private bool Statistics(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
SortedDictionary <int, int> result = new SortedDictionary <int, int>();
Herald.AnnounceExeReport("Statistics", di4B.LambdaSizeStats(out result));
using (StreamWriter writer = new StreamWriter(resultFile))
{
writer.WriteLine("Lambda Size\tCount");
foreach (var item in result)
{
writer.WriteLine("{0}\t{1}", item.Key, item.Value);
}
}
return(true);
}
private bool AccumulationHistogram(string[] args)
{
if (args.Length != 2 && args.Length != 3)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
if (args.Length == 3 && !ParseMux(args[2]))
{
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
ConcurrentDictionary <string, ConcurrentDictionary <char, List <AccEntry <int> > > > results;
Herald.AnnounceExeReport("AccHistogram", di4B.AccumulationHistogram(out results, _maxDegreeOfParallelism));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, results, "chr\tleft\tright\taccumulation\tstrand", mux: _mux));
return(true);
}
private bool tmpLoadVCF(string fileName)
{
if (!ValidateFileName(fileName, out fileName))
{
return(false);
}
_parserSTW.Restart();
VCFParser <Variant, VariantData> vcfParser = new VCFParser <Variant, VariantData>(source: fileName, species: Genomes.HomoSapiens, assembly: Assemblies.hg19);
try { Repository.parsedVariants = vcfParser.Parse(); }
catch (Exception e)
{
if (Path.GetDirectoryName(fileName) + Path.DirectorySeparatorChar == _workingDirectory &&
Path.GetExtension(fileName) == _logFile)
{
Herald.Announce(Herald.MessageType.Error, string.Format("The requested extension should not have same extension as the log file."));
}
else
{
Herald.Announce(Herald.MessageType.Error, string.Format("{0}", e.Message));
}
return(false);
}
_parserSTW.Stop();
_accumulatedLoadET += _parserSTW.Elapsed.TotalSeconds;
Herald.AnnounceExeReport("Loaded", new ExecutionReport(Repository.parsedVariants.intervalsCount, _parserSTW.Elapsed));
return(true);
}
private bool SetIndexingMode(string[] args)
{
if (args.Length < 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Missing argument."));
return(false);
}
switch (args[1].Trim().ToLower())
{
case "single":
_indexingMode = IndexingMode.SinglePass;
break;
case "multi":
_indexingMode = IndexingMode.MultiPass;
break;
default:
Herald.Announce(Herald.MessageType.Error, string.Format("Incorrect argument."));
break;
}
return(GetIndexingMode());
}
public bool Cover(string[] args)
{
if (args.Length < 6)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Missing parameter."));
return(false);
}
char strand;
int minAcc, maxAcc;
string coverOrSummit = args[0].ToLower();
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
if (!char.TryParse(args[2], out strand))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid strand parameter."));
return(false);
}
if (!int.TryParse(args[3], out minAcc))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid minimum accumulation parameter."));
return(false);
}
if (!int.TryParse(args[4], out maxAcc))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid maximum accumulation parameter."));
return(false);
}
Aggregate agg = Aggregate.Count;
if (!String2Aggregate(args[5], out agg))
{
return(false);
}
FunctionOutput <Output <int, Peak, PeakData> > result = null;
switch (coverOrSummit)
{
case "cover":
Herald.AnnounceExeReport("Cover", di4B.Cover(CoverVariation.Cover, strand, minAcc, maxAcc, agg, out result, _maxDegreeOfParallelism), Herald.SpeedUnit.bookmarkPerSecond);
break;
case "summit":
Herald.AnnounceExeReport("Summit", di4B.Cover(CoverVariation.Summit, strand, minAcc, maxAcc, agg, out result, _maxDegreeOfParallelism), Herald.SpeedUnit.bookmarkPerSecond);
break;
}
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, result, "chr\tleft\tright\tcount\tstrand"));
return(true);
}
public bool Index2ndResolution(string[] args)
{
if (args.Length < 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
int binCount = 0;
CuttingMethod cuttingMethod = CuttingMethod.ZeroThresholding;
switch (args[1].ToLower())
{
case "zt":
case "zerothresholding":
cuttingMethod = CuttingMethod.ZeroThresholding;
break;
case "uq":
case "uniformscalarquantization":
cuttingMethod = CuttingMethod.UniformScalarQuantization;
if (args.Length != 3)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
if (!int.TryParse(args[2], out binCount))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
break;
case "nuq":
case "nonuniformscalarquantization":
cuttingMethod = CuttingMethod.NonUniformScalarQuantization;
if (args.Length != 3)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
if (!int.TryParse(args[2], out binCount))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
break;
default:
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
Herald.AnnounceExeReport("2RIndex", di4B.SecondResolutionIndex(cuttingMethod, binCount, _maxDegreeOfParallelism), speedUnit: Herald.SpeedUnit.blockPerSecond);
return(true);
}
private void BenchmarkAccHis()
{
int tries = 20;
ConcurrentDictionary <string, ConcurrentDictionary <char, List <AccEntry <int> > > > results;
for (int i = 0; i < tries; i++)
{
Herald.AnnounceExeReport("Run_" + i, di4B.AccumulationHistogram(out results, _maxDegreeOfParallelism));
}
}
private bool GetPD()
{
Herald.Announce(
Herald.MessageType.Info,
string.Format("Maximum degree of parallelism: \nChr level = {0} {1} \nDi4 level = {2} {3}",
_maxDegreeOfParallelism.chrDegree,
(_maxDegreeOfParallelism.chrDegree > 1 ? "threads" : "thread"),
_maxDegreeOfParallelism.di4Degree,
(_maxDegreeOfParallelism.di4Degree > 1 ? "threads" : "thread")));
return(false);
}
private bool Index(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Missing arguments."));
return(false);
}
if (Path.GetExtension(args[1]) == ".vcf")
{
if (!tmpLoadVCF(args[1]))
{
return(false);
}
var tmp = new Dictionary <string, Dictionary <char, List <Peak> > >();
foreach (var chr in Repository.parsedVariants.intervals)
{
tmp.Add(chr.Key, new Dictionary <char, List <Peak> >());
foreach (var strand in chr.Value)
{
tmp[chr.Key].Add(strand.Key, new List <Peak>());
foreach (var peak in strand.Value)
{
tmp[chr.Key][strand.Key].Add(new Peak()
{
left = peak.left, right = peak.right, hashKey = peak.hashKey
});
}
}
}
var report = di4B.Add(Repository.parsedVariants.fileHashKey, tmp, _indexingMode, _maxDegreeOfParallelism);
Herald.AnnounceExeReport("Indexed", report);
_tN2i += report.count;
}
else
{
if (!Load(args[1]))
{
return(false);
}
var report = di4B.Add(Repository.parsedSample.fileHashKey, Repository.parsedSample.intervals, _indexingMode, _maxDegreeOfParallelism);
Herald.AnnounceExeReport("Indexed", report);
_tN2i += report.count;
}
return(true);
}
private bool ValidateURI(string strUri, out Uri uri)
{
uri = null;
if (Uri.TryCreate(strUri, UriKind.Absolute, out uri) == false)
{
Herald.Announce(Herald.MessageType.Error, "Invalid path URI format.");
return(false);
}
if (!Directory.Exists(uri.AbsolutePath))
{
Herald.Announce(Herald.MessageType.Error, "Path does not exist.");
return(false);
}
return(true);
}
private bool Load(string fileName)
{
if (!ValidateFileName(fileName, out fileName))
{
return(false);
}
_parserSTW.Restart();
BEDParser <Peak, PeakData> bedParser = new BEDParser <Peak, PeakData>(
source: fileName,
species: Genomes.HomoSapiens,
assembly: Assemblies.hg19,
readOnlyValidChrs: true,
startOffset: 0,
chrColumn: UserConfig.ParserParameters.chrColumn,
leftEndColumn: UserConfig.ParserParameters.leftEndColumn,
rightEndColumn: UserConfig.ParserParameters.rightEndColumn,
summitColumn: -1,
nameColumn: UserConfig.ParserParameters.nameColumn,
valueColumn: UserConfig.ParserParameters.valueColumn,
strandColumn: -1,
defaultValue: 0.01,
pValueFormat: pValueFormat.minus10_Log10_pValue,
dropPeakIfInvalidValue: false,
hashFunction: HashFunction.FNV);
try { Repository.parsedSample = bedParser.Parse(); }
catch (Exception e)
{
if (Path.GetDirectoryName(fileName) + Path.DirectorySeparatorChar == _workingDirectory &&
Path.GetExtension(fileName) == _logFile)
{
Herald.Announce(Herald.MessageType.Error, string.Format("The requested extension should not have same extension as the log file."));
}
else
{
Herald.Announce(Herald.MessageType.Error, string.Format("{0}", e.Message));
}
return(false);
}
_parserSTW.Stop();
_accumulatedLoadET += _parserSTW.Elapsed.TotalSeconds;
Herald.AnnounceExeReport("Loaded", new ExecutionReport(Repository.parsedSample.intervalsCount, _parserSTW.Elapsed));
return(true);
}
private bool ReportStats(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
SortedDictionary <string, SortedDictionary <char, Stats> > results = null;
Herald.AnnounceExeReport("Statistics", di4B.Statistics(out results));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, results));
return(true);
}
private bool Dichotomies(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
ConcurrentDictionary <string, ConcurrentDictionary <char, ICollection <BlockKey <int> > > > results = null;
Herald.AnnounceExeReport("Dichotomies", di4B.Dichotomies(out results, _maxDegreeOfParallelism));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, results));
return(true);
}
private bool String2Aggregate(string strAggregate, out Aggregate aggregate)
{
switch (strAggregate.ToLower().Trim())
{
case "count":
aggregate = Aggregate.Count;
return(true);
case "sum":
aggregate = Aggregate.Sum;
return(true);
case "max":
case "maximum":
aggregate = Aggregate.Maximum;
return(true);
case "min":
case "minimum":
aggregate = Aggregate.Minimum;
return(true);
case "mean":
case "average":
aggregate = Aggregate.Mean;
return(true);
case "median":
aggregate = Aggregate.Median;
return(true);
case "std":
case "standarddeviation":
aggregate = Aggregate.StandardDeviation;
return(true);
default:
aggregate = Aggregate.Count;
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid aggregate parameter."));
return(false);
}
}
private bool ExtractResultsFile(string inputFileName, out string outputFileName)
{
Uri resultsFileURI = null;
outputFileName = "";
if (Path.GetDirectoryName(inputFileName).Trim() == "")
{
inputFileName = _workingDirectory + Path.GetFileName(inputFileName);
}
if (Uri.TryCreate(inputFileName, UriKind.Absolute, out resultsFileURI) == false ||
Path.GetFileName(resultsFileURI.AbsolutePath) == null ||
Path.GetFileName(resultsFileURI.AbsolutePath).Trim() == "")
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid results file."));
return(false);
}
outputFileName = resultsFileURI.AbsolutePath;
return(true);
}
private bool BlockInfoDis(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
BlockInfoDis results = null;
Herald.AnnounceExeReport("BlockInfo", di4B.BlocksInfoDistribution(out results, _maxDegreeOfParallelism));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, results));
return(true);
}
private bool Benchmark(string[] args)
{
if (args.Length == 2)
{
if (args[1].ToLower() == "cover")
{
BenchmarkCover();
}
else if (args[1].ToLower() == "acchis")
{
BenchmarkAccHis();
}
return(true);
}
else
{
Herald.Announce(Herald.MessageType.Error, string.Format("Missing argument."));
return(false);
}
}
private bool Map(string[] args)
{
if (args.Length != 5)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[2], out resultFile))
{
return(false); // invalid file URI.
}
char strand = '*';
if (!char.TryParse(args[3], out strand))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid strand argument [{0}].", args[3]));
return(false);
}
Aggregate agg = Aggregate.Count;
if (!String2Aggregate(args[4], out agg))
{
return(false);
}
if (!Load(args[1]))
{
return(false);
}
FunctionOutput <Output <int, Peak, PeakData> > result;
Herald.AnnounceExeReport("Map", di4B.Map(strand, Repository.parsedSample.intervals, agg, out result, _maxDegreeOfParallelism));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, result, "chr\tleft\tright\tcount\tstrand"));
return(true);
}
private bool AccumulationDistribution(string[] args)
{
if (args.Length != 2)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[1], out resultFile))
{
return(false); // invalid file URI.
}
ConcurrentDictionary <string, ConcurrentDictionary <char, SortedDictionary <int, int> > > results;
SortedDictionary <int, int> mergedResults;
Herald.AnnounceExeReport("AccDistribution", di4B.AccumulationDistribution(out results, out mergedResults, _maxDegreeOfParallelism));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, results, mergedResults, "chr\tstrand\taccumulation\tcount"));
return(true);
}
private bool ValidateFileName(string iFileName, out string oFileName)
{
Uri fileUri = null;
oFileName = iFileName;
if (Path.GetDirectoryName(iFileName).Trim() == "")
{
oFileName = _workingDirectory + Path.DirectorySeparatorChar + iFileName;
}
else if (!ValidateURI(Path.GetDirectoryName(iFileName), out fileUri))
{
return(false);
}
if (!File.Exists(oFileName))
{
Herald.Announce(Herald.MessageType.Error, string.Format("File not found [{0}]", oFileName));
return(false);
}
return(true);
}
private bool SetPD(string[] args)
{
int chrDP = 0, di4DP = 0;
if (args.Length != 3 || !int.TryParse(args[1], out chrDP) || !int.TryParse(args[2], out di4DP))
{
Herald.Announce(Herald.MessageType.Error, "Invalid arguments");
return(false);
}
if (chrDP == 0)
{
Herald.Announce(Herald.MessageType.Error, "Invalid arguments; at least one thread for Chr level is required.");
return(false);
}
if (di4DP == 0)
{
Herald.Announce(Herald.MessageType.Error, "Invalid arguments; at least one thread for Di4 level is required.");
return(false);
}
_maxDegreeOfParallelism = new MaxDegreeOfParallelism(chrDP, di4DP);
return(GetPD());
}
private bool GSimData(string[] args)
{
int _sCount = 0, _iCount = 0, _chrCount = 0, _kk = 0, _klambda = 0, _lambdak = 0, _lambdalambda = 0, _fileSizeProb = 0;
if (args.Length != 9 ||
!int.TryParse(args[1], out _sCount) ||
!int.TryParse(args[2], out _iCount) ||
!int.TryParse(args[3], out _chrCount) ||
!int.TryParse(args[4], out _kk) ||
!int.TryParse(args[5], out _klambda) ||
!int.TryParse(args[6], out _lambdak) ||
!int.TryParse(args[7], out _lambdalambda) ||
!int.TryParse(args[8], out _fileSizeProb))
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
var simData = new Di4DataSim(_workingDirectory);
simData.Generate(_sCount, _iCount, _chrCount, new ErlangDistribution(_kk, _klambda), new ErlangDistribution(_lambdak, _lambdalambda), _fileSizeProb);
return(true);
}
private void BenchmarkCover()
{
int tries = 10;
var agg = Aggregate.Count;
FunctionOutput <Output <int, Peak, PeakData> > result = null;
var combinations = new List <int[]>
{
new int[] { 1, 2 },
new int[] { 5, 10 },
new int[] { 10, 20 },
new int[] { 50, 60 },
new int[] { 80, 90 },
new int[] { 100, 200 },
new int[] { 200, 220 },
new int[] { 300, 320 },
new int[] { 400, 500 },
new int[] { 550, 1000 },
new int[] { 1, 1 },
new int[] { 10, 10 },
new int[] { 25, 25 },
new int[] { 50, 50 },
new int[] { 60, 60 },
new int[] { 80, 80 },
new int[] { 100, 100 },
new int[] { 150, 150 },
new int[] { 200, 200 },
new int[] { 500, 500 },
};
foreach (var c in combinations)
{
for (int i = 0; i < tries; i++)
{
Herald.AnnounceExeReport(c[0] + "," + c[1], di4B.Cover(CoverVariation.Cover, '*', c[0], c[1], agg, out result, _maxDegreeOfParallelism), Herald.SpeedUnit.bookmarkPerSecond);
}
}
}
internal bool CommandParse(string command)
{
Herald.Announce(Herald.MessageType.None, "> " + command, Herald.Destination.File);
command = command.Trim();
string[] splittedCommand = command.Split(' ');
switch (splittedCommand[0].ToLower())
{
case "exit":
return(true);
case "index":
_stopWatch.Restart();
if (!Index(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "commit":
_stopWatch.Restart();
if (!Commit())
{
_stopWatch.Stop();
return(false);
}
break;
case "batchindex":
_stopWatch.Restart();
if (!BatchIndex(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
_stopWatch.Stop();
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1}", "Average indexing speed", Math.Round(_tN2i / _stopWatch.Elapsed.TotalSeconds, 2) + " #i\\sec"));
break;
case "statistics":
_stopWatch.Restart();
if (!Statistics(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
_stopWatch.Stop();
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1}", "XYZ", Math.Round(_tN2i / _stopWatch.Elapsed.TotalSeconds, 2) + " #i\\sec"));
break;
case "2pass": // 2nd pass of indexing.
_stopWatch.Restart();
if (!Index2ndPass())
{
_stopWatch.Stop();
return(false);
}
break;
case "2ri": // 2nd resolution index
_stopWatch.Restart();
if (!Index2ndResolution(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "cover":
case "summit":
_stopWatch.Restart();
if (!Cover(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "map": // example: Map E:\refChr.bed * count
_stopWatch.Restart();
if (!Map(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "va":
case "varianta":
case "vanalysis":
case "variantanalysis":
_stopWatch.Restart();
if (!VariantAnalysis(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "merge":
_stopWatch.Restart();
if (!Merge(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "complement":
_stopWatch.Restart();
if (!Complement(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "stats":
ReportStats(splittedCommand);
return(false);
case "dichotomies":
_stopWatch.Restart();
if (!Dichotomies(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "blockinfo":
_stopWatch.Restart();
if (!BlockInfoDis(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "gsimdata":
_stopWatch.Restart();
if (!GSimData(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "getim": // get indexing mode.
return(GetIndexingMode());
case "setim": // set indexing mode.
return(SetIndexingMode(splittedCommand));
case "getdp": // get degree of parallelization
case "getpd": // get parallelization degree
return(GetPD());
case "setdp": // set degree of parallelization
case "setpd": // set parallelization degree
return(SetPD(splittedCommand));
case "getci": // get cache information
return(GetCI());
case "setci": // set cache information
return(SetCI(splittedCommand));
case "acchis": // get Accumulation Histogram.
_stopWatch.Restart();
if (!AccumulationHistogram(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "accdis": // get Accumulation Distribution.
_stopWatch.Restart();
if (!AccumulationDistribution(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
case "benchmark":
_stopWatch.Restart();
if (!Benchmark(splittedCommand))
{
_stopWatch.Stop();
return(false);
}
break;
default:
Herald.Announce(Herald.MessageType.Error, "Unknown Command.");
return(false);
}
_stopWatch.Stop();
Herald.Announce(Herald.MessageType.Success, string.Format(" Overall ET: {0}", _stopWatch.Elapsed.ToString()));
return(false);
}
private bool VariantAnalysis(string[] args)
{
if (args.Length != 3)
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
string resultFile = "";
if (!ExtractResultsFile(args[2], out resultFile))
{
return(false); // invalid file URI.
}
if (!tmpLoadVCF(args[1]))
{
return(false);
}
var tmp = new Dictionary <string, Dictionary <char, List <Peak> > >();
foreach (var chr in Repository.parsedVariants.intervals)
{
tmp.Add(chr.Key, new Dictionary <char, List <Peak> >());
foreach (var s in chr.Value)
{
tmp[chr.Key].Add(s.Key, new List <Peak>());
foreach (var peak in s.Value)
{
tmp[chr.Key][s.Key].Add(new Peak()
{
left = peak.left, right = peak.right, hashKey = peak.hashKey
});
}
}
}
FunctionOutput <Output <int, Peak, PeakData> > result;
Dictionary <uint, int> newRes = new Dictionary <uint, int>();
Herald.AnnounceExeReport("Variant Analysis", di4B.VariantAnalysis('*', tmp, Aggregate.Count, out result, _maxDegreeOfParallelism, out newRes));
Herald.AnnounceExeReport("Export", Exporter.Export(resultFile, result, "chr\tleft\tright\tcount\tstrand"));
var sortedRes = newRes.ToList();
sortedRes.Sort(
delegate(KeyValuePair <uint, int> i, KeyValuePair <uint, int> j)
{
return(j.Value.CompareTo(i.Value));
});
using (StreamWriter writer = new StreamWriter(resultFile))
{
writer.WriteLine("Sampled_ID\tVariations_in_common_with_reference");
foreach (var item in sortedRes)
{
writer.WriteLine("{0}\t{1}", item.Key, item.Value);
}
}
return(true);
}
static void Test2RI()
{
int repeats = 10;
UserConfigSetup.SetGet();
Directory.EnumerateFiles(UserConfig.workingDirectory, "*.idx2R").ToList().ForEach(x => File.Delete(x));
Herald.Initialize(Herald.Destination.Both, UserConfig.logFile);
Orchestrator orchestrator = new Orchestrator();
orchestrator.CommandParse("setdp 4 8");
Console.Clear();
int bin = 0;
Console.WriteLine("Enter bin size :");
int.TryParse(Console.ReadLine(), out bin);
var timer = new Stopwatch();
timer.Start();
orchestrator.Index2ndResolution(new string[] { "2RI", "uq", bin.ToString() });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "2riTimeToCreateTest.txt", true))
{
writter.WriteLine(bin.ToString() + "\t" + timer.Elapsed.TotalSeconds.ToString());
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "1", "2", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t1\t2\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "5", "10", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t5\t10\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "10", "20", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t10\t20\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "50", "60", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t50\t60\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "80", "90", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t80\t90\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "100", "200", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t100\t200\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "200", "220", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t200\t220\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "300", "320", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t300\t320\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "400", "500", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t400\t500\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "550", "1000", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t550\t1000\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "1", "1", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t1\t1\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "10", "10", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t10\t10\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "25", "25", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t25\t25\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "50", "50", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t50\t50\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "60", "60", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t60\t60\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "80", "80", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t80\t80\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "100", "100", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t100\t100\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "150", "150", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t150\t150\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "200", "200", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t200\t200\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
for (int r = 0; r < repeats; r++)
{
timer.Restart();
orchestrator.Cover(new string[] { "cover", "covres.bed", "*", "500", "500", "count" });
timer.Stop();
using (var writter = new StreamWriter(UserConfig.workingDirectory + "CoverResult.txt", true))
{
writter.WriteLine(bin.ToString() + "\t500\t500\t" + timer.Elapsed.TotalSeconds.ToString());
}
}
Herald.Dispose();
}
private bool Index2ndPass()
{
Herald.AnnounceExeReport("2ndPass", di4B.Add2ndPass(_maxDegreeOfParallelism), speedUnit: Herald.SpeedUnit.bookmarkPerSecond);
return(true);
}
private bool BatchIndex(string[] args)
{
_tN2i = 0;
DirectoryInfo dirInfo;
if (args.Length == 2 && args[1].Length > 2 && args[1][0] == '*' && args[1][1] == '.')
{
dirInfo = new DirectoryInfo(_workingDirectory);
}
else if (args.Length == 3)
{
Uri logFileURI = null;
if (!ValidateURI(args[2], out logFileURI))
{
return(false);
}
dirInfo = new DirectoryInfo(logFileURI.AbsolutePath);
}
else
{
Herald.Announce(Herald.MessageType.Error, string.Format("Invalid arguments."));
return(false);
}
/// Checks the validity of the extension
string extension = args[1].Substring(2, args[1].Length - 2);
char[] invalidChars = Path.GetInvalidFileNameChars();
foreach (char c in invalidChars)
{
if (extension.Contains(c))
{
Herald.Announce(Herald.MessageType.Error, "Invalid extension.");
return(false);
}
}
FileInfo[] foundFiles = dirInfo.GetFiles("*." + extension);
if (foundFiles.Length == 0)
{
Herald.Announce(Herald.MessageType.Warrning, string.Format("No file with \"{0}\" extension found!", extension));
return(false);
}
int i = 0;
_indexSTW.Restart();
foreach (FileInfo fileInfo in foundFiles)
{
Herald.Announce(
Herald.MessageType.Info,
string.Format(
/*-*/ "[{0}\\{1}] {2}",
/*0*/ ++i,
/*1*/ foundFiles.Length,
/*2*/ Path.GetFileNameWithoutExtension(fileInfo.FullName)));
if (!Index(new string[] { null, fileInfo.FullName }))
{
return(false);
}
}
_indexSTW.Stop();
_commitSTW.Restart();
Commit();
_commitSTW.Stop();
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1:N0}", "#indexed intervals", _tN2i));
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1}", "Load ET (sec)", _accumulatedLoadET));
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1}", "Index ET (sec)", _indexSTW.Elapsed.TotalSeconds.ToString()));
Herald.Announce(Herald.MessageType.Info, string.Format("{0,29}: {1}", "Commit ET (sec)", _commitSTW.Elapsed.TotalSeconds.ToString()));
return(true);
}
static void Main(string[] args)
{
/*Test2RI();
* Console.WriteLine("");
* Console.WriteLine("Done ... press any key to exit.");
* Console.ReadKey();
* return;*/
Console.Title = "Di4B: 1D intervals incremental inverted index for Bio-informatics";
Console.Clear();
Console.WriteLine("Following are the environment and initialization parameters ...");
try
{
if (!UserConfigSetup.SetGet())
{
return; // Exit application.
}
}
catch (Exception)
{
Console.WriteLine("");
Console.WriteLine("Error !! Invalid URI.");
return;
}
Console.Write("Initializing ...");
Herald.Initialize(Herald.Destination.Both, UserConfig.logFile);
Orchestrator orchestrator = new Orchestrator();
Console.Write(" Done!");
Console.WriteLine("");
Console.Write("Press any key to continue ...");
Console.ReadKey(true);
Console.Clear();
Console.WriteLine("");
Console.WriteLine(".::. Hi, I'm Di4, ready and at your service.");
Console.WriteLine("");
Console.WriteLine(".::. Working Directory : {0}", UserConfig.workingDirectory);
try
{
do
{
Herald.Announce(Herald.MessageType.None, "");
Console.Write("> ");
}while (!orchestrator.CommandParse(Console.ReadLine()));
}
catch (Exception e)
{
if (e.InnerException == null)
{
Herald.Announce(Herald.MessageType.Error,
"My apologies for inconvenience, this was not supposed to happen!" +
" Please restart Di4 and if you experience the issue again, please contact the support.");
}
else
{
Herald.Announce(Herald.MessageType.Error, e.InnerException.Message);
Herald.Announce(Herald.MessageType.None, "Please restart the application having resolved the error(s).");
}
}
Herald.Dispose();
}