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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
private ClinvarTsvWriter(SaTsvWriter saTsvWriter)
{
_writer = saTsvWriter;
}
private EvsTsvWriter(SaTsvWriter writer)
{
_writer = writer;
}
public DbsnpGaTsvWriter(SaTsvWriter dbsnpWriter, SaTsvWriter globalAlleleWriter)
{
_dbsnpWriter = dbsnpWriter;
_globalAlleleWriter = globalAlleleWriter;
}