private void SignalNext(BamWorkRequest workRequest, string chrName)
{
lock (_sync)
{
var remainingWork = _remainingChrByBam[workRequest];
remainingWork.Remove(chrName);
if (remainingWork.Any())
{
_throttleSignalsByBamChr[GetThrottleKey(workRequest, remainingWork.First())].Set();
}
}
}
private void ProcessByBam(BamWorkRequest workRequest, string chrName)
{
var bamFileName = workRequest.BamFileName;
try
{
if (ShouldThrottle)
{
AcquireSignal(workRequest, chrName);
}
if (_maxChrsProcessingAllowed.HasValue)
{
EnforceChrLimit(chrName);
}
var chrReference = GetChrReference(chrName);
if (chrReference == null)
{
return; // missing chr, move on
}
Logger.WriteToLog(string.Format("{0}: Start processing chr '{1}'.", bamFileName, chrName));
var startTime = DateTime.UtcNow;
Process(workRequest, chrReference);
var processingTime = DateTime.UtcNow.Subtract(startTime).TotalSeconds;
Logger.WriteToLog(string.Format("{0}: Completed processing chr '{2}' in {1}s", bamFileName, processingTime, chrName));
TrackTime(workRequest.BamFilePath, processingTime);
}
catch (Exception ex)
{
var wrappedException = new Exception(string.Format("{1}: Error processing chr '{0}': {2}", chrName, bamFileName, ex.Message), ex);
Logger.WriteExceptionToLog(wrappedException);
lock (this)
Exceptions.Add(ex);
}
finally
{
CheckChrComplete(chrName, workRequest);
if (ShouldThrottle)
{
SignalNext(workRequest, chrName);
}
}
}
private void CheckChrComplete(string chrName, BamWorkRequest completedWorkRequest)
{
lock (_sync)
{
var chrWork = _remainingWorkByChr[chrName];
chrWork.Remove(completedWorkRequest);
if (!chrWork.Any()) // no more work left
{
if (_currentlyProcessingChrs.ContainsKey(chrName))
{
_currentlyProcessingChrs[chrName].Sequence = null;
_currentlyProcessingChrs.Remove(chrName);
}
Logger.WriteToLog("Unloaded chromosome '{0}', all jobs complete.", chrName);
}
}
}
private void AcquireSignal(BamWorkRequest workRequest, string chrName)
{
_throttleSignalsByBamChr[GetThrottleKey(workRequest, chrName)].WaitOne();
}
private string GetThrottleKey(BamWorkRequest workRequest, string chrName)
{
return(workRequest.BamFilePath + "-" + chrName);
}
protected abstract void Process(BamWorkRequest workRequest, ChrReference chrReference);