public void write(BamWriter writer,
int index)
{
SerializedBamAlignment alignment = _bamAlignmentList[index];
byte[] byteArray = null;
int smallOffset = 0;
_serializedAlignments.GetByteArrayAndOffset(alignment.SerializedOffset, ref byteArray, ref smallOffset);
writer.Write(byteArray, (uint)alignment.SerializedSize, smallOffset);
}
void WriteListsInOrder(List <BamRecordAccessor> bamContainers, BamWriter bamWriter)
{
List <int> bamAlignmentListIndexes = new List <int>();
for (int i = 0; i < bamContainers.Count; ++i)
{
if (!bamContainers[i].IsEnd())
{
bamAlignmentListIndexes.Add(i);
}
}
if (bamAlignmentListIndexes.Count == 0)
{
return;
}
BamRecordAccessorComparer recordAccessorComparer = new BamRecordAccessorComparer();
SortedList <BamRecordAccessor, BamRecordAccessor> sortedList = new SortedList <BamRecordAccessor, BamRecordAccessor>(bamContainers.Count, recordAccessorComparer);
for (int i = 0; i < bamContainers.Count; ++i)
{
var bamContainer = bamContainers[i];
sortedList.Add(bamContainer, bamContainer);
}
while (sortedList.Count > 1)
{
var bamContainer = sortedList.Values[0];
sortedList.RemoveAt(0);
bamContainer.WriteCurrentAlignment(bamWriter);
bamContainer.MoveToNextRecord();
if (!bamContainer.IsEnd())
{
sortedList.Add(bamContainer, bamContainer);
}
}
// There is only 1 list left
var finalBamContainer = sortedList.Values[0];
while (!finalBamContainer.IsEnd())
{
finalBamContainer.WriteCurrentAlignment(bamWriter);
finalBamContainer.MoveToNextRecord();
}
}
// This method is very specialized. Each list should be the same size, so sorting
// each on its own thread is very efficient. There is one additional pass
// to merge the lists, but the writing occurs during this iteration, so we're
// not waiting to write.
private void SortMemAndWrite()
{
Logger.WriteToLog("Sorting BAM data...");
// Sort each of the lists
Parallel.ForEach(_bamAlignmentLists,
new ParallelOptions {
MaxDegreeOfParallelism = NumThreads
},
bamAlignmentList =>
{
bamAlignmentList.Sort(new BamAlignmentComparer(bamAlignmentList));
}
);
Logger.WriteToLog("BAM sort complete.");
List <BamRecordAccessor> bamListContainer = new List <BamRecordAccessor>();
foreach (SerializedAlignmentContainer bamAlignmentList in _bamAlignmentLists)
{
bamListContainer.Add(new BamListContainer(bamAlignmentList));
}
BamWriter bamWriter = _numTempFiles > 0 ? GetNewTemporaryBamWriter() : this;
WriteListsInOrder(bamListContainer, bamWriter);
Logger.WriteToLog("Finished writing temporary file.");
if (_numTempFiles > 0)
{
bamWriter.Dispose();
foreach (var alignmentContainer in _bamAlignmentLists)
{
alignmentContainer.Clear();
}
}
}
public override void WriteCurrentAlignment(BamWriter writer)
{
byte[] serializedAlignment = BamWriter.SerializeAlignment(ref _currentBamAlignment);
writer.Write(serializedAlignment, (uint)serializedAlignment.Length);
}
public override void WriteCurrentAlignment(BamWriter writer)
{
_bamList.write(writer, _index);
}
public abstract void WriteCurrentAlignment(BamWriter writer);