static void Main(string[] args)
{
var baselineVcfPath = args[0];
var testVcfPath = args[1];
var comparisonConfig = new VcfComparisonConfig();
var configurationManager = new ProgramConfigSettings();
var region = new VcfRegion();
if (args.Length > 2)
{
comparisonConfig.Exact = args.Contains("-Exact");
comparisonConfig.CheckGT = args.Contains("-GT");
comparisonConfig.CheckDP = args.Contains("-DP");
comparisonConfig.CheckVF = args.Contains("-VF");
comparisonConfig.CheckSB = args.Contains("-SB");
comparisonConfig.CheckFilter = args.Contains("-Filter");
comparisonConfig.CheckQual = args.Contains("-Qual");
comparisonConfig.PassingOnly = !args.Contains("-AllVars");
comparisonConfig.ConsiderRefs = args.Contains("-Refs");
comparisonConfig.CheckAD = args.Contains("-AD");
comparisonConfig.AllCheck(args.Contains("-AllCheck"));
comparisonConfig.OutputFile = GetParameterValue(args, "Out");
comparisonConfig.SummaryFile = GetParameterValue(args, "Summary");
comparisonConfig.HideSharedDiffs = args.Contains("-HideShared");
}
region.Chromosome = GetParameterValue(args, "Chrom");
region.Start = int.Parse(GetParameterValue(args, "Start") ?? "0");
region.End = int.Parse(GetParameterValue(args, "End") ?? int.MaxValue.ToString());
var configMargin = configurationManager.MarginOfError;
if (configMargin < 0)
{
comparisonConfig.MarginOfError = configMargin;
}
;
var variantTypes = configurationManager.VariantTypes.Split(',');
var verbose = configurationManager.Verbose;
comparisonConfig.BlockSize = configurationManager.BlockSize;
comparisonConfig.CheckDeletions = variantTypes.Contains("Del");
comparisonConfig.CheckInsertions = variantTypes.Contains("Ins");
comparisonConfig.CheckSnv = variantTypes.Contains("Snv");
comparisonConfig.CheckMnv = variantTypes.Contains("Mnv");
Console.WriteLine();
Console.WriteLine(string.Join(" ", args));
Console.WriteLine("==============================" + Environment.NewLine);
Console.WriteLine("Variant Types: " + string.Join(",", variantTypes));
VcfComparer.BaselineVcfs(baselineVcfPath, testVcfPath, comparisonConfig, region, verbose);
}
public static List <VcfVariant> GetAlleles(string path, VcfRegion region, Logger logger, out bool hitChromEnd)
{
var alleles = new List <VcfVariant>();
hitChromEnd = false;
using (var reader = new VcfReader(path))
{
var stopwatch = Stopwatch.StartNew();
logger.Log("Reading " + path);
if (region.Chromosome != null)
{
var variantsRead = 0;
logger.Log("Looking for chromosome " + region.Chromosome + " " + region.Start + " - " + region.End);
while (true)
{
VcfVariant variant = new VcfVariant();
bool result = reader.GetNextVariant(variant);
variantsRead++;
if (variantsRead % 50000 == 0)
{
logger.Log(string.Format("At chromosome '{0}' position {1} in {2}: {3} variants gathered", variant.ReferenceName, variant.ReferencePosition, stopwatch.Elapsed, alleles.Count));
}
if (!result)
{
hitChromEnd = true;
logger.Log("Reached end of VCF");
break;
}
if (PassedChromosome(variant.ReferenceName, region.Chromosome))
{
hitChromEnd = true;
logger.Log("Passed chromosome " + region.Chromosome);
break;
}
if (variant.ReferenceName != region.Chromosome)
{
continue;
}
if (variant.ReferencePosition < region.Start)
{
continue;
}
if (region.End > 0 && variant.ReferencePosition > region.End)
{
logger.Log("Passed region end");
break;
}
alleles.Add(variant);
}
logger.Log(string.Format("Finished processing VCF {0}", path));
}
else
{
alleles = reader.GetVariants().ToList();
}
}
return(alleles);
}
public static void BaselineVcfs(string baselineVcfPath, string testVcfPath, VcfComparisonConfig config, VcfRegion region = null, bool verbose = false)
{
var logger = new Logger(verbose);
Console.WriteLine("Configuration Options");
Console.WriteLine("------------------------------");
Console.WriteLine(config);
Console.WriteLine("==============================" + Environment.NewLine);
Console.WriteLine("Comparing {0} to {1}", baselineVcfPath, testVcfPath);
var numblocks = region.Chromosome != null ? 1 + ((region.End - region.Start) / config.BlockSize) : 1;
var comparisonKeys = config.GetKeys();
if (config.OutputFile != null)
{
using (StreamWriter sw = File.CreateText(config.OutputFile))
{
sw.WriteLine("Variant\tInBaseline\tInTest," + string.Join("\t", comparisonKeys.Select(x => string.Join("\t", new List <string>()
{
x + "_1", x + "_2", x + "_OK"
}))));
}
}
if (config.SummaryFile != null && !File.Exists(config.SummaryFile))
{
using (StreamWriter sw = File.CreateText(config.SummaryFile))
{
sw.WriteLine("BaselineVcf,TestVcf,SharedDiffs,BaselineOnly,TestOnly");
}
}
for (int i = 0; i < numblocks; i++)
{
bool hitEndOfChromosome;
var subRegion = new VcfRegion();
if (region.Chromosome != null)
{
subRegion.Chromosome = region.Chromosome;
subRegion.Start = region.Start + i * config.BlockSize;
if (region.End > 0)
{
subRegion.End = Math.Min(region.Start + (i + 1) * config.BlockSize, region.End);
}
Console.WriteLine("==============================");
Console.WriteLine("PROCESSING FOR REGION: " + subRegion.ToString());
}
// Get baseline variants
Dictionary <string, List <VcfVariant> > baselineVariantsDict;
var alleles = VcfParser.GetAlleles(baselineVcfPath, subRegion, logger, out hitEndOfChromosome);
var baselineVariants = ProcessVariants(config, alleles, out baselineVariantsDict);
// Get test variants
var testAlleles = VcfParser.GetAlleles(testVcfPath, subRegion, logger, out hitEndOfChromosome);
Dictionary <string, List <VcfVariant> > testVariantsDict;
var testVariants = ProcessVariants(config, testAlleles, out testVariantsDict);
// Compare baseline vs test
var allDiffs = Compare(config, baselineVariants, testVariants, baselineVariantsDict, testVariantsDict);
if (config.SummaryFile != null)
{
FlushSummary(config.SummaryFile, allDiffs, baselineVcfPath, testVcfPath);
}
if (allDiffs.Any() && config.OutputFile != null)
{
foreach (var diff in allDiffs.OrderBy(d => d.Variant.ReferencePosition))
{
FlushDiff(config.OutputFile, diff.GetEntry(comparisonKeys));
}
}
if (hitEndOfChromosome)
{
break;
}
}
}
