public static void DoReformating(ReformatOptions options)
{
var inputFile = options.VcfPath;
var outputFile = inputFile.Replace(".vcf", ".uncrushed.vcf");
var crush = false;
if (options.VcfWritingParams.ForceCrush.HasValue)
{
crush = (bool)options.VcfWritingParams.ForceCrush;
options.VcfWritingParams.AllowMultipleVcfLinesPerLoci = !crush;
}
if (crush)
{
Console.WriteLine("crushing " + inputFile + "...");
outputFile = inputFile.Replace(".vcf", ".crushed.vcf");
}
else
{
Console.WriteLine("uncrushing " + inputFile + "...");
}
if (File.Exists(outputFile))
{
File.Delete(outputFile);
}
//Update Vcf, variant by variant, based on the table data.
VcfUpdater <bool> .UpdateVcfAlleleByAllele(outputFile, options, false, true, UpdateAllele, CanSkipNeverVcfLine,
GetVcfFileWriter);
}
public static void Recalibrate(SignatureSorterResultFiles countsFilePaths, VQROptions options)
{
string vcfFileName = Path.GetFileName(options.VcfPath);
string vcfOut = Path.Combine(options.OutputDirectory, vcfFileName + ".recal");
if (File.Exists(vcfOut))
{
File.Delete(vcfOut);
}
try
{
//Read in the results files that have the data for the error modes detected.
//Decide which types of variants we want to re-Qscore
var recalibrationData = GetRecalibrationTables(countsFilePaths, options);
//Update Vcf, variant by variant, based on the table data.
VcfUpdater <QualityRecalibrationData> .UpdateVcfAlleleByAllele(vcfOut, options, false, recalibrationData, UpdateAllele, CanSkipVcfLines,
VQRVcfWriter.GetVQRVcfFileWriter);
//let the user know it worked
if (File.Exists(vcfOut))
{
Logger.WriteToLog("The following vcf was recalibrated: " + options.VcfPath);
}
}
catch (Exception ex)
{
Logger.WriteToLog("Recalibrate failed for " + options.VcfPath);
Logger.WriteToLog("Exception: " + ex);
}
}
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);
}
public void UpdateVcfTest_TestOnSingleAlleleAction()
{
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "VcfUpdaterTestsOutDir");
var inputDir = Path.Combine(TestPaths.LocalTestDataDirectory);
var inputVcfFilePath = Path.Combine(inputDir, "crushed.genome.vcf");
var outputFile1 = Path.Combine(outDir, "RewriteExample1.vcf");
var outputFile2 = Path.Combine(outDir, "RewriteExample2.vcf");
var outputFile3 = Path.Combine(outDir, "RewriteExample3.vcf");
var outputFile4 = Path.Combine(outDir, "RewriteExample4.vcf");
var outputFile5 = Path.Combine(outDir, "RewriteExample5.vcf");
var outputFile6 = Path.Combine(outDir, "RewriteExample6.vcf");
var expectedFile1 = Path.Combine(inputDir, "VcfReWriter_NoChangeToVariants.vcf");
var expectedFile2 = Path.Combine(inputDir, "VcfReWriter_AllChangeToVariants.vcf");
var expectedFile3 = Path.Combine(inputDir, "VcfReWriter_SomeChangeToVariants.vcf");
var expectedFile4 = Path.Combine(inputDir, "VcfReWriter_RemoveAllVariants.vcf");
var expectedFile5 = Path.Combine(inputDir, "VcfReWriter_RemoveSomeVariants.vcf");
var expectedFile6 = Path.Combine(inputDir, "VcfReWriter_ComplexChangesVariants.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> .UpdateVcfAlleleByAllele(outputFile1, options, true, myData, UpdateChrToFrog, CanAlwaysSkipVcfLine, GetVcfFileWriter);
//edit ALL lines
VcfUpdater <SomeData> .UpdateVcfAlleleByAllele(outputFile2, options, true, myData, UpdateChrToFrog, CanNeverSkipVcfLine, GetVcfFileWriter);
//do something silly to lines with a "C" allele
VcfUpdater <SomeData> .UpdateVcfAlleleByAllele(outputFile3, options, true, myData, UpdateChrToFrog, CanSometimesSkipVcfLine, GetVcfFileWriter);
//remove all vcf entries
VcfUpdater <SomeData> .UpdateVcfAlleleByAllele(outputFile4, options, true, myData, UpdateChrToFrog, CanAlwaysDeleteVcfLine, GetVcfFileWriter);
//remove all vcf entries with a "C" allele
VcfUpdater <SomeData> .UpdateVcfAlleleByAllele(outputFile5, options, true, myData, UpdateChrToFrog, CanSometimesDeleteVcfLine, GetVcfFileWriter);
//Look at lines with a "C" allele.
//If lines with a C allele (ref or alt) have T as an alt, make the chr = "MadeAChangeHERE".
//If lines with a C allele (ref or alt) DO NOT have T as an alt, delete the line entirely.
VcfUpdater <SomeData> .UpdateVcfAlleleByAllele(outputFile6, options, true, myData, UpdateChrToFrogOrDelete, CanSometimesSkipVcfLine, GetVcfFileWriter);
//so, this one is left as is;
//chr1 223906730.G. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//this one, the C->A should get removed, and the C->T should have chr = "MadeAChangeHERE".
//chr1 223906731.C A,T 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 1 / 2:100:254,254:532:0.95:20:-100.0000
// these are also all removed
//chr1 223906744.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 228526603.C. 100 PASS DP = 536 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:536:536:0.00:20:-100.0000
//chr1 228526606.C. 100 PASS DP = 536 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:536:536:0.00:20:-100.0000
//chr1 247812092.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 247812094.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 247812096.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 247812099.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 247812108.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr2 55862775.C. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//check files
TestUtilities.TestHelper.CompareFiles(outputFile1, expectedFile1);
TestUtilities.TestHelper.CompareFiles(outputFile2, expectedFile2);
TestUtilities.TestHelper.CompareFiles(outputFile3, expectedFile3);
TestUtilities.TestHelper.CompareFiles(outputFile4, expectedFile4);
TestUtilities.TestHelper.CompareFiles(outputFile5, expectedFile5);
TestUtilities.TestHelper.CompareFiles(outputFile6, expectedFile6);
//explicit checks for the complicated one, so users can see what we are looking for:
var variantsTest6 = AlleleReader.GetAllVariantsInFile(outputFile6);
var variantsInput = AlleleReader.GetAllVariantsInFile(inputVcfFilePath);
Assert.Equal(91, variantsInput.Count());
Assert.Equal(91 - 10, variantsTest6.Count()); //accounting for removed lines
Assert.Equal(223906728, variantsInput[0].ReferencePosition);
Assert.Equal("chr1", variantsInput[0].Chromosome);
Assert.Equal(223906728, variantsTest6[0].ReferencePosition);
Assert.Equal("chr1", variantsTest6[0].Chromosome);
Assert.Equal(223906731, variantsInput[3].ReferencePosition);
Assert.Equal("chr1", variantsInput[3].Chromosome);
Assert.Equal(223906731, variantsTest6[3].ReferencePosition);
Assert.Equal("FrogChr", variantsTest6[3].Chromosome);
}
