예제 #1
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        public CosmicTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider)
        {
            Console.WriteLine(version.ToString());

            _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
                                      SaTsvCommon.CosmicSchemaVersion, InterimSaCommon.CosmicTag, InterimSaCommon.CosmicVcfTag, false, sequenceProvider, true);
        }
예제 #2
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        public GnomadTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider, string sequencingDataType)
        {
            Console.WriteLine(version.ToString());

            _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
                                      SaTsvCommon.SchemaVersion, _jsonKeyDictionary[sequencingDataType], null, true, sequenceProvider);
        }
예제 #3
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        public CustomAnnoTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, bool isPositional, ISequenceProvider sequenceProvider)
        {
            Console.WriteLine(version.ToString());

            _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
                                      SaTsvCommon.CustomItemSchemaVersion, version.Name, null, !isPositional, sequenceProvider, true);
        }
예제 #4
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        public TopMedTsvWriter(DataSourceVersion version, string outputFileName, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider)
        {
            Console.WriteLine(version.ToString());

            _writer = new SaTsvWriter(outputFileName, version, genomeAssembly.ToString(),
                                      SaTsvCommon.SchemaVersion, InterimSaCommon.TopMedTag, null, true, sequenceProvider);
        }
예제 #5
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        public ExacTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider)
        {
            Console.WriteLine(version.ToString());

            _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
                                      SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.ExacTag, null, true, sequenceProvider);
        }
예제 #6
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        public OnekgTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider)
        {
            Console.WriteLine(version.ToString());

            _onekgWriter = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
                                           SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.OneKgenTag, "AF1000G", true, sequenceProvider);

            _refMinorWriter = new SaMiscTsvWriter(outputDirectory, version, genomeAssembly.ToString(), InterimSaCommon.RefMinorTag, sequenceProvider);
        }
예제 #7
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 public MitoMapVarTsvWriter(DataSourceVersion version, string outputDirectory, string mitoMapDataType, ISequenceProvider sequenceProvider)
 {
     Console.WriteLine(version.ToString());
     _mitoMapVarWriter = new SaTsvWriter(outputDirectory, version, GenomeAssembly.rCRS.ToString(), SaTsvCommon.MitoMapSchemaVersion, mitoMapDataType, null, false, sequenceProvider, true);
 }
예제 #8
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 private ClinvarTsvWriter(SaTsvWriter saTsvWriter)
 {
     _writer = saTsvWriter;
 }
예제 #9
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 private EvsTsvWriter(SaTsvWriter writer)
 {
     _writer = writer;
 }
예제 #10
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 public DbsnpGaTsvWriter(SaTsvWriter dbsnpWriter, SaTsvWriter globalAlleleWriter)
 {
     _dbsnpWriter        = dbsnpWriter;
     _globalAlleleWriter = globalAlleleWriter;
 }