public void CreateIndex()
{
var searchTag = $"\"{SectionToIndex}\":[";
const string headerTag = "{\"header\":";
var index = new JasixIndex();
string line;
//skipping lines before the sectionToIndex arrives
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith(headerTag))
{
index.HeaderLine = ExtractHeader(line);
}
if (line.EndsWith(searchTag))
{
break;
}
}
// we need the location before accessing the line
var fileLoc = _reader.Position;
string previousChr = "";
int previousPos = 0;
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith("]"))
{
break;
}
line = line.TrimEnd(',');
var chrPos = GetChromPosition(line);
CheckFileSorted(chrPos.chr, chrPos.position, previousChr, previousPos);
index.Add(chrPos.chr, chrPos.position, chrPos.end, fileLoc);
fileLoc = _reader.Position;
previousChr = chrPos.chr;
previousPos = chrPos.position;
}
index.Write(_writeStream);
Console.WriteLine();
var peakMemoryUsageBytes = MemoryUtilities.GetPeakMemoryUsage();
var wallTimeSpan = _benchmark.GetElapsedTime();
Console.WriteLine();
if (peakMemoryUsageBytes > 0)
{
Console.WriteLine("Peak memory usage: {0}", MemoryUtilities.ToHumanReadable(peakMemoryUsageBytes));
}
Console.WriteLine("Time: {0}", Benchmark.ToHumanReadable(wallTimeSpan));
}
private static ExitCodes ProgramExecution()
{
(string hostName, string remoteCacheDir, string remoteReferencesDir, string manifestGRCh37,
string manifestGRCh38) = Configuration.Load();
List <GenomeAssembly> genomeAssemblies = GenomeAssemblyHelper.GetGenomeAssemblies(_genomeAssembly);
var client = new Client(hostName);
Console.Write("- downloading manifest... ");
Dictionary <GenomeAssembly, List <string> > remotePathsByGenomeAssembly =
Manifest.GetRemotePaths(client, genomeAssemblies, manifestGRCh37, manifestGRCh38);
(string cacheDir, string referencesDir, string saDir, List <string> outputDirectories) =
OutputDirectory.Create(_outputDirectory, genomeAssemblies);
var fileList = new List <RemoteFile>();
fileList.AddCacheFiles(genomeAssemblies, remoteCacheDir, cacheDir)
.AddReferenceFiles(genomeAssemblies, remoteReferencesDir, referencesDir)
.AddSupplementaryAnnotationFiles(remotePathsByGenomeAssembly, saDir);
Console.WriteLine($"{fileList.Count} files.\n");
// get rid of extra files in the output directories
OutputDirectory.Cleanup(fileList, outputDirectories);
// get length, checksum, and checks existence
Console.WriteLine("- downloading file metadata:");
AnnotationRepository.DownloadMetadata(client, fileList);
// remove obsolete files from the output directory
OutputDirectory.RemoveOldFiles(fileList);
// remove skipped files from our list
List <RemoteFile> filesToDownload = OutputDirectory.RemoveSkippedFiles(fileList);
// download the latest files
if (filesToDownload.Count > 0)
{
long numBytesToDownload = OutputDirectory.GetNumDownloadBytes(filesToDownload);
Console.WriteLine($"- downloading files ({MemoryUtilities.ToHumanReadable(numBytesToDownload)}):");
AnnotationRepository.DownloadFiles(client, filesToDownload);
}
// sanity check
OutputDirectory.CheckFiles(fileList);
bool foundError = fileList.Any(x => !x.Pass);
return(foundError ? ExitCodes.InvalidData : ExitCodes.Success);
}
public void CreateIndex()
{
var index = new JasixIndex();
IndexHeader(index);
string lastLine = IndexPositions(index);
IndexGenes(lastLine, index);
index.Write(_writeStream);
Console.WriteLine();
long peakMemoryUsageBytes = MemoryUtilities.GetPeakMemoryUsage();
var wallTimeSpan = _benchmark.GetElapsedTime();
Console.WriteLine();
if (peakMemoryUsageBytes > 0)
{
Console.WriteLine("Peak memory usage: {0}", MemoryUtilities.ToHumanReadable(peakMemoryUsageBytes));
}
Console.WriteLine("Time: {0}", Benchmark.ToHumanReadable(wallTimeSpan));
}
/// <summary>
/// executes the command-line workflow
/// </summary>
public void Execute(string[] args)
{
var bench = new Benchmark();
try
{
List <string> unsupportedOps = null;
if (args == null || args.Length == 0)
{
SetExitCode(ExitCodes.MissingCommandLineOption);
_showHelpMenu = true;
}
else
{
try
{
unsupportedOps = _commandLineOps.Parse(args);
if (unsupportedOps.Count > 0)
{
SetExitCode(ExitCodes.UnknownCommandLineOption);
_showHelpMenu = true;
}
}
catch (OptionException oe)
{
_errorBuilder.AppendFormat("{0}ERROR: {1}\n", _errorSpacer, oe.Message);
SetExitCode(ExitCodes.UnknownCommandLineOption);
_showHelpMenu = true;
}
}
if (_showVersion)
{
Console.WriteLine("{0} {1}", _versionProvider.GetProgramVersion(), _versionProvider.GetDataVersion());
SetExitCode(ExitCodes.Success);
}
else
{
if (!Console.IsOutputRedirected)
{
CommandLineUtilities.DisplayBanner(_programAuthors);
}
if (_showHelpMenu)
{
Help.Show(_commandLineOps, _commandLineExample, _programDescription);
CommandLineUtilities.ShowUnsupportedOptions(unsupportedOps);
Console.WriteLine();
Console.WriteLine(_versionProvider.GetDataVersion());
Console.WriteLine();
// print the errors if any were found
if (FoundParsingErrors())
{
return;
}
}
else
{
ValidateCommandLine();
// print the errors if any were found
if (FoundParsingErrors())
{
return;
}
ProgramExecution();
}
}
}
catch (Exception e)
{
ExitCode = ExitCodeUtilities.ShowException(e);
}
_peakMemoryUsageBytes = MemoryUtilities.GetPeakMemoryUsage();
_wallTimeSpan = bench.GetElapsedTime();
if (!_showVersion && !_showHelpMenu && !Console.IsOutputRedirected)
{
Console.WriteLine();
if (_peakMemoryUsageBytes > 0)
{
Console.WriteLine("Peak memory usage: {0}", MemoryUtilities.ToHumanReadable(_peakMemoryUsageBytes));
}
Console.WriteLine("Time: {0}", Benchmark.ToHumanReadable(_wallTimeSpan));
}
}
public void ToHumanReadable(long numBytes, string expectedResult)
{
Assert.Equal(expectedResult, MemoryUtilities.ToHumanReadable(numBytes));
}
public void ToHumanReadable_Convert_Bytes()
{
var observedValue = MemoryUtilities.ToHumanReadable(123);
Assert.Equal("123 B", observedValue);
}
