public MerDictionary(long dictionarySize, int merSize)
{
if (dictionarySize > maxTable)
{
partitioned = true;
keySize = (int)Math.Ceiling(Math.Log(dictionarySize / maxTable, 4)); // find minimum key size
if (keySize < 1)
{
keySize = 1; // must partition on at least one base
}
noOfPartitions = (int)Math.Pow(4, keySize); // giving this many partitions
keyBaseShift = 64 - keySize * 2; // shift right this many bits to extract the partition no.
int partitionLength = (int)(dictionarySize / noOfPartitions); // with this average length (but scaled to reflect canonical distributions)
dictionaryPartitions = new kMerDictionary <TV> [noOfPartitions];
for (int i = 0; i < noOfPartitions; i++)
{
int scaledPartitionLength = 2 * partitionLength * (noOfPartitions - i) / noOfPartitions; // =(16-I2)/16*2*(F19/16)
dictionaryPartitions[i] = new kMerDictionary <TV>(scaledPartitionLength, merSize);
}
}
else
{
partitioned = false;
dictionary = new kMerDictionary <TV>((int)dictionarySize, merSize);
}
capacity = dictionarySize;
}
private void CopyToTable(int partitionNo, ulong[] orderedMers, TV[] orderedValues, int merCount, int merSize)
{
//Console.WriteLine("starting copy for partition " + partitionNo);
kMerDictionary <TV> pmp = new kMerDictionary <TV>(merCount, merSize);
pmers[partitionNo] = pmp;
for (int i = 0; i < merCount; i++)
{
pmp.AddNoCheck(orderedMers[i], orderedValues[i]);
}
pmp.Optimise();
//Console.WriteLine(merCount + " mers copied for partition " + partitionNo);
}
int keyBaseShift = 0; // # of bits to shift to get partition-key bases (bits)
public MerTable(long tableSize, int merSize)
{
this.merSize = merSize;
if (tableSize > maxTable)
{
partitioned = true;
int keySizeBases = (int)Math.Ceiling(Math.Log(tableSize / maxTable, 4)); // find minimum key size
if (keySizeBases < 1)
{
keySizeBases = 1; // must partition on at least one base
}
keyBaseShift = 64 - keySizeBases * 2;
noParts = (int)Math.Pow(4, keySizeBases); // giving this many partitions
int partitionLength = (int)(tableSize / noParts); //
int scaledPartitionLength = 2 * partitionLength; // rough guess as to space needed to hold the first (largest) partition of loaded kmers
orderedMers = new ulong[2][];
orderedValues = new TV[2][];
for (int b = 0; b < 2; b++)
{
orderedMers[b] = new ulong[scaledPartitionLength];
orderedValues[b] = new TV[scaledPartitionLength];
}
ctd = new CopyToTableDelegate(CopyToTable);
pmers = new kMerDictionary <TV> [noParts];
ulong fillBases = 0xffffffffffffffff >> (keySizeBases * 2);
partitionBoundaries = new ulong[noParts];
for (ulong k = 0; k < (ulong)noParts; k++)
{
partitionBoundaries[k] = k << keyBaseShift | fillBases;
}
}
else
{
mers = new kMerDictionary <TV>((int)tableSize, merSize);
}
}
public bool LoadFinished()
{
if (dataNeedsSorting)
{
Console.WriteLine("kmers being loaded into table were not in sorted order");
return(false);
}
if (partitioned)
{
// wait for previous buffer copy to complete
if (iarCopyToTable != null && !iarCopyToTable.IsCompleted)
{
//Console.WriteLine("waiting for copy to finish before final copy");
iarCopyToTable.AsyncWaitHandle.WaitOne();
}
// copy final buffer into its hash table partition
//Console.WriteLine("calling copy from LoadFinished for partition " + currentPartition + " for buffer " + currentBuffer);
CopyToTable(currentPartition, orderedMers[currentBuffer], orderedValues[currentBuffer], cpi, merSize);
for (int p = 0; p < pmers.Length; p++)
{
if (pmers[p] == null)
{
pmers[p] = new kMerDictionary <TV>(1, merSize);
}
}
}
// finished with these buffers now
orderedMers = null;
orderedValues = null;
//Console.WriteLine(mersAdded + " mers added, " + mersCopied + " mers copied");
return(true);
}
