/// <summary>
/// Adds the links between the nodes of the graph.
/// </summary>
private void GenerateLinks(KmerDictionary kmerManager)
{
// Prepare a mask to remove the bits representing the first nucleotide (or left most bits in the encoded kmer)
// First calculate how many bits do you have to move down a character until you are at the start of the kmer encoded sequence
int distancetoShift = 2 * (KmerLength - 1);
ulong rightMask = ~(((ulong)3) << distancetoShift);
Parallel.ForEach(_nodes, node =>
{
DeBruijnNode searchResult = null;
KmerData32 searchNodeValue = new KmerData32();
// Right Extensions - Remove first position from the value
// Remove the left most value by using an exclusive
ulong nextKmer = node.NodeValue.KmerData & rightMask;
// Move it over two to get make a position for the next pair of bits to represent a new nucleotide
nextKmer = nextKmer << 2;
for (ulong i = 0; i < 4; i++)
{
ulong tmpNextKmer = nextKmer | i; // Equivalent to "ACGTA"+"N" where N is the 0-3 encoding for A,C,G,T
// Now to set the kmer value to this, the orientationForward value is equal to false if the
// reverse compliment of the kmer is used instead of the kmer value itself.
bool matchIsRC = searchNodeValue.SetKmerData(tmpNextKmer, KmerLength);
searchResult = kmerManager.TryGetOld(searchNodeValue);
if (searchResult != null)
{
node.SetExtensionNode(true, matchIsRC, searchResult);
}
}
// Left Extensions
nextKmer = node.NodeValue.KmerData;
//Chop off the right most basepair
nextKmer >>= 2;
for (ulong i = 0; i < 4; i++) // Cycle through A,C,G,T
{
// Add the character on to the left side of the kmer
// Equivalent to "N" + "ACGAT" where the basepair is added on as the 2 bits
ulong tmpNextKmer = (i << distancetoShift) | nextKmer;
bool matchIsRC = searchNodeValue.SetKmerData(tmpNextKmer, KmerLength);
searchResult = kmerManager.TryGetOld(searchNodeValue);
if (searchResult != null)
{
node.SetExtensionNode(false, matchIsRC, searchResult);
}
}
});
LinkGenerationCompleted = true;
}
/// <summary>
/// Adds the links between the nodes of the graph.
/// </summary>
private void GenerateLinks(KmerDictionary kmerManager)
{
// Prepare a mask to remove the bits representing the first nucleotide (or left most bits in the encoded kmer)
// First calculate how many bits do you have to move down a character until you are at the start of the kmer encoded sequence
int distancetoShift=2*(KmerLength-1);
ulong rightMask = ~( ((ulong)3) << distancetoShift);
Parallel.ForEach(_nodes, node =>
{
DeBruijnNode searchResult = null;
KmerData32 searchNodeValue = new KmerData32();
// Right Extensions - Remove first position from the value
// Remove the left most value by using an exclusive
ulong nextKmer = node.NodeValue.KmerData & rightMask;
// Move it over two to get make a position for the next pair of bits to represent a new nucleotide
nextKmer= nextKmer << 2;
for (ulong i = 0; i < 4; i++)
{
ulong tmpNextKmer = nextKmer | i;// Equivalent to "ACGTA"+"N" where N is the 0-3 encoding for A,C,G,T
// Now to set the kmer value to this, the orientationForward value is equal to false if the
// reverse compliment of the kmer is used instead of the kmer value itself.
bool matchIsRC = searchNodeValue.SetKmerData(tmpNextKmer, KmerLength);
searchResult = kmerManager.TryGetOld(searchNodeValue);
if (searchResult != null)
{
node.SetExtensionNode(true, matchIsRC, searchResult);
}
}
// Left Extensions
nextKmer = node.NodeValue.KmerData;
//Chop off the right most basepair
nextKmer >>= 2;
for (ulong i = 0; i < 4; i++) // Cycle through A,C,G,T
{
// Add the character on to the left side of the kmer
// Equivalent to "N" + "ACGAT" where the basepair is added on as the 2 bits
ulong tmpNextKmer = (i<<distancetoShift) | nextKmer;
bool matchIsRC=searchNodeValue.SetKmerData(tmpNextKmer, KmerLength);
searchResult = kmerManager.TryGetOld(searchNodeValue);
if (searchResult != null)
{
node.SetExtensionNode(false, matchIsRC, searchResult);
}
}
});
LinkGenerationCompleted = true;
}
