private static Dictionary <int, FqNucleotideRead> createHashMap()
{
Dictionary <int, FqNucleotideRead> hashmap = new Dictionary <int, FqNucleotideRead>();
char[] nucleotides = { 'A', 'G', 'C', 'T', 'U', 'N' };
char[] qualities = { '!', '"', '#', '$', '%', '&', '\'', '(', ')', '*', '+', ',', '-',
'.', '/', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':',
';', '<', '=', '>', '?', '@', 'A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T',
'U', 'V', 'W', 'X', 'Y', 'Z', '[', '\\', ']', '^', '_', '`', 'a',
'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n',
'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', '{',
'|', '}', '~' };
FqNucleotideRead fqRead;
HashSet <int> existance = new HashSet <int>();
for (int i = 0; i < nucleotides.Length; i++)
{
for (int j = 0; j < qualities.Length; j++)
{
fqRead = new FqNucleotideRead(nucleotides[i], qualities[j]);
int hashcode = fqRead.getProxyCode();
if (existance.Contains(hashcode) == false)
{
existance.Add(hashcode);
hashmap.Add(hashcode, fqRead);
}
}
}
return(hashmap);
}
public void addNucleotide(FqNucleotideRead fqRead, int hashcode)
{
if (checkExists.Contains(hashcode) == false)
{
checkExists.Add(hashcode);
map.Add(hashcode, fqRead);
}
}
public IFqFile ParseStandardFormat()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0)
{
continue;
}
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.Close();
}
return(fastqFile);
}
public IFqFile parseByteFastq()
{
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
FqNucleotideRead fqRead = new FqNucleotideRead();
FqSequence fqSeq;
sw = new Stopwatch();
sw.Start();
const int LINES_IN_BLOCK = 4, HEADER_LINE = 0, SEQLINE = 1, INFO_LINE = 2, QUAL_LINE = 3, MAX_LINE = 250;
int lineIter = 0, bitIter = 1, seqIndex = 0;
byte[][] fqBlocks = new byte[4][]
{
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE]
};
for (int i = 0; i < byteArray.Length; i++)
{
if (byteArray[i] == CARRIDGE_RETURN)
{
fqBlocks[lineIter][0] = (byte)bitIter;
bitIter = 1;
lineIter++;
if (lineIter == LINES_IN_BLOCK)
{
lineIter = 0;
fqSeq = new FqSequence(seqIndex, System.Text.Encoding.ASCII.GetString(fqBlocks[HEADER_LINE]), System.Text.Encoding.ASCII.GetString(fqBlocks[INFO_LINE]), fqBlocks[SEQLINE][0]);
for (int j = 1; j < (fqBlocks[SEQLINE][0]); j++)
{
fqRead.resetFqNucleotideRead((char)fqBlocks[SEQLINE][j], (char)fqBlocks[QUAL_LINE][j]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
seqIndex++;
}
}
else
{
fqBlocks[lineIter][bitIter] = byteArray[i];
bitIter++;
}
}
Console.WriteLine("PARSED: File read in {0} s from byte array", sw.Elapsed);
return(fastqFile);
}
public IEnumerable<FqFile_Component> ParseStandardFormatComponent()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
int blockNumber = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
FqFile_Component fastqFileComponent = new FqFile_Component();
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0) continue;
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFileComponent.addFastqSequence(fqSeq);
nLine += 3;
blockNumber ++;
if (blockNumber == FqFileMap.FQ_BLOCK_LIMIT)
{
yield return fastqFileComponent;
blockNumber = 0;
fastqFileComponent = new FqFile_Component();
}
}
yield return fastqFileComponent;
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.FlushAsync();
fileReader.Close();
}
}
public IFqFile ParseStandardFormat()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0) continue;
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.Close();
}
return fastqFile;
}
public IFqFile parseByteFastq()
{
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
FqNucleotideRead fqRead = new FqNucleotideRead();
FqSequence fqSeq;
sw = new Stopwatch();
sw.Start();
const int LINES_IN_BLOCK = 4, HEADER_LINE = 0, SEQLINE = 1, INFO_LINE = 2, QUAL_LINE = 3, MAX_LINE = 250;
int lineIter = 0, bitIter = 1, seqIndex = 0;
byte[][] fqBlocks = new byte[4][]
{
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE]
};
for (int i = 0; i < byteArray.Length; i++)
{
if (byteArray[i] == CARRIDGE_RETURN)
{
fqBlocks[lineIter][0] = (byte) bitIter;
bitIter = 1;
lineIter++;
if (lineIter == LINES_IN_BLOCK)
{
lineIter = 0;
fqSeq = new FqSequence(seqIndex, System.Text.Encoding.ASCII.GetString(fqBlocks[HEADER_LINE]), System.Text.Encoding.ASCII.GetString(fqBlocks[INFO_LINE]), fqBlocks[SEQLINE][0]);
for (int j = 1; j < (fqBlocks[SEQLINE][0]); j++)
{
fqRead.resetFqNucleotideRead((char)fqBlocks[SEQLINE][j], (char)fqBlocks[QUAL_LINE][j]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
seqIndex++;
}
}
else
{
fqBlocks[lineIter][bitIter] = byteArray[i];
bitIter++;
}
}
Console.WriteLine("PARSED: File read in {0} s from byte array", sw.Elapsed);
return fastqFile;
}
public void addNucleotide(FqNucleotideRead fqRead, int hashcode)
{
if (checkExists.Contains(hashcode) == false)
{
checkExists.Add(hashcode);
map.Add(hashcode, fqRead);
}
}
private static Dictionary<int, FqNucleotideRead> createHashMap()
{
Dictionary<int, FqNucleotideRead> hashmap = new Dictionary<int, FqNucleotideRead>();
char[] nucleotides = { 'A', 'G', 'C', 'T', 'U', 'N' };
char[] qualities = { '!', '"', '#', '$', '%', '&', '\'', '(', ')', '*', '+', ',', '-',
'.', '/', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':',
';', '<', '=', '>', '?', '@', 'A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T',
'U', 'V', 'W', 'X', 'Y', 'Z', '[', '\\', ']', '^', '_', '`', 'a',
'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n',
'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', '{',
'|', '}', '~' };
FqNucleotideRead fqRead;
HashSet<int> existance = new HashSet<int>();
for (int i = 0; i < nucleotides.Length; i++)
{
for (int j = 0; j < qualities.Length; j++)
{
fqRead = new FqNucleotideRead(nucleotides[i], qualities[j]);
int hashcode = fqRead.getProxyCode();
if (existance.Contains(hashcode) == false)
{
existance.Add(hashcode);
hashmap.Add(hashcode, fqRead);
}
}
}
return hashmap;
}
public IEnumerable <FqFile_Component> ParseMultiLineFormatComponent()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
int blockNumber = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
FqFile_Component fastqFileComponent = new FqFile_Component();
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 6 != 0)
{
continue;
}
String seqlist = reader.ReadLine();
String seqlist2 = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
String qscore2 = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, (seqlist.Length + seqlist2.Length));
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
if (seqlist2.Length > 0 && (seqlist2.Length == qscore2.Length))
{
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist2[i], qscore2[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
blockNumber++;
if (blockNumber == FqFileMap.FQ_BLOCK_LIMIT)
{
yield return(fastqFileComponent);
blockNumber = 0;
fastqFileComponent = new FqFile_Component();
}
}
yield return(fastqFileComponent);
}
}
finally
{
fileReader.Close();
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
