private void ExecuteParsingTest(string arguments, bool shouldPass, Action <ApplicationOptions> assertions = null)
{
var options = new ApplicationOptions();
if (shouldPass)
{
options.UpdateOptions(arguments.Split(' '));
if (assertions != null)
{
assertions(options);
}
}
else
{
Assert.Throws <Exception>(() => options.UpdateOptions(arguments.Split(' ')));
}
}
public void InvalidVcfOutputFolder()
{
var appOptions = new ApplicationOptions
{
BAMPaths = new[] { _bamChr19, _bamChr17Chr19, _bamChr17Chr19Dup },
IntervalPaths = new[] { _intervalsChr17, _intervalsChr19, null },
GenomePaths = new[] { _genomeChr17Chr19 }
};
Assert.False(Directory.Exists("56:\\Illumina\\OutputFolder"));
var outputFolder = Path.Combine("56:\\Illumina\\OutputFolder");
// var outputFile = Path.Combine(outputFolder, "VcfFileWriterTests.vcf");
var outputFileOptions = new[] { "-OutFolder", outputFolder };
appOptions.UpdateOptions(outputFileOptions);
Assert.Throws <ArgumentException>(() => appOptions.Validate());
}
public void GvcfHeaderFormat()
{
var appOptions = new ApplicationOptions
{
BAMPaths = new[] { _bamChr19, _bamChr17Chr19, _bamChr17Chr19Dup },
IntervalPaths = new[] { _intervalsChr17, _intervalsChr19, null },
GenomePaths = new[] { _genomeChr17Chr19 }
};
var gVCFOption = new[] { "-gVCF", "true" };
appOptions.UpdateOptions(gVCFOption);
var factory = new Factory(appOptions);
var context = new VcfWriterInputContext
{
CommandLine = new[] { "myCommandLine" },
SampleName = "mySample",
ReferenceName = "myReference",
ContigsByChr = new List <Tuple <string, long> >
{
new Tuple <string, long>("chr1", 10001),
new Tuple <string, long>("chrX", 500)
}
};
var outputFile = factory.GetOutputFile(appOptions.BAMPaths[0]);
var writer = factory.CreateVcfWriter(outputFile, context);
var candidates = _defaultCandidates;
writer.WriteHeader();
writer.Write(candidates);
writer.Dispose();
// Time to read the header
VcfFileWriterTests.VcfFileFormatValidation(outputFile, 5);
}
public void DefaultGVCFOutput()
{
var appOptions = new ApplicationOptions
{
BAMPaths = new[] { _bamChr19, _bamChr17Chr19, _bamChr17Chr19Dup },
IntervalPaths = new[] { _intervalsChr17, _intervalsChr19, null },
GenomePaths = new[] { _genomeChr17Chr19 }
};
var gVCFOption = new[] { "-gVCF", "true" };
appOptions.UpdateOptions(gVCFOption);
var factory = new Factory(appOptions);
var context = new VcfWriterInputContext
{
CommandLine = new[] { "myCommandLine" },
SampleName = "mySample",
ReferenceName = "myReference",
ContigsByChr = new List <Tuple <string, long> >
{
new Tuple <string, long>("chr1", 10001),
new Tuple <string, long>("chrX", 500)
}
};
var outputFile = factory.GetOutputFile(appOptions.BAMPaths[0]);
var writer = factory.CreateVcfWriter(outputFile, context);
var candidates = _defaultCandidates;
writer.WriteHeader();
writer.Write(candidates);
writer.Dispose();
Assert.True(File.Exists(outputFile));
Assert.Equal(outputFile, Path.ChangeExtension(_bamChr19, "genome.vcf"));
}