//add peak to an existing region
region addPeakToRegion(peak nextpeak, region openReg)
{
openReg.name += "," + nextpeak.name;
openReg.score++;
openReg.peakList.Add(nextpeak);
return(openReg);
}
/// <summary>
/// returns the distance of two consecutive peaks according to the parameters given by the user
/// true && true: summit of narrowed peak to summit of narrowed peak
/// true && false: summit of non-narrowed peak to summit of non-narrowed peak
/// false && true: start of narrowed peak to end of narrowed peak
/// false && false: start of non-narrowed peak to end of non-narrowed peak
/// </summary>
/// <param name="firstpeak">examined peak</param>
/// <param name="nextpeak">next peak</param>
/// <returns>the distance between the peaks based in the given parameters</returns>
int distanceOfConsecutivePeaks(peak firstpeak, peak nextpeak)
{
if (distanceOption)
{
return((nextpeak.startIndex + nextpeak.summit) - (firstpeak.startIndex + firstpeak.summit));
}
else
{
return((nextpeak.startIndex + nextpeak.middle) - (firstpeak.startIndex + firstpeak.middle));
}
}
/// <summary>
/// check if the combined peak file is sorted properly
/// in the following comments the x marks the distance that we consider
/// in general:
/// distanceOption is true when we calculate the distance from summit to summit and false when we calculate the distance from midpoint to midpoint
/// </summary>
/// <param name="examinedPeak"></param>
/// <returns>an integer that denotes what to compare</returns>
int checkSorting(peak examinedPeak)
{
if (distanceOption)
{
return(examinedPeak.startIndex + examinedPeak.summit);
}
else
{
return(examinedPeak.startIndex + examinedPeak.middle);
}
}
//just open a new region
region openNewRegion(peak firstpeak, peak nextpeak, int cnt, char strd)
{
return(new region()
{
chromosome = firstpeak.chromosome,
regionName = "reg" + cnt,
name = "reg" + cnt + "-" + firstpeak.name + "," + nextpeak.name,
score = 2,
strand = strd,
peakList = new List <peak>()
{
firstpeak, nextpeak
}
});
}
public void prepareNetwork(List <Tuple <string, int> > tfsInReg, peak newPeak)
{
if (!tfsInReg.Any(x => x.Item1 == newPeak.TFname))
{
foreach (Tuple <string, int> s in tfsInReg)
{
if (_tfOccsperChr.ContainsKey(s.Item1))
{
if (_tfOccsperChr[s.Item1].ContainsKey(newPeak.TFname))
{
_tfOccsperChr[s.Item1][newPeak.TFname].increaseCount(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2));
}
else
{
_tfOccsperChr[s.Item1].Add(newPeak.TFname, new tfOccurrences(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2)));
}
}
else
{
_tfOccsperChr.Add(s.Item1, new Dictionary <string, tfOccurrences>()
{
{ newPeak.TFname, new tfOccurrences(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2)) }
});
}
if (_tfOccsperChr.ContainsKey(newPeak.TFname))
{
if (_tfOccsperChr[newPeak.TFname].ContainsKey(s.Item1))
{
_tfOccsperChr[newPeak.TFname][s.Item1].increaseCount(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2));
}
else
{
_tfOccsperChr[newPeak.TFname].Add(s.Item1, new tfOccurrences(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2)));
}
}
else
{
_tfOccsperChr.Add(newPeak.TFname, new Dictionary <string, tfOccurrences>()
{
{ s.Item1, new tfOccurrences(Math.Abs((newPeak.startIndex + newPeak.summit) - s.Item2)) }
});
}
}
}
}
//just to avoid some more lines of code
//called only from regionFinder and is used only when we detect a region that contains only one peak in it
region singleRegion(peak peakToAdd, int cnt)
{
return(new region()
{
chromosome = peakToAdd.chromosome,
regionName = "reg" + cnt,
name = "reg" + cnt + "-" + peakToAdd.name,
score = 1,
peakList = new List <peak>()
{
peakToAdd
},
strand = strandSpecificity ? peakToAdd.strand : '.',
startIndex = peakToAdd.startIndex,
endIndex = peakToAdd.endIndex,
pValue = peakToAdd.pValue
});
}
/// <summary>
/// Prints the given peak.
/// </summary>
/// <param name="prntPk">the peak to print.</param>
/// <param name="output">the output stream where to print the peak.</param>
public void printPeak(peak prntPk, StreamWriter output)
{
switch (numOfCols)
{
case 3:
output.WriteLine(string.Format("{0}\t{1}\t{2}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex));
break;
case 4:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name));
break;
case 5:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score));
break;
case 6:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score, prntPk.strand));
break;
case 7:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score, prntPk.strand, prntPk.signalValue));
break;
case 8:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score, prntPk.strand, prntPk.signalValue, prntPk.pValue));
break;
case 9:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score, prntPk.strand, prntPk.signalValue, prntPk.pValue, prntPk.qValue));
break;
case 10:
output.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}", prntPk.chromosome, prntPk.startIndex, prntPk.endIndex, prntPk.name, prntPk.score, prntPk.strand, prntPk.signalValue, prntPk.pValue, prntPk.qValue, prntPk.summit));
break;
default:
exit("something went wrong while printing");
break;
}
}
/// <summary>
/// converts an loaded peak to a region. checks if the region name is in the correct format and adds all the peaks in the peak list
/// </summary>
/// <param name="newPeak">the loaded peak (that is actually a region)</param>
/// <param name="lineCounter">the line counter</param>
/// <returns>the loaded region</returns>
public region peakToRegion(peak newPeak, int lineCounter)
{
List <Tuple <string, int> > tfsInReg;
#region convert peak to region
region newRegion = new region()
{
chromosome = newPeak.chromosome,
startIndex = newPeak.startIndex,
endIndex = newPeak.endIndex,
name = newPeak.name,
score = newPeak.score,
strand = newPeak.strand,
signalValue = newPeak.signalValue,
pValue = newPeak.pValue,
qValue = newPeak.qValue,
summit = newPeak.summit,
peakList = new List <peak>()
};
#endregion
#region check if region name correct
if (newRegion.name.Split('-').Length != 2 || !newRegion.name.Split('-').First().StartsWith("reg"))
{
exit("the name field of the input file in line " + lineCounter + " is in a wrong format");
}
else
{
newRegion.regionName = newRegion.name.Split('-').First();
}
#endregion
#region add peaks to peak list
tfsInReg = new List <Tuple <string, int> >();
foreach (string sp in newRegion.name.Split('-').Last().Split(','))
{
if (sp.Split('_').Length < 2)
{
exit("the name field of the input file in line " + lineCounter + " is in a wrong format");
}
else
{
newRegion.peakList.Add(new peak()
{
chromosome = newRegion.chromosome,
startIndex = 1,
endIndex = 1,
TFname = sp.Split('_').First(),
peakName = sp.Split('_').Last(),
name = sp,
score = 0,
strand = '.',
signalValue = 0,
pValue = -1,
qValue = -1,
summit = 1
});
#region add peak statistical data
statistics.addToTfStatsPre(sp.Split('_').First(), new List <int>()
{
0
}, 1);
#endregion
#region keep some stats for network
if (!tfsInReg.Any(x => x.Item1 == sp.Split('_').First()))
{
foreach (Tuple <string, int> s in tfsInReg)
{
if (tfOccs.ContainsKey(s.Item1))
{
if (tfOccs[s.Item1].ContainsKey(sp.Split('_').First()))
{
tfOccs[s.Item1][sp.Split('_').First()].increaseCount(0);
}
else
{
tfOccs[s.Item1].Add(sp.Split('_').First(), new tfOccurrences(0));
}
}
else
{
tfOccs.Add(s.Item1, new Dictionary <string, tfOccurrences>()
{
{ sp.Split('_').First(), new tfOccurrences(0) }
});
}
if (tfOccs.ContainsKey(sp.Split('_').First()))
{
if (tfOccs[sp.Split('_').First()].ContainsKey(s.Item1))
{
tfOccs[sp.Split('_').First()][s.Item1].increaseCount(0);
}
else
{
tfOccs[sp.Split('_').First()].Add(s.Item1, new tfOccurrences(0));
}
}
else
{
tfOccs.Add(sp.Split('_').First(), new Dictionary <string, tfOccurrences>()
{
{ s.Item1, new tfOccurrences(0) }
});
}
}
}
tfsInReg.Add(new Tuple <string, int>(sp.Split('_').First(), 0));
#endregion
}
}
#endregion
return(newRegion);
}
/// <summary>
/// construct a peak from an xml file element
/// </summary>
/// <param name="peakElement">xml peak element</param>
/// <param name="inputFile">the name of the input xml file</param>
/// <param name="elementCounter">region element counter</param>
/// <param name="attributeCounter">peak within region attribute counter</param>
/// <param name="lineCounter">the xml file line counter</param>
/// <returns>returns the constructed peak</returns>
public peak peakFromXML(XElement peakElement, string inputFile, int elementCounter, int attributeCounter, int lineCounter)
{
int tmpInt;
double tmpDbl;
peak newPeak = new peak();
#region test chromosome 0
try
{
if (!chromosomeNamesAndLength.ContainsKey(peakElement.Attribute("chr").Value) && !ignoreChromosomeLength)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid chromosome entry in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
else
{
newPeak.chromosome = peakElement.Attribute("chr").Value;
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain chromosome information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test start position 1
try
{
if (!int.TryParse(peakElement.Attribute("s").Value, out tmpInt))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid start index entry in element " + elementCounter + " attribute " + attributeCounter + ". Integer expected" + " (line " + lineCounter + ")");
}
if (tmpInt < 0)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid start index entry in element " + elementCounter + " attribute " + attributeCounter + ". Positive expected" + " (line " + lineCounter + ")");
}
newPeak.startIndex = tmpInt;
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain start index information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test end position 2
try
{
if (!int.TryParse(peakElement.Attribute("e").Value, out tmpInt))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid end index entry in element " + elementCounter + " attribute " + attributeCounter + ". Integer expected" + " (line " + lineCounter + ")");
}
if (tmpInt < 0)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid end index entry in element " + elementCounter + " attribute " + attributeCounter + ". Positive expected" + " (line " + lineCounter + ")");
}
if (!ignoreChromosomeLength)
{
if (tmpInt > chromosomeNamesAndLength[newPeak.chromosome])
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid end index entry in element " + elementCounter + " attribute " + attributeCounter + ". Exceeding chromosome's limits" + " (line " + lineCounter + ")");
}
}
newPeak.endIndex = tmpInt;
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain end index information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test name 3
try
{
newPeak.name = peakElement.Attribute("n").Value;
if (newPeak.name.Split('_').Length > 1)
{
newPeak.TFname = newPeak.name.Split('_').First();
newPeak.peakName = newPeak.name.Split('_').Last();
}
else
{
newPeak.TFname = "TF";
newPeak.peakName = "peak" + Convert.ToString(lineCounter - ((2 * elementCounter) - 2));
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain name information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test score 4
try
{
if (numOfCols > 4)
{
if (!double.TryParse(peakElement.Attribute("scr").Value, out tmpDbl))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid score entry in element " + elementCounter + " attribute " + attributeCounter + ". Integer expected" + " (line " + lineCounter + ")");
}
newPeak.score = tmpDbl;
}
else
{
newPeak.score = 0;
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain score information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test strand 5
try
{
if (numOfCols > 5)
{
if (!strandSymbols.Exists(x => x == peakElement.Attribute("strd").Value[0]))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid strand entry in element " + elementCounter + " attribute " + attributeCounter + ". +/-/. expected" + " (line " + lineCounter + ")");
}
newPeak.strand = peakElement.Attribute("strd").Value[0];
}
else
{
newPeak.strand = '.';
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain strand information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test signalValue 6
try
{
if (numOfCols > 6)
{
if (!double.TryParse(peakElement.Attribute("sv").Value, out tmpDbl))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid signalValue entry in element " + elementCounter + " attribute " + attributeCounter + ". Numeric expected" + " (line " + lineCounter + ")");
}
newPeak.signalValue = tmpDbl;
}
else
{
newPeak.signalValue = 0;
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain signalValue information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test pValue 7
try
{
if (numOfCols > 7)
{
if (!double.TryParse(peakElement.Attribute("pv").Value, out tmpDbl))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid pValue entry in element " + elementCounter + " attribute " + attributeCounter + ". Numeric expected" + " (line " + lineCounter + ")");
}
newPeak.pValue = tmpDbl;
}
else
{
newPeak.pValue = -1;
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain pValue information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test qValue 8
try
{
if (numOfCols > 8)
{
if (!double.TryParse(peakElement.Attribute("qv").Value, out tmpDbl))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid qValue entry in element " + elementCounter + " attribute " + attributeCounter + ". Numeric expected" + " (line " + lineCounter + ")");
}
newPeak.qValue = tmpDbl;
}
else
{
newPeak.qValue = -1;
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain qValue information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
#region test summit 9
try
{
if (numOfCols > 9)
{
if (!int.TryParse(peakElement.Attribute("sm").Value, out tmpInt))
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid summit entry in element " + elementCounter + " attribute " + attributeCounter + ". Integer expected" + " (line " + lineCounter + ")");
}
if (tmpInt < 0 && tmpInt != -1)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " has an invalid summit entry in element " + elementCounter + " attribute " + attributeCounter + ". Positive or -1 expected" + " (line " + lineCounter + ")");
}
newPeak.summit = tmpInt;
}
else
{
newPeak.summit = Convert.ToInt32((newPeak.endIndex - newPeak.startIndex) / 2);
}
}
catch (Exception)
{
exit("the file " + inputFile.Split(OSseparator).Last() + " does not contain summit information in element " + elementCounter + " attribute " + attributeCounter + " (line " + lineCounter + ")");
}
#endregion
return(newPeak);
}
int peakStartPlusSummit(peak newPeak)
{
return(newPeak.startIndex + newPeak.summit);
}
int peakStartPlusSummit(peak newPeak, bool narrowThePeak, int summitWindow)
{
return(newPeak.startIndex + newPeak.summit);
}
/// <summary>
/// Creates a peak instance from a bed file line.
/// </summary>
/// <returns>The generated peak.</returns>
/// <param name="line">bed format line.</param>
/// <param name="numOfCols">number of columns.</param>
/// <param name="peakFile">the name of the input peak file. Used for error checking purposes.</param>
/// <param name="lineCounter">line counter of the peak file. Used for error checking purposes.</param>
/// <param name="TFname">transcription factor name.</param>
public peak peakFromLine(string line, int numOfCols, string peakFile, int lineCounter, string TFname)
{
int tmpInt;
double tmpDbl;
peak newPeak = new peak();
List <string> breakAtTab = line.Split('\t').ToList();
#region check num of cols
if (breakAtTab.Count != numOfCols)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has different number on columns in line " + lineCounter);
}
#endregion
#region test chromosome 0
if (!chromosomeNamesAndLength.ContainsKey(breakAtTab[0]) && !ignoreChromosomeLength)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 1 line " + lineCounter);
}
else
{
newPeak.chromosome = breakAtTab[0];
}
#endregion
#region test start position 1
if (!int.TryParse(breakAtTab[1], out tmpInt))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 2 line " + lineCounter + ". Integer expected");
}
if (tmpInt < 0)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 2 line " + lineCounter + ". Positive expected");
}
newPeak.startIndex = tmpInt;
#endregion
#region test end position 2
if (!int.TryParse(breakAtTab[2], out tmpInt))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 3 line " + lineCounter + ". Integer expected");
}
if (tmpInt < 0)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 3 line " + lineCounter + ". Positive expected");
}
if (!ignoreChromosomeLength)
{
if (tmpInt > chromosomeNamesAndLength[breakAtTab[0]])
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 3 line " + lineCounter + ". Exceeding chromosome's limits");
}
}
newPeak.endIndex = tmpInt;
#endregion
#region check for equality betwen start and end
if (newPeak.startIndex == newPeak.endIndex)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in line " + lineCounter + ". Start is equal to end index!");
}
#endregion
#region test name 3
if (mode == "regions" || mode == "tfNet" || mode == "peaks")
{
newPeak.peakName = "peak" + lineCounter;
newPeak.TFname = TFname;
if (numOfCols > 3)
{
newPeak.name = newPeak.TFname + "_" + newPeak.peakName + "_" + breakAtTab[3];
}
else
{
newPeak.name = newPeak.TFname + "_" + newPeak.peakName;
}
if (mode == "regions")
{
if (breakAtTab[3].Split('_').Length > 1)
{
newPeak.TFname = breakAtTab[3].Split('_').First();
newPeak.peakName = breakAtTab[3].Split('_').ElementAt(1);
newPeak.name = newPeak.TFname + "_" + newPeak.peakName;
}
}
}
else
{
newPeak.name = breakAtTab[3];
}
#endregion
#region test score 4
if (numOfCols > 4)
{
if (!double.TryParse(breakAtTab[4], out tmpDbl))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 5 line " + lineCounter + ". Integer expected");
}
if (filterByScore != 0 && tmpDbl < filterByScore)
{
return(null);
}
newPeak.score = tmpDbl;
}
else
{
newPeak.score = 0;
}
#endregion
#region test strand 5
if (numOfCols > 5)
{
if (breakAtTab[5].Length == 0)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an empty element in column 6 line " + lineCounter + ". +/-/. expected");
}
if (!strandSymbols.Exists(x => x == breakAtTab[5][0]))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 6 line " + lineCounter + ". +/-/. expected");
}
newPeak.strand = breakAtTab[5][0];
}
else
{
newPeak.strand = '.';
}
#endregion
#region test signalValue 6
if (numOfCols > 6)
{
if (!double.TryParse(breakAtTab[6], out tmpDbl))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 7 line " + lineCounter + ". Numeric expected");
}
if (!(mode == "filter" || mode == "network"))
{
if (filterBySV != 0 && tmpDbl < filterBySV)
{
return(null);
}
}
newPeak.signalValue = tmpDbl;
}
else
{
newPeak.signalValue = 0;
}
#endregion
#region test pValue 7
if (numOfCols > 7)
{
if (!double.TryParse(breakAtTab[7], out tmpDbl))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 8 line " + lineCounter + ". Numeric expected");
}
if (!(mode == "filter" || mode == "network"))
{
if (filterByPvalue != 0 && tmpDbl > filterByPvalue)
{
return(null);
}
if (tmpDbl == -1.0 && !noValueAssigned)
{
return(null);
}
}
newPeak.pValue = tmpDbl;
//if (tmpDbl != -1 && regionPvalue)
//{
// if (minusLog10)
// {
// newPeak.pValue = Math.Pow(10, -tmpDbl);
// }
// else
// {
// newPeak.pValue = tmpDbl;
// }
//}
//else
//{
// newPeak.pValue = tmpDbl;
//}
}
else
{
newPeak.pValue = -1;
}
#endregion
#region test qValue 8
if (numOfCols > 8)
{
if (!double.TryParse(breakAtTab[8], out tmpDbl))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 9 line " + lineCounter + ". Numeric expected");
}
if (!(mode == "filter" || mode == "network"))
{
if (filterByQvalue != 0 && tmpDbl > filterByQvalue)
{
return(null);
}
if (tmpDbl == -1.0 && !noValueAssigned)
{
return(null);
}
}
newPeak.qValue = tmpDbl;
//if (tmpDbl != -1 && regionPvalue)
//{
// if (minusLog10)
// {
// newPeak.qValue = Math.Pow(10, -tmpDbl);
// }
// else
// {
// newPeak.qValue = tmpDbl;
// }
//}
//else
//{
// newPeak.qValue = tmpDbl;
//}
}
else
{
newPeak.qValue = -1;
}
#endregion
#region test summit 9
if (numOfCols > 9)
{
if (!int.TryParse(breakAtTab[9], out tmpInt))
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 10 line " + lineCounter + ". Integer expected");
}
if (tmpInt < 0 && tmpInt != -1)
{
exit("the file " + peakFile.Split(OSseparator).Last() + " has an invalid element in column 10 line " + lineCounter + ". Positive expected");
}
if (!(mode == "filter" || mode == "network"))
{
if (!unknownSummit && tmpInt < 1)
{
return(null);
}
}
if (tmpInt == -1)
{
newPeak.summit = narrowThePeak ? summitWindow : middlePoint(newPeak.startIndex, newPeak.endIndex);
}
else
{
newPeak.summit = tmpInt;
}
}
else if (!(mode == "filter" || mode == "network"))
{
if (!unknownSummit)
{
return(null);
}
}
else
{
newPeak.summit = narrowThePeak ? summitWindow : middlePoint(newPeak.startIndex, newPeak.endIndex);
}
#endregion
newPeak.middle = narrowThePeak ? summitWindow : middlePoint(newPeak.startIndex, newPeak.endIndex);
newPeak.startIndex = narrowThePeak ? newStartIndex(newPeak.startIndex, newPeak.summit, summitWindow) : newPeak.startIndex;
newPeak.endIndex = narrowThePeak ? newEndIndex(newPeak.startIndex, newPeak.summit, summitWindow, newPeak.endIndex, newPeak.chromosome) : newPeak.endIndex;
return(newPeak);
}
