Main(string[] args)
{
int i;
for (i = 0; i < args.Length; ++i)
{
using (System.IO.FileStream fs = new System.IO.FileStream(
args[i],
System.IO.FileMode.Open,
System.IO.FileAccess.Read))
{
System.Console.Write(args[i] + @": {0:d} bytes ... ", fs.Length);
byte[] T = new byte[fs.Length];
int[] SA = new int[fs.Length];
fs.Read(T, 0, T.Length);
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
sw.Start();
SAIS.sufsort(T, SA, T.Length);
sw.Stop();
double sec = (double)sw.ElapsedTicks / (double)System.Diagnostics.Stopwatch.Frequency;
System.Console.WriteLine(@"{0:f4} sec", sec);
check(T, SA, T.Length, true);
T = null;
SA = null;
}
}
}
private static IBigArray <ulong> buildSuffixArray(string str)
{
//Initialise the array that will hold the suffix array
MemoryEfficientBigULongArray suffixArray = new MemoryEfficientBigULongArray(str.Length);
//Calculate the suffix array
long status = SAIS.sufsort(str, suffixArray, str.Length);
if (status != 0)
{
string error = String.Format("Error occurred whilst generating the suffix array: {0}", status);
Console.WriteLine(error);
throw new Exception(error);
}
return(suffixArray);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="fastaDatabase"></param>
public SearchableDatabase(FastaDatabase fastaDatabase)
{
FastaDatabase = fastaDatabase;
_sequence = fastaDatabase.GetSequence();
_suffixArray = new int[_sequence.Length];
SAIS.sufsort(_sequence, _suffixArray, _sequence.Length);
var neighboringLcps = new byte[_suffixArray.Length];
neighboringLcps[0] = 0;
for (var i = 1; i < _suffixArray.Length; i++)
{
var lcp = IndexedDatabase.GetLcp(_sequence, _suffixArray[i - 1], _suffixArray[i]);
neighboringLcps[i] = lcp;
}
_leftLcps = new byte[_suffixArray.Length];
_rightLcps = new byte[_suffixArray.Length];
InitializeLcps(neighboringLcps, _leftLcps, _rightLcps, 0, _suffixArray.Length - 1);
}
private void CreatePermutedLongestCommonPrefixFile()
{
if (File.Exists(_pLcpFilePath))
{
File.Delete(_pLcpFilePath);
}
var sequence = FastaDatabase.GetSequence();
//Console.WriteLine("Annotation: {0}", System.Text.Encoding.ASCII.GetString(sequence));
var suffixArray = new int[sequence.Length - 1];
SAIS.sufsort(sequence, suffixArray, sequence.Length - 1);
var prevIndex = sequence.Length - 1;
var pLcp = new byte[suffixArray.Length];
// Data dependency: cannot run in parallel
foreach (var index in suffixArray)
{
var lcp = GetLcp(sequence, prevIndex, index);
pLcp[index] = lcp;
//Console.WriteLine("{0}\t{1}", System.Text.Encoding.ASCII.GetString(sequence, offset, sequence.Length - offset - 1), lcp);
prevIndex = index;
}
using (var fs = new FileStream(_pLcpFilePath, FileMode.OpenOrCreate, FileAccess.Write))
{
foreach (var lcp in pLcp)
{
//Console.WriteLine("LCP: {0}", lcp);
fs.WriteByte(lcp);
}
fs.Write(BitConverter.GetBytes(FastaDatabase.FileFormatId), 0, sizeof(int));
fs.Write(BitConverter.GetBytes(FastaDatabase.GetLastWriteTimeHash()), 0, sizeof(int));
}
}