public static int Main(string[] args)
{
var ops = new Dictionary <string, TopLevelOption>
{
["createSA"] = new TopLevelOption("create Nirvana supplementary annotation database", MergeIntermediateTsvs.Run),
["createTSV"] = new TopLevelOption("create intermediate tsv file for supplementary annotation", CreateIntermediateTsvsMain.Run),
["createOmimTsv"] = new TopLevelOption("create omim tsv file", CreateOmimTsvMain.Run),
["geneScoresTsv"] = new TopLevelOption("create gene scores tsv file", GeneScoresMain.Run),
["extractMiniSA"] = new TopLevelOption("extracts mini SA", ExtractMiniSaMain.Run),
["extractMiniXml"] = new TopLevelOption("extracts mini SA", ExtractMiniXmlMain.Run),
["createGnomadTsv"] = new TopLevelOption("create gnomAD tsv file", CreateGnomadTsvMain.Run),
["createTopMedTsv"] = new TopLevelOption("create TOPMed tsv file", CreateTopMedTsvMain.Run),
["createCosmicSvs"] = new TopLevelOption("create COSMIC SV tsv files", ExtractCosmicSvsMain.Run),
["remapWithDbsnp"] = new TopLevelOption("remap a VCF file given source and destination rsID mappings", DbSnpRemapperMain.Run),
};
var exitCode = new TopLevelAppBuilder(args, ops)
.Parse()
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Utilities focused on supplementary annotation")
.ShowErrors()
.Execute();
return((int)exitCode);
}
public void Parse_Nominal()
{
var exitCode = new TopLevelAppBuilder(new[] { "combine", "dummy" }, _ops)
.Parse()
.ShowBanner("banner")
.ShowHelpMenu("help")
.ShowErrors()
.Execute();
Assert.Equal(ExitCodes.Success, exitCode);
}
public static int Main(string[] args)
{
var ops = new Dictionary <string, TopLevelOption>
{
["clinvar"] = new TopLevelOption("create ClinVar database", ClinVarMain.Run),
["cosmic"] = new TopLevelOption("create COSMIC database", CreateCosmicDb.Main.Run),
["ClinGen"] = new TopLevelOption("create ClinGen database", MakeClinGenDb.Main.Run),
["CustomVar"] = new TopLevelOption("create custom variant annotation database", Custom.VariantMain.Run),
["CustomGene"] = new TopLevelOption("create custom gene annotation database", Custom.GeneMain.Run),
["OneKGenSvVcfToBed"] = new TopLevelOption("convert 1000 Genomes structural variants VCF file into a BED-like file", OneKGenSvDb.VcfToBed.Run),
["OneKGenSv"] = new TopLevelOption("create 1000 Genomes structural variants database", OneKGenSvDb.Create.Run),
["OneKGen"] = new TopLevelOption("create 1000 Genome small variants database", CreateOneKgDb.Main.Run),
["RefMinor"] = new TopLevelOption("create Reference Minor database from 1000 Genome ", RefMinorDb.Main.Run),
["ancestralAllele"] = new TopLevelOption("create Ancestral allele database from 1000Genomes data", MakeAaDb.Main.Run),
["dbsnp"] = new TopLevelOption("create dbSNP database", CreateDbsnpDb.Main.Run),
["globalMinor"] = new TopLevelOption("create global minor allele database", CreateGlobalAllelesDb.Main.Run),
["Dgv"] = new TopLevelOption("create DGV database", makeDgvDb.Main.Run),
["Omim"] = new TopLevelOption("create OMIM database", Omim.Main.Run),
["downloadOmim"] = new TopLevelOption("download OMIM database", Omim.Downloader.Run),
["ExacScores"] = new TopLevelOption("create ExAC gene scores database", ExacScores.Main.Run),
["extractMiniSA"] = new TopLevelOption("extracts mini SA", ExtractMiniSaMain.Run),
["extractMiniXml"] = new TopLevelOption("extracts mini XML (ClinVar)", ExtractMiniXmlMain.Run),
["gnomad"] = new TopLevelOption("create gnomAD database", GnomadSnvMain.Run),
["gnomad-lcr"] = new TopLevelOption("create gnomAD low complexity region database", LcrRegionsMain.Run),
["gnomadGeneScores"] = new TopLevelOption("create gnomAD gene scores database", GnomadGenesMain.Run),
["TopMed"] = new TopLevelOption("create TOPMed database", CreateTopMedDb.Main.Run),
["PhyloP"] = new TopLevelOption("create PhyloP database", PhyloP.Main.Run),
["CosmicSv"] = new TopLevelOption("create COSMIC SV tsv files", ExtractCosmicSvsMain.Run),
["remapWithDbsnp"] = new TopLevelOption("remap a VCF file given source and destination rsID mappings", DbSnpRemapperMain.Run),
["filterSpliceNetTsv"] = new TopLevelOption("filter SpliceNet predictions", SpliceNetPredictionFilterMain.Run),
["mitomapVarDb"] = new TopLevelOption("create MITOMAP small variants database", SmallVarDb.Run),
["mitomapSvDb"] = new TopLevelOption("create MITOMAP structural variants database", StructVarDb.Run),
["spliceAi"] = new TopLevelOption("create SpliceAI database", SpliceAiDb.Run),
["primateAi"] = new TopLevelOption("create PrimateAI database", PrimateAiDb.Run),
["dosageMapRegions"] = new TopLevelOption("create dosage map regions", DosageMapRegions.Run),
["dosageSensitivity"] = new TopLevelOption("create dosage sensitivity database", DosageSensitivity.Run),
["diseaseValidity"] = new TopLevelOption("create disease validity database", GeneDiseaseValidity.Run),
["MitoHet"] = new TopLevelOption("create mitochondrial Heteroplasmy database", MitoHeteroplasmyDb.Run),
["Revel"] = new TopLevelOption("create REVEL database", Revel.Create.Run),
["index"] = new TopLevelOption("edit an index file", UpdateIndex.Run),
["concat"] = new TopLevelOption("merge multiple NSA files for the same data source having non-overlapping regions", NsaConcatenator.NsaConcatenator.Run),
["AaCon"] = new TopLevelOption("create AA conservation database", AAConservation.AaConservationMain.Run)
};
var exitCode = new TopLevelAppBuilder(args, ops)
.Parse()
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Utilities focused on supplementary annotation")
.ShowErrors()
.Execute();
return((int)exitCode);
}
public void Parse_ShowHelpMenu()
{
var validator = new TopLevelAppBuilder(null, _ops).Parse();
Assert.True(validator.Data.ShowHelpMenu);
var exitCode = validator
.ShowBanner("banner")
.ShowHelpMenu("help")
.ShowErrors()
.Execute();
Assert.Equal(ExitCodes.MissingCommandLineOption, exitCode);
}
public void Parse_UnsupportedOption()
{
var validator = new TopLevelAppBuilder(new[] { "--if", "-" }, _ops).Parse();
Assert.True(validator.Data.Errors.Count > 0);
var exitCode = validator
.ShowBanner("banner")
.ShowHelpMenu("help")
.ShowErrors()
.Execute();
Assert.Equal(ExitCodes.UnknownCommandLineOption, exitCode);
}
private static int Main(string[] args)
{
var ops = new Dictionary <string, TopLevelOption>
{
["create"] = new TopLevelOption("creates a full reference file", CreateReferenceMain.Run),
["substring"] = new TopLevelOption("creates a reference substring file", CreateSubstringMain.Run),
["testseq"] = new TopLevelOption("creates a TestSeq_reference.dat file", CreateTestSeqMain.Run)
};
var exitCode = new TopLevelAppBuilder(args, ops)
.Parse()
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Utilities focused on creating the reference files")
.ShowErrors()
.Execute();
return((int)exitCode);
}
public static int Main(string[] args)
{
var ops = new Dictionary <string, TopLevelOption>
{
["clinvar"] = new TopLevelOption("create ClinVar database", CreateClinvarDb.Main.Run),
["cosmic"] = new TopLevelOption("create COSMIC database", CreateCosmicDb.Main.Run),
["ClinGen"] = new TopLevelOption("create ClinGen database", MakeClinGenDb.Main.Run),
["Custom"] = new TopLevelOption("create custom annotation database", Custom.Main.Run),
["OneKGenSv"] = new TopLevelOption("create 1000 Genomes structural variants database", MakeOnekSvDb.Main.Run),
["OneKGen"] = new TopLevelOption("create 1000 Genome small variants database", CreateOneKgDb.Main.Run),
["RefMinor"] = new TopLevelOption("create Reference Minor database from 1000 Genome ", RefMinorDb.Main.Run),
["ancestralAllele"] = new TopLevelOption("create Ancestral allele database from 1000Genomes data", MakeAaDb.Main.Run),
["Dbsnp"] = new TopLevelOption("create dbSNP database", CreateDbsnpDb.Main.Run),
["globalMinor"] = new TopLevelOption("create global minor allele database", CreateGlobalAllelesDb.Main.Run),
["Dgv"] = new TopLevelOption("create DGV database", makeDgvDb.Main.Run),
["Omim"] = new TopLevelOption("create OMIM database", Omim.Main.Run),
["ExacScores"] = new TopLevelOption("create ExAC gene scores database", ExacScores.Main.Run),
["extractMiniSA"] = new TopLevelOption("extracts mini SA", ExtractMiniSaMain.Run),
["extractMiniXml"] = new TopLevelOption("extracts mini XML (ClinVar)", ExtractMiniXmlMain.Run),
["Gnomad"] = new TopLevelOption("create gnomAD database", CreateGnomadDb.Main.Run),
["GnomadGeneScores"] = new TopLevelOption("create gnomAD gene scores database", GnomadGenesMain.Run),
["TopMed"] = new TopLevelOption("create TOPMed database", CreateTopMedDb.Main.Run),
["PhyloP"] = new TopLevelOption("create PhyloP database", PhyloP.Main.Run),
["CosmicSv"] = new TopLevelOption("create COSMIC SV tsv files", ExtractCosmicSvsMain.Run),
["remapWithDbsnp"] = new TopLevelOption("remap a VCF file given source and destination rsID mappings", DbSnpRemapperMain.Run),
["filterSpliceNetTsv"] = new TopLevelOption("filter SpliceNet predictions", SpliceNetPredictionFilterMain.Run),
["mitomapVarDb"] = new TopLevelOption("create MITOMAP small variants database", SmallVarDb.Run),
["mitomapSvDb"] = new TopLevelOption("create MITOMAP structural variants database", StructVarDb.Run),
["spliceAi"] = new TopLevelOption("create SpliceAI database", SpliceAiDb.Run),
["dosageSensitivity"] = new TopLevelOption("create dosage sensitivity database", DosageSensitivity.Run)
};
var exitCode = new TopLevelAppBuilder(args, ops)
.Parse()
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Utilities focused on supplementary annotation")
.ShowErrors()
.Execute();
return((int)exitCode);
}
private static int Main(string[] args)
{
var ops = new Dictionary <string, TopLevelOption>
{
["combine"] = new TopLevelOption("combine cache directories", CombineCacheDirectoriesMain.Run),
["create"] = new TopLevelOption("create Nirvana cache files", CreateNirvanaDatabaseMain.Run),
["download"] = new TopLevelOption("downloads required files", DownloadMain.Run),
["extract"] = new TopLevelOption("extracts transcripts", ExtractTranscriptsMain.Run),
["gene"] = new TopLevelOption("updates the universal gene archive", UniversalGeneArchiveMain.Run),
["gff"] = new TopLevelOption("export transcripts to GFF", CreateGffMain.Run),
["header"] = new TopLevelOption("displays the header information", HeaderMain.Run),
["parse"] = new TopLevelOption("parses the VEP cache files", ParseVepCacheDirectoryMain.Run),
["rgff"] = new TopLevelOption("export regulatory regions to GFF", CreateRegulatoryGffMain.Run)
};
var exitCode = new TopLevelAppBuilder(args, ops)
.Parse()
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Utilities focused on querying the cache directory")
.ShowErrors()
.Execute();
return((int)exitCode);
}
