public Sequencer(uint[] c, OccurrenceArray[] occurrences, OccurrenceArray[] occurrencesRev,
CompressedSuffixArray suffixArray, CompressedSuffixArray suffixArrayRev,
int threadCount)
{
_c = c;
_occurrences = occurrences;
_occurrencesRev = occurrencesRev;
_suffixArray = suffixArray;
_suffixArrayRev = suffixArrayRev;
_database = new AlignmentDatabase("temp.db");
_threadCount = threadCount;
}
public static CompressedSuffixArray CreateFromFile(string fileName, DnaBwt bwt, OccurrenceArray[] occ, uint[] c)
{
var buffer = File.ReadAllBytes(fileName);
uint[] compressedSufArray = new uint[buffer.Length/4];
for (int i = 0; i < compressedSufArray.Length; i++)
{
compressedSufArray[i] = BitConverter.ToUInt32(buffer, i*4);
}
CompressedSuffixArray csa = new CompressedSuffixArray(compressedSufArray, bwt, occ, c);
return csa;
}
public Sequencer(uint[] c, OccurrenceArray[] occurrences, OccurrenceArray[] occurrencesRev,
CompressedSuffixArray suffixArray, CompressedSuffixArray suffixArrayRev)
: this(c, occurrences, occurrencesRev,
suffixArray, suffixArrayRev, Environment.ProcessorCount + 2)
{
}