/// <summary>
/// Public method mapping Reads to Contigs.
/// </summary>
/// <param name="contigs">List of sequences of contigs.</param>
/// <param name="reads">List of input reads.</param>
/// <param name="kmerLength">Length of kmer.</param>
/// <returns>Contig Read Map.</returns>
public ReadContigMap Map(IList <ISequence> contigs, IList <ISequence> reads, int kmerLength)
{
KmerIndexerDictionary map = SequenceToKmerBuilder.BuildKmerDictionary(contigs, kmerLength);
ReadContigMap maps = new ReadContigMap();
using (ThreadLocal <char[]> rcBuilder = new ThreadLocal <char[]>(() => new char[kmerLength]))
{
Parallel.ForEach(reads, (ISequence readSequence) =>
{
IEnumerable <string> kmers = SequenceToKmerBuilder.GetKmerStrings(readSequence, kmerLength);
ReadIndex read = new ReadIndex(readSequence);
IList <KmerIndexer> positions;
foreach (string kmer in kmers)
{
if (map.TryGetValue(kmer, out positions) ||
map.TryGetValue(kmer.GetReverseComplement(rcBuilder.Value), out positions))
{
read.ContigReadMatchIndexes.Add(positions);
}
}
IList <Task <IList <ReadMap> > > tasks =
new List <Task <IList <ReadMap> > >();
//Stores information about contigs for which tasks has been generated.
IList <int> visitedContigs = new List <int>();
//Creates Task for every read in nodes for a given contig.
for (int index = 0; index < read.ContigReadMatchIndexes.Count; index++)
{
int readPosition = index;
foreach (KmerIndexer kmer in read.ContigReadMatchIndexes[index])
{
int contigIndex = kmer.SequenceIndex;
if (!visitedContigs.Contains(contigIndex))
{
visitedContigs.Add(contigIndex);
tasks.Add(Task <IList <ReadMap> > .Factory.StartNew(t =>
MapRead(readPosition, read.ContigReadMatchIndexes, contigIndex, read.ReadSequence.Count, kmerLength),
TaskCreationOptions.AttachedToParent));
}
}
}
Dictionary <ISequence, IList <ReadMap> > overlapMaps =
new Dictionary <ISequence, IList <ReadMap> >();
for (int index = 0; index < visitedContigs.Count; index++)
{
overlapMaps.Add(contigs[visitedContigs[index]], tasks[index].Result);
}
lock (maps)
{
if (!maps.ContainsKey(read.ReadSequence.DisplayID))
{
maps.Add(read.ReadSequence.DisplayID, overlapMaps);
}
else
{
throw new ArgumentException(
string.Format(CultureInfo.CurrentCulture, Resource.DuplicatingReadIds, read.ReadSequence.DisplayID));
}
}
});
}
return(maps);
}
/// <summary>
/// Aligns reads to contigs using kmer method of alignment.
/// </summary>
/// <param name="contigs">List of contig sequences.</param>
/// <param name="reads">List of read sequences.</param>
/// <param name="kmerLength">Kmer Length.</param>
/// <returns>List of Contig</returns>
public static IList <Contig> ReadContigAlignment(IList <ISequence> contigs, IList <ISequence> reads, int kmerLength)
{
KmerIndexerDictionary map = SequenceToKmerBuilder.BuildKmerDictionary(reads, kmerLength);
IList <ContigIndex> contigDatas;
using (ThreadLocal <char[]> rcBuilder = new ThreadLocal <char[]>(() => new char[kmerLength]))
{
contigDatas = contigs.AsParallel().Select(contig =>
{
IEnumerable <string> kmers = SequenceToKmerBuilder.GetKmerStrings(contig, kmerLength);
ContigIndex index = new ContigIndex(contig);
IList <KmerIndexer> positions;
foreach (string kmer in kmers)
{
if (map.TryGetValue(kmer, out positions) ||
map.TryGetValue(kmer.GetReverseComplement(rcBuilder.Value), out positions))
{
index.ContigReadMatchIndexes.Add(positions);
}
else
{
index.ContigReadMatchIndexes.Add(new List <KmerIndexer>());
}
}
return(index);
}).ToList();
}
return(contigDatas.Select(contigData =>
{
IList <Task <IList <ReadMap> > > tasks =
new List <Task <IList <ReadMap> > >();
//Stores information about contigs for which tasks has been generated.
IList <int> visitedReads = new List <int>();
//Creates Task for every read in nodes for a given contig.
for (int index = 0; index < contigData.ContigReadMatchIndexes.Count; index++)
{
int readPosition = index;
foreach (KmerIndexer kmer in contigData.ContigReadMatchIndexes[index])
{
int contigIndex = kmer.SequenceIndex;
if (!visitedReads.Contains(contigIndex))
{
visitedReads.Add(contigIndex);
tasks.Add(Task <IList <ReadMap> > .Factory.StartNew(t =>
MapRead(readPosition, contigData.ContigReadMatchIndexes, contigIndex, contigData.ContigSequence.Count, kmerLength),
TaskCreationOptions.AttachedToParent));
}
}
}
Contig contigOutputStructure = new Contig();
contigOutputStructure.Consensus = contigData.ContigSequence;
for (int index = 0; index < visitedReads.Count; index++)
{
foreach (ReadMap maps in tasks[index].Result)
{
Contig.AssembledSequence assembledSeq = new Contig.AssembledSequence()
{
Length = maps.Length,
Position = maps.StartPositionOfContig,
ReadPosition = maps.StartPositionOfRead,
Sequence = reads[visitedReads[index]]
};
if (contigOutputStructure.Consensus.Range(assembledSeq.Position, assembledSeq.Length).ToString().
Equals(assembledSeq.Sequence.Range(assembledSeq.ReadPosition, assembledSeq.Length).ToString()))
{
assembledSeq.IsComplemented = false;
assembledSeq.IsReversed = false;
}
else
{
assembledSeq.IsComplemented = true;
assembledSeq.IsReversed = true;
}
contigOutputStructure.Sequences.Add(assembledSeq);
}
}
return contigOutputStructure;
}).ToList());
}