/// <summary>
/// Cleans adapter sequences from seqeuences
/// </summary>
public override void cleanAdapters()
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
Adapters.getInstance();
removedAdapters = new Dictionary <int, string>();
Parallel.For(0, index, new ParallelOptions {
MaxDegreeOfParallelism = Preferences.getInstance().getCoresToUse()
},
// Initialize the local states
() => new FqSequence_IO(sequencerType, "Adapter Removal", this),
// Accumulate the thread-local computations in the loop body
(i, loop, adapters) =>
{
adapters.removedAdapters = fastqSeq[i].cleanAdapters(adapters.adapters, Fq_FILE_MAP);
return(adapters);
},
adapters =>
{
Object locker = new object();
lock (locker)
{
if (adapters.removedAdapters != null)
{
removedAdapters.Add(adapters.removedAdapters.SequenceIndex, adapters.removedAdapters.AdapterName);
}
}
});
stopwatch.Stop();
Console.WriteLine("Statistics Performed in " + stopwatch.Elapsed);
}
public FqSequence_IO(String sequencerType, String taskType, FqFile_Component fqFile)
{
if (taskType == SEQUENCE_TESTS_TASK)
{
distributes = new List <int>(40);
for (int j = 0; j <= SequencerDiscriminator.getSequencerSpecifier(sequencerType).getDistributionSpread(); j++)
{
distributes.Add(0);
}
perSeqQuals = new int[fqFile.getMaxSeqSize()];
subZeroOffset = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getSubZeroQualities();
}
else if (taskType == ADAPTER_TASK)
{
adapters = Adapters.getInstance().getAdaptersList();
removedAdapters = null;
}
}