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));
}
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));
}
}
