public static void RewriteVcf(string vcfIn, string outDir, AdaptiveGtOptions options, RecalibrationResults results)
{
Logger.WriteToLog("Rewriting VCF.");
string vcfFileName = Path.GetFileName(vcfIn);
if (vcfFileName.Contains("genome."))
{
vcfFileName = vcfFileName.Replace("genome", "recal");
}
else
{
vcfFileName = vcfFileName.Replace(".vcf", ".recal.vcf");
}
string vcfOut = Path.Combine(outDir, vcfFileName);
if (File.Exists(vcfOut))
{
File.Delete(vcfOut);
}
VcfUpdater <RecalibrationResults> .UpdateVcfLociByLoci(vcfOut, options, false, results, LocusProcessor.ProcessLocus,
(List <string> vcfLine) => TypeOfUpdateNeeded.Modify, GetAdaptiveGtWriter);
Logger.WriteToLog("filtering complete.");
}
public void DoFiltering()
{
Logger.WriteToLog("filtering " + _psaraOptions.VcfPath + "...");
if (File.Exists(_outputFile))
{
File.Delete(_outputFile);
}
VcfUpdater <GeometricFilter> .UpdateVcfLociByLoci(_outputFile, _psaraOptions, false, _geometricFilter,
UpdateColocatedAlleles, CanNeverSkipVcfLine, GetPsaraVcfWriter);
Logger.WriteToLog("filtering complete.");
}
public void UpdateVcfTest_TestOnAllLociAlleleAction()
{
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "ModifyCoLocated");
var inputDir = Path.Combine(TestPaths.LocalTestDataDirectory);
var inputVcfFilePath = Path.Combine(inputDir, "colocated.genome.vcf");
var outputFile1 = Path.Combine(outDir, "Rewrite_NoChangeToVariants.vcf");
var outputFile2 = Path.Combine(outDir, "Rewrite_TagMultiAllelicSites.vcf");
var outputFile3 = Path.Combine(outDir, "Rewrite_TagIndelSites.vcf");
var expectedFile1 = Path.Combine(inputDir, "VcfReWriter_NoChangeToLoci.vcf");
var expectedFile2 = Path.Combine(inputDir, "VcfReWriter_TagMultiAllelicSites.vcf");
var expectedFile3 = Path.Combine(inputDir, "VcfReWriter_TagIndelSites.vcf");
TestUtilities.TestHelper.RecreateDirectory(outDir);
var myData = new SomeData();
var options = new VcfConsumerAppOptions();
options.VcfPath = inputVcfFilePath;
options.VariantCallingParams.AmpliconBiasFilterThreshold = null;//turning this off because these tests predate the AB filter. This allows the pre-exisiting vcf headers to stay the same.
//edit NO lines
VcfUpdater <SomeData> .UpdateVcfLociByLoci(outputFile1, options, true, myData, VcfUpdater <SomeData> .NeverUpdateByLoci, CanAlwaysSkipVcfLine, GetVcfFileWriter);
//TagMultiAllelicSites
VcfUpdater <SomeData> .UpdateVcfLociByLoci(outputFile2, options, true, myData, TagMultiAllelicSites, CanNeverSkipVcfLine, GetVcfFileWriter);
//TagIndelSites
VcfUpdater <SomeData> .UpdateVcfLociByLoci(outputFile3, options, true, myData, TagIndelSites, CanNeverSkipVcfLine, GetVcfFileWriter);
//check files
TestUtilities.TestHelper.CompareFiles(outputFile1, expectedFile1);
TestUtilities.TestHelper.CompareFiles(outputFile2, expectedFile2);
TestUtilities.TestHelper.CompareFiles(outputFile3, expectedFile3);
}
