/// <summary>
/// detect and annotate region based on low memory consumption
/// </summary>
/// <returns>data needed for statistics printing</returns>
returnLists regionFinderLowMemory()
{
returnLists rLists = new returnLists();
int pkCounter = 1, realDistance = -1, numOfCols = checkNumberOfFieldsInBedFile(combinedPeakfile);
region newRegion = null;
peak firstPeak, nextPeak;
bool openRegion = false;
FileStream fs = File.Open(@"" + combinedPeakfile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
BufferedStream bs = new BufferedStream(fs);
StreamReader sr = new StreamReader(bs);
string firstLine = sr.ReadLine(), nextLine;
Dictionary <string, int> checkIfSorted = new Dictionary <string, int>();
List <int> tmpAllPkDist = new List <int>(), tmpPkInRegDist = new List <int>();
#region printing results
string regionsFileName = resultsDirectory + OSseparator + outfileName + "_regions." + fileType;
StreamWriter outputRegion = new StreamWriter(@"" + regionsFileName);
string peaksInRegionsFileName = resultsDirectory + OSseparator + outfileName + "_regions_peaks." + fileType;
StreamWriter outputPeak = new StreamWriter(@"" + peaksInRegionsFileName);
string xmlFileName = resultsDirectory + OSseparator + outfileName + "_regions.xml";
XmlWriterSettings settings = new XmlWriterSettings();
settings.Indent = true;
settings.IndentChars = "\t";
XmlWriter writer = XmlWriter.Create(@"" + xmlFileName, settings);
writer.WriteStartDocument();
writer.WriteStartElement("regs");
#endregion
#region load the very first peak
if ((firstPeak = peakFromLine(firstLine, numOfCols, combinedPeakfile, pkCounter, null)) == null)
{
firstLine = sr.ReadLine();
pkCounter++;
if ((firstPeak = peakFromLine(firstLine, numOfCols, combinedPeakfile, pkCounter, null)) == null)
{
exit("wrong file format in the combined peak file " + combinedPeakfile.Split(OSseparator).Last());
}
}
//check sorted
if (checkIfSorted.ContainsKey(firstPeak.chromosome))
{
if (checkIfSorted[firstPeak.chromosome] > checkSorting(firstPeak))
{
exit("the combined peak file " + combinedPeakfile.Split(OSseparator).Last() + " is not sorted properly! line: " + pkCounter);
}
else
{
checkIfSorted[firstPeak.chromosome] = checkSorting(firstPeak);
}
}
else
{
checkIfSorted.Add(firstPeak.chromosome, checkSorting(firstPeak));
}
statistics.addToPeaksPerChromosomePre(firstPeak.chromosome, 1);
statistics.addToTfStatsPre(firstPeak.TFname, new List <int>()
{
firstPeak.endIndex - firstPeak.startIndex
}, 1);
#endregion
#region check format
if (numOfCols < 3 || numOfCols > 10)
{
exit("the file " + combinedPeakfile.Split(OSseparator).Last() + " has a non-acceptable format");
}
#endregion
while ((nextLine = sr.ReadLine()) != null)
{
pkCounter++;
nextPeak = peakFromLine(nextLine, numOfCols, combinedPeakfile, pkCounter, null); //as long as you are not at the last element of the peak list you have a nextpeak to assign
#region check for sorting
if (checkIfSorted.ContainsKey(nextPeak.chromosome))
{
if (checkIfSorted[nextPeak.chromosome] > checkSorting(nextPeak))
{
exit("the combined peak file " + combinedPeakfile.Split(OSseparator).Last() + " is not sorted properly! line: " + pkCounter);
}
else
{
checkIfSorted[nextPeak.chromosome] = checkSorting(nextPeak);
}
}
else
{
checkIfSorted.Add(nextPeak.chromosome, checkSorting(nextPeak));
}
statistics.addToPeaksPerChromosomePre(firstPeak.chromosome, 1);
statistics.addToTfStatsPre(firstPeak.TFname, new List <int>()
{
firstPeak.endIndex - firstPeak.startIndex
}, 1);
#endregion
#region change chromosome
if (nextPeak.chromosome != firstPeak.chromosome)
{
if (openRegion) //close the last opened region
{
newRegion = closeTheRegion(newRegion);
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
openRegion = false;
}
else //you have reached the end of the list and you have no left
{
newRegion = singleRegion(firstPeak, nextRegionCounter());
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
}
firstPeak = nextPeak;
nextLine = sr.ReadLine();
nextPeak = peakFromLine(nextLine, numOfCols, combinedPeakfile, pkCounter, null);
statistics.addToPeaksPerChromosomePre(firstPeak.chromosome, 1);
statistics.addToTfStatsPre(firstPeak.TFname, new List <int>()
{
firstPeak.endIndex - firstPeak.startIndex
}, 1);
}
#endregion
tmpAllPkDist.Add(realDistance = distanceOfConsecutivePeaks(firstPeak, nextPeak));
switch (strandSpecificRegionDetectionHelp(firstPeak.strand, nextPeak.strand, realDistance, openRegion))
{
case 1:
newRegion = openNewRegion(firstPeak, nextPeak, nextRegionCounter(), '.');
openRegion = true;
tmpPkInRegDist.Add(realDistance);
break;
case 2:
newRegion = addPeakToRegion(nextPeak, newRegion);
tmpPkInRegDist.Add(realDistance);
break;
case 3:
newRegion = singleRegion(firstPeak, nextRegionCounter());
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
break;
case 4:
newRegion = closeTheRegion(newRegion);
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
openRegion = false;
break;
default:
exit("something went wrong in region creation");
break;
}
firstPeak = nextPeak;
}
sr.Close();
#region last line of the input file
if (openRegion) //close the last opened region
{
newRegion = closeTheRegion(newRegion);
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
}
else //you have reached the end of the list and you have no left
{
newRegion = singleRegion(firstPeak, nextRegionCounter());
if (filterRegion(newRegion))
{
printRegion(newRegion, outputRegion, outputPeak);
writeRegionInXML(writer, newRegion);
rLists.updateVariablesLowMemory(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
}
#endregion
rLists.allRegDist.AddRange(rLists.allPkDist.Where(x => x > peakDistance).ToList());
#region closing printings
outputRegion.Close();
outputPeak.Close();
if (!peakFile)
{
File.Delete(@"" + peaksInRegionsFileName);
}
writer.WriteEndElement();
writer.WriteEndDocument();
writer.Close();
if (!xmlFile)
{
File.Delete(@"" + xmlFileName);
}
#endregion
return(rLists);
}
/// <summary>
/// For threads generated for every chromosome
/// </summary>
/// <param name="a"></param>
/// <param name="distance"></param>
/// <param name="allregions"></param>
/// </summary>
/// <returns>data needed for statistics printing</returns>
returnLists regionFinder(List <peak> listOfPeaks)
{
returnLists rLists = new returnLists();
int pkCounter = 1, realDistance = -1, numOfPeaks = listOfPeaks.Count;
region newRegion = null;
peak nextPeak;
bool openRegion = false;
List <int> tmpAllPkDist = new List <int>(), tmpPkInRegDist = new List <int>();
rLists.pkPerChr.Add(listOfPeaks.First().chromosome, 0);
rLists.regPerChr.Add(listOfPeaks.First().chromosome, 0);
foreach (peak examinedPeak in listOfPeaks)
{
#region check for last peak
if (pkCounter != numOfPeaks)
{ //as long as you are not at the last element of the peak list you have a nextpeak to assign
nextPeak = listOfPeaks.ElementAt(pkCounter);
}
else if (openRegion) //close the last opened region
{
newRegion = closeTheRegion(newRegion);
if (filterRegion(newRegion))
{
newRegion.peakList = peakSorting(newRegion.peakList, distanceOption);
rLists.updateVariables(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak, summitWindow);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
break;
}
else //you have reached the end of the list and you have no left
{
newRegion = singleRegion(examinedPeak, nextRegionCounter());
if (filterRegion(newRegion))
{
newRegion.peakList = peakSorting(newRegion.peakList, distanceOption);
rLists.updateVariables(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak, summitWindow);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
break;
}
#endregion
tmpAllPkDist.Add(realDistance = distanceOfConsecutivePeaks(examinedPeak, nextPeak));
switch (strandSpecificRegionDetectionHelp(examinedPeak.strand, nextPeak.strand, realDistance, openRegion))
{
case 1:
newRegion = openNewRegion(examinedPeak, nextPeak, nextRegionCounter(), '.');
openRegion = true;
tmpPkInRegDist.Add(realDistance);
pkCounter++;
break;
case 2:
newRegion = addPeakToRegion(nextPeak, newRegion);
tmpPkInRegDist.Add(realDistance);
pkCounter++;
break;
case 3:
newRegion = singleRegion(examinedPeak, nextRegionCounter());
if (filterRegion(newRegion))
{
newRegion.peakList = peakSorting(newRegion.peakList, distanceOption);
rLists.updateVariables(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak, summitWindow);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
pkCounter++;
break;
case 4:
newRegion = closeTheRegion(newRegion);
if (filterRegion(newRegion))
{
newRegion.peakList = peakSorting(newRegion.peakList, distanceOption);
rLists.updateVariables(newRegion, tmpAllPkDist, tmpPkInRegDist, narrowThePeak, summitWindow);
}
tmpAllPkDist = new List <int>();
tmpPkInRegDist = new List <int>();
openRegion = false;
pkCounter++;
break;
default:
exit("something went wrong in region creation");
break;
}
}
rLists.allRegDist.AddRange(rLists.allPkDist.Where(x => x > peakDistance).ToList());
rLists.pkPerChr[listOfPeaks.First().chromosome] = rLists.detectedRegs.Sum(x => x.peakList.Count);
rLists.regPerChr[listOfPeaks.First().chromosome] = rLists.detectedRegs.Count;
return(rLists);
}
