/// <summary>
/// For each sequence read by the parser, pass it to the metric handler. Also update GUI summary panels
/// </summary>
private void ProcessSequences(string filename, BAMParser parser)
{
double incrementOne = 1; // the progress bar will update every [incrementOne] many clusters
double incrementTwo = 1; // the progress bar will update every [incrementTwo] many clusters
int increaseIncrementAfter = 100; // after this many clusters, increase the increment at which we update the gui
double increment; // the current increment at which progress bar will update
int updateDisplayForClusterIndex = -1, clusterCount = -1; // whether we have already updated the gui for this cluster
foreach (SAMAlignedSequence se in parser.ParseSequenceAsEnumerable(filename))
{
if (metricHandler.Add(se))
{
clusterCount = metricHandler.ClusterCount;
increment = (clusterCount < increaseIncrementAfter) ? incrementOne : incrementTwo;
if ((clusterCount == 1 || (double)clusterCount % increment == 0) && clusterCount != updateDisplayForClusterIndex)
{
updateDisplayForClusterIndex = clusterCount;
Dispatcher.BeginInvoke(
System.Windows.Threading.DispatcherPriority.Normal,
new StatsDelegate(UpdateStatsPanel), metricHandler.GoodCount, clusterCount,
metricHandler.MaxSampleCount, metricHandler.MaxAlignmentQuality, metricHandler.MaxReadQuality,
metricHandler.AverageDirt, metricHandler.AverageMapQ, metricHandler.AverageReadQ,
metricHandler.AverageDirtGood, metricHandler.AverageMapQGood, metricHandler.AverageReadQGood);
}
}
else
{
Console.WriteLine(Properties.Resources.HANDLER_FINISHED);
break;
}
}
// Tell the handler that there are no more sequences to receive
metricHandler.SetComplete();
}
/// <summary>
/// Processess a bam file dividing it into Cluster that it then yields back.
/// </summary>
public IEnumerable <Cluster> ProcessSequences(string filename)
{
//keep track of last cluster and last position
Cluster curCluster = null;
//also make sure things are sorted
int lastPos = int.MinValue;
int lastEnd = int.MinValue;
BAMParser bp = new BAMParser();
foreach (SAMAlignedSequence seq in bp.ParseSequenceAsEnumerable(filename))
{
ReadsProcessed++;
if (seq.Pos < 1 || seq.CIGAR == "*" || seq.Flag.HasFlag(SAMFlags.UnmappedQuery))
{
UnmappedReadsProcessed++;
continue;
}
//SKIP POSITION AND GET
if (seq.Pos > 0 && curCluster != null &&
seq.RName == curCluster.GenomeLocation.ID && seq.Pos < lastPos)
{
throw new PloidulatorException("BAM file is not in sorted order. Problem appeared at read: " + seq.ToString());
}
if (seq.Pos > lastEnd || seq.RName != curCluster.GenomeLocation.ID)
{
if (curCluster != null)
{
yield return(curCluster);
}
curCluster = new Cluster(seq.RName, seq.Pos);
}
curCluster.AddRead(seq);
lastPos = seq.Pos;
lastEnd = seq.RefEndPos;
if (ReadsProcessed % updateInterval == 0)
{
if (UpdateHandler != null && curCluster != null)
{
ClusterProcessorUpdate cu = new ClusterProcessorUpdate()
{
CurrentCluster = curCluster.GenomeLocation.ID,
ReadsProcessed = ReadsProcessed,
UnMappedReads = UnmappedReadsProcessed
};
UpdateHandler(cu);
}
}
}
if (curCluster != null)
{
yield return(curCluster);
}
}
