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);
}
static void Main(string[] args)
{
var baselineVcfPath = args[0];
var testVcfPath = args[1];
var config = new VcfComparisonConfig();
if (args.Length > 2)
{
config.Exact = args.Contains("-Exact");
config.CheckGT = args.Contains("-GT");
config.CheckDP = args.Contains("-DP");
config.CheckVF = args.Contains("-VF");
config.CheckSB = args.Contains("-SB");
config.CheckFilter = args.Contains("-Filter");
config.CheckQual = args.Contains("-Qual");
config.PassingOnly = !args.Contains("-AllVars");
config.ConsiderRefs = args.Contains("-Refs");
config.CheckAD = args.Contains("-AD");
}
double marginOfError = 0;
var configMargin = ConfigurationManager.AppSettings["MarginOfError"];
if (configMargin != "N/A")
{
config.MarginOfError = float.Parse(configMargin);
}
;
var variantTypes = ConfigurationManager.AppSettings["VariantTypes"].Split(',');
config.CheckDeletions = variantTypes.Contains("Del");
config.CheckInsertions = variantTypes.Contains("Ins");
config.CheckSnv = variantTypes.Contains("Snv");
config.CheckMnv = variantTypes.Contains("Mnv");
Console.WriteLine();
Console.WriteLine(string.Join(" ", args));
Console.WriteLine("==============================" + Environment.NewLine);
Console.WriteLine("Variant Types: " + string.Join(",", variantTypes));
BaselineVcfs(baselineVcfPath, testVcfPath, config, args.Contains("-AllComparisons"));
}
private static List <VcfVariant> ProcessVariants(VcfComparisonConfig config, List <VcfVariant> testAlleles, out Dictionary <string, List <VcfVariant> > testVariantsDict)
{
var testVariants = new List <VcfVariant>();
testVariantsDict = new Dictionary <string, List <VcfVariant> >();
var variantCalls = config.ConsiderRefs ? testAlleles : testAlleles.Where(a => a.VariantAlleles[0] != ".").ToList();
foreach (var variantCall in variantCalls)
{
var type = GetVariantType(variantCall);
if ((config.CheckSnv && type == Program.VariantType.Snv) || (config.CheckMnv && type == Program.VariantType.Mnv) ||
(config.CheckDeletions && type == Program.VariantType.Deletion) ||
(config.CheckInsertions && type == Program.VariantType.Insertion))
{
testVariants.Add(variantCall);
if (!testVariantsDict.ContainsKey(variantCall.ReferenceName))
{
testVariantsDict[variantCall.ReferenceName] = new List <VcfVariant>();
}
testVariantsDict[variantCall.ReferenceName].Add(variantCall);
}
}
return(testVariants);
}
public static void BaselineVcfs(string baselineVcfPath, string testVcfPath, VcfComparisonConfig config, bool showAllComparisons)
{
Console.WriteLine("Configuration Options");
Console.WriteLine("------------------------------");
Console.WriteLine(config);
Console.WriteLine("==============================" + Environment.NewLine);
Console.WriteLine("Comparing {0} to {1}", baselineVcfPath, testVcfPath);
var baselineVariantsMissingInTest = new List <VcfVariant>();
var testVariantsMissingInBaseline = new List <VcfVariant>();
var sharedVariants = new List <Tuple <VcfVariant, VcfVariant> >();
var baselineVariants = new List <VcfVariant>();
var baselineVariantsDict = new Dictionary <string, List <VcfVariant> >();
using (var reader = new VcfReader(baselineVcfPath))
{
var alleles = reader.GetVariants().ToList();
var variantCalls = config.ConsiderRefs ? alleles : alleles.Where(a => a.VariantAlleles[0] != ".").ToList();
foreach (var variantCall in variantCalls)
{
var type = GetVariantType(variantCall);
if ((config.CheckSnv && type == VariantType.Snv) || (config.CheckMnv && type == VariantType.Mnv) ||
(config.CheckDeletions && type == VariantType.Deletion) ||
(config.CheckInsertions && type == VariantType.Insertion))
{
baselineVariants.Add(variantCall);
if (!baselineVariantsDict.ContainsKey(variantCall.ReferenceName))
{
baselineVariantsDict[variantCall.ReferenceName] = new List <VcfVariant>();
}
baselineVariantsDict[variantCall.ReferenceName].Add(variantCall);
}
}
}
var testVariants = new List <VcfVariant>();
var testVariantsDict = new Dictionary <string, List <VcfVariant> >();
using (var reader = new VcfReader(testVcfPath))
{
var alleles = reader.GetVariants().ToList();
var variantCalls = config.ConsiderRefs ? alleles : alleles.Where(a => a.VariantAlleles[0] != ".").ToList();
foreach (var variantCall in variantCalls)
{
var type = GetVariantType(variantCall);
if ((config.CheckSnv && type == VariantType.Snv) || (config.CheckMnv && type == VariantType.Mnv) ||
(config.CheckDeletions && type == VariantType.Deletion) ||
(config.CheckInsertions && type == VariantType.Insertion))
{
testVariants.Add(variantCall);
if (!testVariantsDict.ContainsKey(variantCall.ReferenceName))
{
testVariantsDict[variantCall.ReferenceName] = new List <VcfVariant>();
}
testVariantsDict[variantCall.ReferenceName].Add(variantCall);
}
}
}
var numBaselines = baselineVariants.Count(v => !config.PassingOnly || v.Filters == "PASS");
var numTestVars = testVariants.Count(v => !config.PassingOnly || v.Filters == "PASS");
Console.WriteLine("Baseline Variants : " + numBaselines);
Console.WriteLine("Test Variants : " + numTestVars);
foreach (var testVariant in testVariants)
{
var variantInOtherVcf = FindVariantInOtherVcf(testVariant, baselineVariants, baselineVariantsDict, config.PassingOnly);
if (variantInOtherVcf == null)
{
testVariantsMissingInBaseline.Add(testVariant);
}
}
foreach (var baselineVariant in baselineVariants)
{
var variantInOtherVcf = FindVariantInOtherVcf(baselineVariant, testVariants, testVariantsDict, config.PassingOnly);
if (variantInOtherVcf == null)
{
baselineVariantsMissingInTest.Add(baselineVariant);
}
else if (variantInOtherVcf.ReferenceName != null)
{
sharedVariants.Add(new Tuple <VcfVariant, VcfVariant>(baselineVariant, variantInOtherVcf));
}
}
Console.WriteLine(Environment.NewLine + "------------------------------" + Environment.NewLine);
Console.WriteLine("Baseline Missing In Test : {0} ({1}%)", baselineVariantsMissingInTest.Count(), Math.Round(100 * (float)baselineVariantsMissingInTest.Count() / numBaselines, 2));
Console.WriteLine("------------------------------");
PrintVariants(baselineVariantsMissingInTest);
Console.WriteLine(Environment.NewLine + "------------------------------" + Environment.NewLine);
Console.WriteLine("Test Missing In Baseline : {0} ({1}%)", testVariantsMissingInBaseline.Count(), Math.Round(100 * (float)testVariantsMissingInBaseline.Count() / numTestVars, 2));
Console.WriteLine("------------------------------");
PrintVariants(testVariantsMissingInBaseline);
Console.WriteLine(Environment.NewLine + "------------------------------" + Environment.NewLine);
Console.WriteLine("Comparison of Shared Variants ({0})", sharedVariants.Count());
Console.WriteLine("------------------------------");
var allDiffs = new List <Dictionary <string, string> >();
foreach (var sharedVariant in sharedVariants)
{
if (sharedVariant.Item1.ToString() == sharedVariant.Item2.ToString())
{
//these are exactly the same.
continue;
}
var matchDict = new Dictionary <string, string>();
var okResult = "OK";
var matchStrings = new List <string>();
bool allOk = true;
var variantString = string.Format("{0} {1} {2} {3}", sharedVariant.Item1.ReferenceName, sharedVariant.Item1.ReferencePosition, sharedVariant.Item1.ReferenceAllele, sharedVariant.Item1.VariantAlleles.First());
matchStrings.Add(variantString);
matchDict["Variant"] = variantString;
if (config.CheckVF)
{
var result = okResult;
var vf1 = GetVF(sharedVariant.Item1);
var vf2 = GetVF(sharedVariant.Item2);
var vfsEqual = ApproximatelyEqual(vf1, vf2, config.MarginOfError);
if (!vfsEqual)
{
matchStrings.Add(string.Format("VF: ({0} vs {1})", vf1, vf2));
allOk = false;
result = ((float)(vf2) / vf1).ToString();
}
matchDict["VF"] = result;
}
if (config.CheckDP)
{
var result = okResult;
var dp1 = GetDP(sharedVariant.Item1);
var dp2 = GetDP(sharedVariant.Item2);
var dpsEqual = ApproximatelyEqual(dp1, dp2, config.MarginOfError);
if (!dpsEqual)
{
matchStrings.Add(string.Format("DP: ({0} vs {1})", dp1, dp2));
allOk = false;
result = ((float)(dp2) / dp1).ToString();
}
matchDict["DP"] = result;
}
if (config.CheckGT)
{
var result = okResult;
var gt1 = GetGT(sharedVariant.Item1);
var gt2 = GetGT(sharedVariant.Item2);
var gtsEqual = gt1 == gt2;
if (!gtsEqual)
{
matchStrings.Add(string.Format("GT: ({0} vs {1})", gt1, gt2));
allOk = false;
}
matchDict["GT"] = result;
}
if (config.CheckFilter)
{
var result = okResult;
var filtersEqual = sharedVariant.Item1.Filters == sharedVariant.Item2.Filters;
if (!filtersEqual)
{
matchStrings.Add(string.Format("Filters: ({0} vs {1})", sharedVariant.Item1.Filters,
sharedVariant.Item2.Filters));
allOk = false;
result = "False";
}
matchDict["Filters"] = result;
}
if (config.CheckSB)
{
var result = okResult;
var sb1 = GetSB(sharedVariant.Item1);
var sb2 = GetSB(sharedVariant.Item2);
var sbsEqual = ApproximatelyEqual(sb1, sb2, config.MarginOfError);
if (!sbsEqual)
{
matchStrings.Add(string.Format("SB: ({0} vs {1})", sb1, sb2));
allOk = false;
result = ((float)(sb2) / sb1).ToString();
}
matchDict["SB"] = result;
}
if (config.CheckAD)
{
var result = okResult;
var ad1 = GetAD(sharedVariant.Item1);
var ad2 = GetAD(sharedVariant.Item2);
var adsEqual = ad1 == ad2;
//var adsEqual = ApproximatelyEqual(ad1, ad2, config.MarginOfError);
if (!adsEqual)
{
matchStrings.Add(string.Format("AD: ({0} vs {1})", ad1, ad2));
allOk = false;
result = "False";
}
matchDict["AD"] = result;
var ad1split = ad1.Split(',');
var ad2split = ad2.Split(',');
matchDict["RefDepthRatio"] = ((float)(int.Parse(ad2split[0])) / int.Parse(ad1split[0])).ToString();
matchDict["AltDepthRatio"] = ((float)(int.Parse(ad2split[1])) / int.Parse(ad1split[1])).ToString();
}
if (config.CheckQual)
{
var result = okResult;
var qualsEqual = ApproximatelyEqual(sharedVariant.Item1.Quality, sharedVariant.Item2.Quality);
if (!qualsEqual)
{
matchStrings.Add(string.Format("Qual: ({0} vs {1})", sharedVariant.Item1.Quality,
sharedVariant.Item2.Quality));
allOk = false;
result = ((float)sharedVariant.Item2.Quality / sharedVariant.Item1.Quality).ToString();
}
matchDict["Qual"] = result;
}
if (allOk || config.Exact)
{
if (sharedVariant.Item1.ToString() != sharedVariant.Item2.ToString())
{
matchStrings.Add(
string.Format(
Environment.NewLine + "{0}" + Environment.NewLine + "vs" + Environment.NewLine + "{1}" + Environment.NewLine,
sharedVariant.Item1.ToString(), sharedVariant.Item2.ToString()));
allOk = false;
}
}
if (!allOk && !showAllComparisons)
{
Console.WriteLine(string.Join("\t", matchStrings));
}
if (!allOk)
{
allDiffs.Add(matchDict);
}
}
if (showAllComparisons && allDiffs.Any())
{
var allDiffKeys = allDiffs.First().Keys;
Console.WriteLine(string.Join(",", allDiffKeys));
foreach (var allDiff in allDiffs)
{
var resultsList = new List <string>();
foreach (var allDiffKey in allDiffKeys)
{
resultsList.Add(allDiff[allDiffKey]);
}
Console.WriteLine(string.Join(",", resultsList));
}
}
}
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;
}
}
}
private static List <Comparison> CompareSharedVariants(VcfComparisonConfig config, List <Tuple <VcfVariant, VcfVariant> > sharedVariants)
{
var allDiffs = new List <Dictionary <string, string> >();
var allComparisons = new List <Comparison>();
foreach (var sharedVariant in sharedVariants)
{
if (sharedVariant.Item1.ToString() == sharedVariant.Item2.ToString())
{
//these are exactly the same.
continue;
}
var okResult = "OK";
bool allOk = true;
var comparison = new Comparison(sharedVariant.Item1, true, true);
if (config.CheckVF)
{
var result = okResult;
var vf1 = GetVF(sharedVariant.Item1);
var vf2 = GetVF(sharedVariant.Item2);
var vfsEqual = ApproximatelyEqual(vf1, vf2, config.MarginOfError);
if (!vfsEqual)
{
allOk = false;
result = ((float)(vf2) / vf1).ToString();
}
comparison.AddResult(new ComparisonResult("VF", vf1, vf2, vfsEqual, result));
}
if (config.CheckDP)
{
var result = okResult;
var dp1 = GetDP(sharedVariant.Item1);
var dp2 = GetDP(sharedVariant.Item2);
var dpsEqual = ApproximatelyEqual(dp1, dp2, config.MarginOfError);
if (!dpsEqual)
{
allOk = false;
result = ((float)(dp2) / dp1).ToString();
}
comparison.AddResult(new ComparisonResult("DP", dp1, dp2, dpsEqual, result));
}
if (config.CheckGT)
{
var result = okResult;
var gt1 = GetGT(sharedVariant.Item1);
var gt2 = GetGT(sharedVariant.Item2);
var gtsEqual = gt1 == gt2;
if (!gtsEqual)
{
allOk = false;
result = "False";
}
comparison.AddResult(new ComparisonResult("GT", gt1, gt2, gtsEqual));
}
if (config.CheckFilter)
{
var result = okResult;
var filtersEqual = sharedVariant.Item1.Filters == sharedVariant.Item2.Filters;
if (!filtersEqual)
{
allOk = false;
result = "False";
}
comparison.AddResult(new ComparisonResult("Filters", sharedVariant.Item1.Filters, sharedVariant.Item2.Filters, filtersEqual, result));
}
if (config.CheckSB)
{
var result = okResult;
var sb1 = GetSB(sharedVariant.Item1);
var sb2 = GetSB(sharedVariant.Item2);
var sbsEqual = ApproximatelyEqual(sb1, sb2, config.MarginOfError);
if (!sbsEqual)
{
allOk = false;
result = ((float)(sb2) / sb1).ToString();
}
comparison.AddResult(new ComparisonResult("SB", sb1, sb2, sbsEqual, result));
}
if (config.CheckAD)
{
var result = okResult;
var ad1 = GetAD(sharedVariant.Item1);
var ad2 = GetAD(sharedVariant.Item2);
var adsEqual = ad1 == ad2;
if (!adsEqual)
{
var ad1split = ad1.Split(',');
var ad2split = ad2.Split(',');
allOk = false;
result = "RefDepthRatio:" + ((float)(int.Parse(ad2split[0])) / int.Parse(ad1split[0])).ToString() + ";AltDepthRatio:" + (ad1split.Length > 1 && ad2split.Length > 1 ? ((float)(int.Parse(ad2split[1])) / int.Parse(ad1split[1])).ToString() : "NA");
}
comparison.AddResult(new ComparisonResult("AD", ad1, ad2, adsEqual, result));
}
if (config.CheckQual)
{
var result = okResult;
var qualsEqual = ApproximatelyEqual(sharedVariant.Item1.Quality, sharedVariant.Item2.Quality);
if (!qualsEqual)
{
allOk = false;
result = ((float)sharedVariant.Item2.Quality / sharedVariant.Item1.Quality).ToString();
}
comparison.AddResult(new ComparisonResult("Qual", sharedVariant.Item1.Quality, sharedVariant.Item2.Quality, qualsEqual, result));
}
if (allOk && config.Exact)
{
if (sharedVariant.Item1.ToString() != sharedVariant.Item2.ToString())
{
comparison.AddResult(new ComparisonResult("Exact", sharedVariant.Item1.ToString(), sharedVariant.Item2.ToString(), false));
allOk = false;
}
}
if (!allOk)
{
Console.WriteLine(comparison.Variant + "\t" + string.Join("\t", comparison.GetDiffs()));
allComparisons.Add(comparison);
}
}
return(allComparisons);
}
private static List <Comparison> Compare(VcfComparisonConfig config, List <VcfVariant> baselineVariants,
List <VcfVariant> testVariants, Dictionary <string, List <VcfVariant> > baselineVariantsDict, Dictionary <string, List <VcfVariant> > testVariantsDict)
{
var numBaselines = baselineVariants.Count(v => !config.PassingOnly || v.Filters == "PASS");
var numTestVars = testVariants.Count(v => !config.PassingOnly || v.Filters == "PASS");
Console.WriteLine("Baseline Variants : " + numBaselines);
Console.WriteLine("Test Variants : " + numTestVars);
// Check for variants missing from either baseline or test
var baselineVariantsMissingInTest = new List <VcfVariant>();
var testVariantsMissingInBaseline = new List <VcfVariant>();
var sharedVariants = new List <Tuple <VcfVariant, VcfVariant> >();
foreach (var testVariant in testVariants)
{
var variantInOtherVcf = FindVariantInOtherVcf(testVariant, baselineVariantsDict, config.PassingOnly);
if (variantInOtherVcf == null)
{
testVariantsMissingInBaseline.Add(testVariant);
}
}
foreach (var baselineVariant in baselineVariants)
{
var variantInOtherVcf = FindVariantInOtherVcf(baselineVariant, testVariantsDict, config.PassingOnly);
if (variantInOtherVcf == null)
{
baselineVariantsMissingInTest.Add(baselineVariant);
}
else if (variantInOtherVcf.ReferenceName != null)
{
sharedVariants.Add(new Tuple <VcfVariant, VcfVariant>(baselineVariant, variantInOtherVcf));
}
}
Console.WriteLine(Environment.NewLine + "------------------------------");
Console.WriteLine("Baseline Missing In Test : {0} ({1}%)", baselineVariantsMissingInTest.Count(),
Math.Round(100 * (float)baselineVariantsMissingInTest.Count() / numBaselines, 2));
Console.WriteLine("------------------------------");
if (baselineVariantsMissingInTest.Any())
{
PrintVariants(baselineVariantsMissingInTest);
Console.WriteLine("------------------------------" + Environment.NewLine);
}
Console.WriteLine("Test Missing In Baseline : {0} ({1}%)", testVariantsMissingInBaseline.Count(),
Math.Round(100 * (float)testVariantsMissingInBaseline.Count() / numTestVars, 2));
Console.WriteLine("------------------------------");
if (testVariantsMissingInBaseline.Any())
{
PrintVariants(testVariantsMissingInBaseline);
Console.WriteLine("------------------------------" + Environment.NewLine);
}
var allDiffs = new List <Comparison>();
if (!config.HideSharedDiffs)
{
Console.WriteLine("Comparison of Shared Variants ({0})", sharedVariants.Count());
Console.WriteLine("------------------------------");
// Compare shared variants
allDiffs = CompareSharedVariants(config, sharedVariants);
Console.WriteLine("------------------------------");
}
allDiffs.AddRange(baselineVariantsMissingInTest.Select(variant => new Comparison(variant, true, false)));
allDiffs.AddRange(testVariantsMissingInBaseline.Select(variant => new Comparison(variant, false, true)));
return(allDiffs);
}
