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 void ReformatTest()
{
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "UncrushOutDir");
//For added challenge, this is a none-pisces vcf we are parsing and reformatting.
var inputDir = Path.Combine(TestPaths.LocalTestDataDirectory);
var testVcf = Path.Combine(inputDir, "CrushedExample.vcf");
var inputFile = Path.Combine(outDir, "CrushedExample.vcf");
TestHelper.RecreateDirectory(outDir);
if (!Directory.Exists(outDir))
{
Directory.CreateDirectory(outDir);
}
if (File.Exists(inputFile))
{
File.Delete(inputFile);
}
File.Copy(testVcf, inputFile);
var crushedOutFile = Path.Combine(outDir, "crushedexample.crushed.vcf");
var uncrushedOutFile = Path.Combine(outDir, "crushedexample.uncrushed.vcf");
var options = new ReformatOptions();
options.VcfPath = inputFile;
options.VariantCallingParams.AmpliconBiasFilterThreshold = null; //just to keep vcf header the same as before we added this filter.
//ouput uncrushed
options.VcfWritingParams.ForceCrush = false;
ReformatVcf.Reformat.DoReformating(options);
//output crushed
options.VcfWritingParams.ForceCrush = true;
ReformatVcf.Reformat.DoReformating(options);
//check files
TestHelper.CompareFiles(crushedOutFile, Path.Combine(TestPaths.LocalTestDataDirectory, "expected.crushed.vcf"));
TestHelper.CompareFiles(uncrushedOutFile, Path.Combine(TestPaths.LocalTestDataDirectory, "expected.uncrushed.vcf"));
}
public ASParser(ITokenStream input, ReformatOptions opt)
: base(input)
{
options = opt;
InitializeCyclicDFAs();
ruleMemo = new IDictionary[307 + 1];
}
public ReformatOptionsParser()
{
Options = new ReformatOptions();
}
