/// <summary>
/// Sorts the SequenceAlignmentMap based on the sort by fields,
/// either chromosome coordinates or read names and retuns sorted BAM indexer
/// </summary>
/// <example>
/// 1. Sort by chromosome name.
/// BAMSort sorter = new BAMSort([SequenceAlignmentMap], BAMSortByFields.ChromosomeCoordinates);
/// IList<BAMSortedIndex> sortedGroups = sorter.Sort();
/// foreach (BAMSortedIndex sortedGroup in sortedGroups)
/// {
/// sortedGroup.GroupName // Containes the RName
/// foreach (int index in sortedGroup)
/// {
/// index // index of SequenceAlignmentMap.QuerySequences
/// }
/// }
/// 2. Sort by read name.
/// BAMSort sorter = new BAMSort([SequenceAlignmentMap], BAMSortByFields.ChromosomeCoordinates);
/// IList<BAMSortedIndex> sortedGroups = sorter.Sort();
/// foreach (int index in sortedGroups[0]) // There will be only Group in list.
/// {
/// index // index of SequenceAlignmentMap.QuerySequences
/// }
/// </example>
/// <returns>sorted BAM indexer</returns>
public IList<BAMSortedIndex> Sort()
{
IList<BAMSortedIndex> sortedIndices = new List<BAMSortedIndex>();
switch (sortField)
{
case BAMSortByFields.ChromosomeNameAndCoordinates:
// Sort by Chromosomes (RName) and then by Positions (Pos) and retun "BAMSortedIndex"
// containing the indices of sorted SequenceAlignmentMap.QuerySequences items.
SortedDictionary<string, IList<string>> sortedFiles = SortByChromosomeCoordinates();
foreach (KeyValuePair<string, IList<string>> sortedFile in sortedFiles)
{
BAMSortedIndex sortedIndex = new BAMSortedIndex(sortedFile.Value, sortField);
sortedIndex.GroupName = sortedFile.Key;
sortedIndices.Add(sortedIndex);
}
break;
case BAMSortByFields.ChromosomeCoordinates:
// Sort by Chromosomes Positions (Pos) and retun "BAMSortedIndex"
// containing the indices of sorted SequenceAlignmentMap.QuerySequences items.
sortedFiles = SortByChromosomeCoordinates();
foreach (string refName in sequenceAlignMap.GetRefSequences())
{
IList<string> filenames =null;
if (sortedFiles.TryGetValue(refName, out filenames))
{
BAMSortedIndex sortedIndex = new BAMSortedIndex(filenames, sortField);
sortedIndex.GroupName = refName;
sortedIndices.Add(sortedIndex);
}
}
break;
case BAMSortByFields.ReadNames:
// Sort by Read name (QName) and retun "BAMSortedIndex" containing the indices of
// sorted SequenceAlignmentMap.QuerySequences items.
sortedIndices.Add(new BAMSortedIndex(SortByReadNames(), sortField));
break;
}
return sortedIndices;
}
/// <summary>
/// Sort and merge multiple SAM objects
/// </summary>
/// <param name="sortedIndexes">Sorted Indexes of SAM object.</param>
/// <param name="fstemp">Temporary tream to write alignments.</param>
/// <param name="formatter">Format aligned sequences in BAM format.</param>
/// <param name="sequenceAlignmentMaps">List of SAM objects to be merged.</param>
private void WriteMergeFile(IList <IList <BAMSortedIndex> > sortedIndexes, FileStream fstemp, BAMFormatter formatter, IList <SequenceAlignmentMap> sequenceAlignmentMaps)
{
List <SAMAlignedSequence> alignedSeqs = new List <SAMAlignedSequence>();
int[] sortedIndex = new int[sequenceAlignmentMaps.Count];
for (int i = 0; i < sortedIndexes.Count; i++)
{
BAMSortedIndex bamSortedIndex = sortedIndexes[i].ElementAt(sortedIndex[i]);
if (bamSortedIndex != null)
{
if (bamSortedIndex.MoveNext())
{
alignedSeqs.Add(sequenceAlignmentMaps[i].QuerySequences[bamSortedIndex.Current]);
}
else
{
alignedSeqs.Add(null);
}
}
else
{
alignedSeqs.Add(null);
}
}
int smallestIndex = -1;
do
{
for (int index = 0; index < alignedSeqs.Count; index++)
{
if (alignedSeqs[index] != null)
{
if (smallestIndex == -1)
{
smallestIndex = index;
}
else
{
if (0 < string.Compare(alignedSeqs[smallestIndex].RName, alignedSeqs[index].RName, StringComparison.OrdinalIgnoreCase))
{
smallestIndex = index;
}
else if (alignedSeqs[smallestIndex].RName.Equals(alignedSeqs[index].RName))
{
if (alignedSeqs[smallestIndex].Pos > alignedSeqs[index].Pos)
{
smallestIndex = index;
}
}
}
}
}
if (smallestIndex > -1)
{
SAMAlignedSequence alignSeqTowrite = alignedSeqs[smallestIndex];
if (sortedIndexes[smallestIndex].ElementAt(sortedIndex[smallestIndex]).MoveNext())
{
int nextIndex = sortedIndexes[smallestIndex].ElementAt(sortedIndex[smallestIndex]).Current;
alignedSeqs[smallestIndex] = sequenceAlignmentMaps[smallestIndex].QuerySequences[nextIndex];
}
else
{
sortedIndex[smallestIndex]++;
if (sortedIndex[smallestIndex] < sortedIndexes[smallestIndex].Count &&
sortedIndexes[smallestIndex].ElementAt(sortedIndex[smallestIndex]).MoveNext())
{
int nextIndex = sortedIndexes[smallestIndex].ElementAt(sortedIndex[smallestIndex]).Current;
alignedSeqs[smallestIndex] = sequenceAlignmentMaps[smallestIndex].QuerySequences[nextIndex];
}
else
{
alignedSeqs[smallestIndex] = null;
smallestIndex = -1;
}
}
formatter.WriteAlignedSequence(_header, alignSeqTowrite, fstemp);
}
} while (!alignedSeqs.All(a => a == null));
}
