public static DnaSequence CreateReverseGenomeFromBinaryFile(string forwardBinaryFile)
{
DnaSequence forward = CreateFromBinaryFile(forwardBinaryFile);
DnaSequence reverse = new DnaSequence(new byte[forward.Bytes.Length], forward.Length);
for (long i = 0, j = forward.Length - 1; i < reverse.Length; i++, j--)
{
reverse[i] = forward[j];
}
return reverse;
}
public static DnaSequence CreateGenomeFromReverseTextFile(string refFile)
{
using (var file = File.OpenRead(refFile))
{
var reader = new BinaryReader(file);
long length = file.Length;
byte[] binaryText = new byte[length / 4 + (length % 4 == 0 ? 0 : 1)];
DnaSequence dna = new DnaSequence(binaryText, length);
for (long i = file.Length-1; i >= 0; i--)
{
var character = reader.ReadChar();
switch (character)
{
case 'A':
dna[i] = 0;
break;
case 'C':
dna[i] = 1;
break;
case 'G':
dna[i] = 2;
break;
case 'T':
dna[i] = 3;
break;
}
}
return dna;
}
}
public static void SavePrecomputedDataToFiles(string baseFileName, DnaSequence referenceGenome)
{
Level0String level0String = new Level0String(referenceGenome);
LongSuffixArray suffixArray = LongSuffixArray.CreateSuffixArray(level0String);
suffixArray.WriteToFile(baseFileName + ".csa", 32);
DnaBwt bwt = new DnaBwt(level0String, suffixArray);
bwt.WriteToFile(baseFileName + ".bwt");
WriteCToFile(baseFileName + ".c", bwt);
OccurrenceArray[] occs = OccurrenceArray.CreateOccurrenceArrays(bwt);
OccurrenceArray.WriteToFile(baseFileName + ".occ", occs);
}
public Level0String(DnaSequence text)
{
_text = text.Bytes;
_length = (uint)(text.Length + 1);
}
private List<System.Tuple<uint, uint>> GetSuffixArrayBoundsSansRecursion(DnaSequence shortRead, int allowedDiff,
byte[] minDiffs)
{
var maxHeap = new BinaryHeap<Tuple<int, int, uint, uint, int>>((x, y) => y.Item2.CompareTo(x.Item2));
var curAllowedDiff = 0;
var alignments = new List<System.Tuple<uint, uint>>();
for (int dnaBase = 0; dnaBase < 4; dnaBase++)
{
if (dnaBase == shortRead[shortRead.Length - 1])
{
uint minSAIndex = 0;
var maxSAIndex = (uint)(_suffixArray.Length - 1);
maxHeap.Add(new Tuple<int, int, uint, uint, int>((int)(shortRead.Length - 2), allowedDiff,
minSAIndex, maxSAIndex, dnaBase));
}
else
{
if (allowedDiff - 1 >= minDiffs[shortRead.Length - 1])
{
uint minSAIndex = 0;
var maxSAIndex = (uint)(_suffixArray.Length - 1);
maxHeap.Add(new Tuple<int, int, uint, uint, int>((int)(shortRead.Length - 2), allowedDiff-1,
minSAIndex, maxSAIndex, dnaBase));
}
}
}
while (maxHeap.Count > 0)
{
var tuple = maxHeap.Remove();
int remainingAllowedDiff = tuple.Item2;
if (remainingAllowedDiff < curAllowedDiff)
break;
int readIndex = tuple.Item1;
int dbase = tuple.Item5;
uint minSAIndex = (uint) (_c[dbase] + _occurrences[dbase][tuple.Item3 - 1] + 1);
uint maxSAIndex = (uint)(_c[dbase] + _occurrences[dbase][tuple.Item4]);
if (minSAIndex > maxSAIndex)
continue;
if (readIndex < 0)
{
if (remainingAllowedDiff > curAllowedDiff)
{
alignments.Clear();
curAllowedDiff = remainingAllowedDiff;
}
alignments.Add(new System.Tuple<uint, uint>(minSAIndex, maxSAIndex));
continue;
}
for (int dnaBase = 0; dnaBase < 4; dnaBase++)
{
if (dnaBase == shortRead[readIndex])
{
maxHeap.Add(new Tuple<int, int, uint, uint, int>(readIndex - 1, remainingAllowedDiff,
minSAIndex, maxSAIndex, dnaBase));
}
else
{
if (remainingAllowedDiff - 1 >= minDiffs[readIndex])
{
maxHeap.Add(new Tuple<int, int, uint, uint, int>(readIndex - 1, remainingAllowedDiff - 1,
minSAIndex, maxSAIndex, dnaBase));
}
}
}
}
return alignments;
}
/// <summary>
/// Calculates a loose bound of the minimum number of differences needed to align shortRead[0..i]
/// </summary>
/// <param name="?"></param>
/// <param name="shortRead"></param>
/// <param name="minSAIndex"></param>
/// <param name="maxSAIndex"></param>
private byte[] CalculateMinimumDifferences(DnaSequence shortRead, out uint minSAIndex, out uint maxSAIndex)
{
minSAIndex = 1;
maxSAIndex = (uint) (_suffixArrayRev.Length - 1);
byte differences = 0;
byte[] minDifferences = new byte[shortRead.Length];
for (uint readIndex = 0;
readIndex < shortRead.Length;
readIndex++)
{
var character = shortRead[readIndex];
minSAIndex = (uint)(_c[character] + _occurrencesRev[character][minSAIndex - 1] + 1);
maxSAIndex = (uint) (_c[character] + _occurrencesRev[character][maxSAIndex]);
if (minSAIndex > maxSAIndex)
{
minSAIndex = 1;
maxSAIndex = (uint) (_suffixArrayRev.Length - 1);
differences++;
}
minDifferences[readIndex] = differences;
}
return minDifferences;
}
public void ConstructGenome(string outFile)
{
int readLength;
long genomeLength;
using (var session = _database.SessionFactory.OpenStatelessSession())
{
var metadata = session.Query<Metadata>().First();
readLength = metadata.ReadLength;
genomeLength = metadata.GenomeLength;
}
using (var file = File.Open(outFile, FileMode.Create))
{
var writer = new BinaryWriter(file);
var positionsToReads = new Dictionary<uint, byte[][]>();
long maxInserted = 0;
ThreadPool.QueueUserWorkItem(o =>
{
Queue<ILookup<uint, byte[]>> queue = new Queue<ILookup<uint, byte[]>>();
long[] maxQueried = {0};
ManualResetEvent enqueueEvent = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(o2 =>
{
using (var session = _database.SessionFactory.OpenStatelessSession())
{
const long readInterval = 1000000;
for (long i = 0; i < genomeLength; i += readInterval)
{
long i1 = i;
var lookup = LinqExtensionMethods.Query<Alignment>(session)
.Where(
a =>
a.Position >= i1 &&
a.Position < i1 + readInterval)
.ToLookup(a => a.Position, a => a.ShortRead);
lock (queue)
{
queue.Enqueue(lookup);
Interlocked.Add(ref maxQueried[0], readInterval);
enqueueEvent.Set();
}
}
}
Interlocked.Exchange(ref maxQueried[0], long.MaxValue);
});
while (Volatile.Read(ref maxQueried[0]) != long.MaxValue)
{
ILookup<uint, byte[]> lookup;
enqueueEvent.WaitOne();
lock (queue)
{
lookup = queue.Dequeue();
enqueueEvent.Reset();
}
var keys = lookup.Select(g => g.Key).ToArray();
Array.Sort(keys);
foreach (var key in keys)
{
lock (positionsToReads)
{
positionsToReads.Add(key, lookup[key].ToArray());
Interlocked.Exchange(ref maxInserted, key);
}
}
}
while (queue.Any())
{
ILookup<uint, byte[]> lookup = queue.Dequeue();
var keys = lookup.Select(g => g.Key).ToArray();
Array.Sort(keys);
foreach (var key in keys)
{
lock (positionsToReads)
{
positionsToReads.Add(key, lookup[key].ToArray());
Interlocked.Exchange(ref maxInserted, key);
}
}
}
Interlocked.Exchange(ref maxInserted, long.MaxValue);
});
for (long textIndex = 0; textIndex < genomeLength; textIndex++)
{
lock (positionsToReads)
{
positionsToReads.Remove((uint)(textIndex - readLength));
}
if (textIndex%100000 == 0)
{
Console.WriteLine(textIndex);
}
int[] characterCounts = new int[4];
for (uint i = (uint)textIndex; i > textIndex - readLength && i > 0; i--)
{
uint i1 = i;
SpinWait.SpinUntil(() => Volatile.Read(ref maxInserted) >= i1);
bool gotValue;
byte[][] reads;
lock (positionsToReads)
{
gotValue = positionsToReads.TryGetValue(i, out reads);
}
if (!gotValue) continue;
foreach (var read in reads)
{
DnaSequence sequence = new DnaSequence(read, readLength);
var character = sequence[textIndex - i];
characterCounts[character]++;
}
}
var finalCharacter = 'N';
var maxCount = 0;
var maxIndex = -1;
for (int i = 0; i < 4; i++)
{
if (characterCounts[i] > maxCount)
{
maxCount = characterCounts[i];
maxIndex = i;
}
}
switch (maxIndex)
{
case 0:
finalCharacter = 'A';
break;
case 1:
finalCharacter = 'C';
break;
case 2:
finalCharacter = 'G';
break;
case 3:
finalCharacter = 'T';
break;
}
writer.Write(finalCharacter);
}
}
}
public void AlignReads(string readsFile)
{
using (var session = _database.SessionFactory.OpenStatelessSession())
using (var transaction = session.BeginTransaction())
using (var file = File.OpenRead(readsFile))
{
var reader = new BinaryReader(file);
var readLength = reader.ReadInt32();
var numReads = (file.Length - 4) / DnaSequence.ByteArrayLength(readLength);
Metadata metadata = new Metadata()
{
Id = 1,
GenomeLength = _suffixArray.Length - 1,
ReadLength = readLength
};
session.Insert(metadata);
Random[] randoms = new Random[_threadCount];
var manualResetEvents = new ManualResetEvent[_threadCount];
bool[] doneReading = {false};
Queue<byte[]> queue = new Queue<byte[]>();
long[] readsAligned = {0};
ManualResetEvent queueReadyForMore = new ManualResetEvent(true);
for (int i = 0; i < manualResetEvents.Length; i++)
{
randoms[i] = new Random();
manualResetEvents[i] = new ManualResetEvent(false);
var i1 = i;
ThreadPool.QueueUserWorkItem(o =>
{
while (Volatile.Read(ref readsAligned[0]) != numReads)
{
byte[] shortReadBytes;
long readId;
lock (queue)
{
if (!queue.Any())
continue;
shortReadBytes = queue.Dequeue();
if (queue.Count < 20000)
queueReadyForMore.Set();
readId = Volatile.Read(ref readsAligned[0]);
Interlocked.Increment(ref readsAligned[0]);
}
var shortRead = new DnaSequence(shortReadBytes, readLength);
AddAlignmentsToDatabase(shortRead, 2, randoms[i1], session, readId);
if (readId%20000 == 0)
{
Console.WriteLine(readId);
GC.Collect();
}
}
manualResetEvents[i1].Set();
});
readsAligned[0]++;
}
long readsRead = 0;
while (readsRead < numReads)
{
byte[] shortReadBytes = reader.ReadBytes(DnaSequence.ByteArrayLength(readLength));
queueReadyForMore.WaitOne();
lock (queue)
{
queue.Enqueue(shortReadBytes);
if (queue.Count > 40000)
queueReadyForMore.Reset();
}
readsRead++;
}
lock (doneReading)
{
doneReading[0] = true;
}
WaitHandle.WaitAll(manualResetEvents);
transaction.Commit();
}
}
public void AddAlignmentsToDatabase(DnaSequence shortRead, int allowedDifferences, Random rng,
IStatelessSession session, long readId)
{
uint revMinSAIndex, revMaxSAIndex;
var minDifferences = CalculateMinimumDifferences(shortRead, out revMinSAIndex, out revMaxSAIndex);
if (minDifferences[minDifferences.Length - 1] > allowedDifferences)
return;
if (minDifferences[minDifferences.Length - 1] == 0)
{
var randomIndex = revMinSAIndex + rng.Next((int) (revMaxSAIndex+1-revMinSAIndex));
var textPos = (uint)(_suffixArray.Length - 1 - _suffixArrayRev[randomIndex] - shortRead.Length);
Alignment alignment = new Alignment {Id = readId, Position = textPos, ShortRead = shortRead.Bytes};
lock (session)
{
session.Insert(alignment);
}
}
else
{
var sufBounds =
GetSuffixArrayBoundsSansRecursion(shortRead, allowedDifferences, minDifferences);
if (sufBounds.Any())
{
var indices = new HashSet<uint>();
foreach (var sufBound in sufBounds)
{
for (uint saIndex = sufBound.Item1; saIndex <= sufBound.Item2; saIndex++)
indices.Add(saIndex);
}
var indicesArray = indices.ToArray();
var randomIndex = rng.Next(indicesArray.Count());
var textPos = (uint) _suffixArray[indicesArray[randomIndex]];
Alignment alignment = new Alignment {Id = readId, Position = textPos, ShortRead = shortRead.Bytes};
lock (session)
{
session.Insert(alignment);
}
}
}
}
