_SET_KEY = "PS";
    public static final String OLD_DEPTH_KEY = "RD";
    public static final String STRAND_BIAS_KEY = "SB";
    public static final String SOMATIC_KEY = "SOMATIC";
    public static final String VALIDATED_KEY = "VALIDATED";
    public static final String THOUSAND_GENOMES_KEY = "1000G";
    
    // reserved INFO for structural variants
    /** INFO Type of structural variant */
    public static final String SVTYPE = "SVTYPE";    

    // separators
    public static final String FORMAT_FIELD_SEPARATOR = ":";
    public static final String GENOTYPE_FIELD_SEPARATOR = ":";
    public static final char   GENOTYPE_FIELD_SEPARATOR_CHAR = ':';
    public static final String FIELD_SEPARATOR = "\t";
    public static final char   FIELD_SEPARATOR_CHAR = '\t';
    public static final String FILTER_CODE_SEPARATOR = ";";
    public static final String INFO_FIELD_ARRAY_SEPARATOR = ",";
    public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR = ',';
    public static final String ID_FIELD_SEPARATOR = ";";
    public static final String INFO_FIELD_SEPARATOR = ";";
    public static final char INFO_FIELD_SEPARATOR_CHAR = ';';
    public static final String UNPHASED = "/";
    public static final String PHASED = "|";
    public static final String PHASED_SWITCH_PROB_v3 = "\\";
    public static final String PHASING_TOKENS = "/|\\";

    // header lines
    public static final String FILTER_HEADER_START = "##FILTER";
    public static final String FORMAT_HEADER_START = "##FORMAT";
    public static final String INFO_HEADER_START = "##INFO";
    public static final String ALT_HEADER_KEY = "ALT";
    public static final String ALT_HEADER_START = VCFHeader.METADATA_INDICATOR + ALT_HEADER_KEY ;
    public static final String CONTIG_HEADER_KEY = "contig";
    public static final String CONTIG_HEADER_START = "##" + CONTIG_HEADER_KEY;

    public static final int ALT_HEADER_OFFSET = ALT_HEADER_START.length() + 1;

    public static final String PEDIGREE_HEADER_KEY = "PEDIGREE";
    public static final String PEDIGREE_HEADER_START = VCFHeader.METADATA_INDICATOR + PEDIGREE_HEADER_KEY;
    public static final int PEDIGREE_HEADER_OFFSET = PEDIGREE_HEADER_START.length() + 1;

    public static final String SAMPLE_HEADER_KEY = "SAMPLE";
    public static final String SAMPLE_HEADER_START = VCFHeader.METADATA_INDICATOR + SAMPLE_HEADER_KEY;
    public static final int SAMPLE_HEADER_OFFSET = SAMPLE_HEADER_START.length() + 1;

    public static final String META_HEADER_KEY = "META";
    public static final String META_HEADER_START = VCFHeader.METADATA_INDICATOR + META_HEADER_KEY;
    public static final int META_HEADER_OFFSET = META_HEADER_START.length() + 1;

    // old indel alleles
    public static final char DELETION_ALLELE_v3 = 'D';
    public static final char INSERTION_ALLELE_v3 = 'I';

    // special alleles
    public static final char SPANNING_DELETION_ALLELE = '*';
    public static final char NO_CALL_ALLELE = '.';
    public static final char NULL_ALLELE = '-';


    // missing/default values
    public static final String UNFILTERED = ".";
    public static final String PASSES_FILTERS_v3 = "0";
    public static final String PASSES_FILTERS_v4 = "PASS";
    public static final String EMPTY_ID_FIELD = ".";
    public static final String EMPTY_INFO_FIELD = ".";
    public static final String EMPTY_ALTERNATE_ALLELE_FIELD = ".";
    public static final String MISSING_VALUE_v4 = ".";
    public static final String MISSING_QUALITY_v3 = "-1";
    public static final Double MISSING_QUALITY_v3_DOUBLE = Double.valueOf(MISSING_QUALITY_v3);

    public static final String MISSING_GENOTYPE_QUALITY_v3 = "-1";
    public static final String MISSING_HAPLOTYPE_QUALITY_v3 = "-1";
    public static final String MISSING_DEPTH_v3 = "-1";
    public static final String UNBOUNDED_ENCODING_v4 = ".";
    public static final String UNBOUNDED_ENCODING_v3 = "-1";
    public static final String PER_ALTERNATE_COUNT = "A";
    public static final String PER_ALLELE_COUNT = "R";
    public static final String PER_GENOTYPE_COUNT = "G";
    public static final String EMPTY_ALLELE = ".";
    public static final String EMPTY_GENOTYPE = "./.";
    public static final int MAX_GENOTYPE_QUAL = 99;

    public static final Double VCF_ENCODING_EPSILON = 0.00005; // when we consider fields equal(), used in the Qual compare
}
