public void Execute()
{
if (_knownIndels != null)
{
_stateManager.AddCandidates(_knownIndels);
}
var read = new Read();
const int chunkSize = 10000;
var minLogThreshold = TimeSpan.FromSeconds(2);
int lastChunk = 0;
using (var tracker = new ElapsedTimeLogger($"Realign {_chrReference.Name}"))
while (_extractorForCandidates.GetNextAlignment(read))
{
// do not take candidates from reads with MapQ of zero, or secondary alignments
var doSkip = ((_skipDuplicates || _skipAndRemoveDuplicates) && read.IsPcrDuplicate) || read.MapQuality == 0 || !read.IsPrimaryAlignment;
if (!doSkip)
{
var candidates = _indelFinder.FindIndels(read, _chrReference.Sequence, _chrReference.Name);
_stateManager.AddCandidates(candidates);
_stateManager.AddAlleleCounts(read);
}
Realign(read.Position - 1);
var thisChunk = read.Position / chunkSize;
if (thisChunk > lastChunk)
{
tracker.LogIncrement(
$"Realign {_chrReference.Name}:{lastChunk*chunkSize}-{thisChunk*chunkSize}", minLogThreshold);
}
lastChunk = thisChunk;
}
Realign(null);
Logger.WriteToLog("Total realigned reads: " + TotalRealignedReads);
}
public void NullLogTest()
{
var log = loggerFactory.CreateLogger <ElapsedTimeLoggerTests>();
log.LogInformation("Normal log");
using (ElapsedTimeLogger etl = ElapsedTimeLogger.Create(null, "toto", "beginContext", "endContext", " "))
{
log.LogDebug("Normal log");
Thread.Sleep(600);
etl.LogInformation("ETL log 10");
Thread.Sleep(20);
using (etl.BeginScope("foo"))
{
etl.LogDebug("ETL log 20");
Thread.Sleep(400);
etl.LogWarning("ETL log 30");
Thread.Sleep(500);
}
}
log.LogInformation("Normal log");
}