Adding information to filenames of GC profile and subclones

BoevaLab · Nov 30, 2016 · 2a0b5c7 · 2a0b5c7
1 parent 8778faf
commit 2a0b5c7
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Showing 6 changed files with 23 additions and 17 deletions.
diff --git a/src/SVfinder.h b/src/SVfinder.h
@@ -70,7 +70,7 @@ void runWithDefinedPloidy(int ploidy, GenomeCopyNumber & sampleCopyNumber, Genom
         int degree,int intercept,bool logLogNorm,float minExpectedGC,float maxExpectedGC,float knownContamination,float breakPointThreshold,int breakPointType,int minCNAlength,
         int teloCentroFlanks, std::vector<double> & RSS, std::vector<double> &percentage_GenExpl,bool contaminationAdjustment,std::vector<double> &contamination,
         ThreadPool * thrPool,ThreadPoolManager * thrPoolManager,std::string makePileup, float seekSubclones,
-         std::string outputDir,std::vector<int> &unexplainedChromosomes, bool CompleteGenomicsData) ;
+         std::string myName,std::vector<int> &unexplainedChromosomes, bool CompleteGenomicsData) ;
 
 
 #endif //SVFINDER_H

diff --git a/src/SeekSubclones.cpp b/src/SeekSubclones.cpp
@@ -11,19 +11,19 @@ SeekSubclones::~SeekSubclones(void)
 }
 
 
-SeekSubclones::SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string outputDir, float minimal_pop) {
+SeekSubclones::SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string myName, float minimal_pop) {
     ploidy_ = ploidy;
     minimal_pop_  = minimal_pop/100;
-    getSegmentsInfo(samplecopynumber, outputDir);
+    getSegmentsInfo(samplecopynumber, myName);
 }
 
 
-void SeekSubclones::getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string outputDir)
+void SeekSubclones::getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string myName)
 {
     string::size_type pos = 0;
 	map<string,int>::iterator it;
     ofstream myfile;
-    std::string Newfile = outputDir + "Subclones" +  ".txt";
+    std::string Newfile = myName + "_subclones" +  ".txt";
     double bonfer_correction = 0;
     int thresholdOnChrLengthForSubcloneDetection=20;
     int numberOfChromosomes = samplecopynumber.getNumberOfChromosomes();

diff --git a/src/SeekSubclones.h b/src/SeekSubclones.h
@@ -17,10 +17,10 @@
 class SeekSubclones
 {
     public:
-        SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string outputDir, float minimal_pop);
+        SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string myName, float minimal_pop);
         SeekSubclones();
         ~SeekSubclones(void);
-        void getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string outputDir);
+        void getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string myName);
         bool SignTest(std::vector <float>& data, float& threshold, int bonfer_correction);
         void EstimateSubclonalPopulation(std::vector <float> data, float threshold, int ploidy_);
         bool PercentageTest(std::vector <float>& data, float& threshold);

diff --git a/src/freec b/src/freec
diff --git a/src/main.cpp b/src/main.cpp
@@ -835,7 +835,17 @@ int main(int argc, char *argv[])
 
     //If GC profile for exome is needed
     //sampleCopyNumber.fillCGprofile(dirWithFastaSeq);
-    //GCprofileFile = outputDir+"GC_profile.cnp";
+
+    if (!has_GCprofile || GCprofileFile=="") {
+        if (sampleCopyNumber.getWindowSize()==0)
+            GCprofileFile = outputDir+"GC_profile.targetedRegions.cnp";
+        else {
+            stringstream ss;
+            ss << outputDir <<"GC_profile." <<window <<"bp.cnp";
+            GCprofileFile = ss.str();
+        }
+    }
+
     //sampleCopyNumber.printCGprofile(GCprofileFile);
 
     //READ GC-CONTENT:
@@ -849,14 +859,12 @@ int main(int argc, char *argv[])
 			}
         } else {// has_dirWithFastaSeq is true
 			sampleCopyNumber.fillCGprofile(dirWithFastaSeq);
-			GCprofileFile = outputDir+"GC_profile.cnp";
 			if (!has_MapFile)
                 sampleCopyNumber.printCGprofile(GCprofileFile); //if has_MapFile will print out GC-content later
         }
         if (has_MapFile) {  //read mappability file
             sampleCopyNumber.readGemMappabilityFile(gemMapFile);
             //rewrite GC-profile with mappability as the last (5th) colomn
-            GCprofileFile = outputDir+"GC_profile.cnp";
             sampleCopyNumber.printCGprofile(GCprofileFile);
             cout << "..Mappability track from "<< gemMapFile <<" has been added to "<< GCprofileFile <<"\n";
         }
@@ -867,14 +875,12 @@ int main(int argc, char *argv[])
         }
         if (has_dirWithFastaSeq) {// has_dirWithFastaSeq is true
 			sampleCopyNumber.fillCGprofile(dirWithFastaSeq);
-			GCprofileFile = outputDir+"GC_profile.cnp";
 			if (!has_MapFile)
                 sampleCopyNumber.printCGprofile(GCprofileFile); //if has_MapFile will print out GC-content later
         } else {cerr << "Error: Cannot read chromosome fasta files for the GC content correction\n";}
         if (has_MapFile) {  //read mappability file
             sampleCopyNumber.readGemMappabilityFile(gemMapFile);
             //rewrite GC-profile with mappability as the last (5th) colomn
-            GCprofileFile = outputDir+"GC_profile.cnp";
             sampleCopyNumber.printCGprofile(GCprofileFile);
             cout << "..Mappability track from "<< gemMapFile <<" has been added to "<< GCprofileFile <<"\n";
         }
@@ -918,7 +924,7 @@ int main(int argc, char *argv[])
         runWithDefinedPloidy(ploidy,sampleCopyNumber,controlCopyNumber,isControlIsPresent,forceGC,has_BAF,ifTargeted,WESanalysis,
         degree,intercept,logLogNorm,minExpectedGC,maxExpectedGC,knownContamination,breakPointThreshold,breakPointType,minCNAlength,
         teloCentroFlanks, RSS,percentage_GenExpl,contaminationAdjustment,contamination, thrPool,thrPoolManager,
-        makePileup,seekSubclones,outputDir,unexplainedChromosomes, CompleteGenomicsData);
+        makePileup,seekSubclones,myName,unexplainedChromosomes, CompleteGenomicsData);
 
     }
 
@@ -954,7 +960,7 @@ int main(int argc, char *argv[])
         runWithDefinedPloidy(bestPloidy,sampleCopyNumber,controlCopyNumber,isControlIsPresent,forceGC,has_BAF,ifTargeted,WESanalysis,
         degree,intercept,logLogNorm,minExpectedGC,maxExpectedGC,knownContamination,breakPointThreshold,breakPointType,minCNAlength,
         teloCentroFlanks, RSS,percentage_GenExpl,contaminationAdjustment,contamination, thrPool,thrPoolManager,makePileup,seekSubclones,
-         outputDir,unexplainedChromosomes, CompleteGenomicsData);
+         myName,unexplainedChromosomes, CompleteGenomicsData);
     }
 
 	if (has_BAF || makePileup != "false") {
@@ -1024,7 +1030,7 @@ void runWithDefinedPloidy(int ploidy, GenomeCopyNumber & sampleCopyNumber, Genom
         bool has_BAF,bool ifTargeted,bool WESanalysis,
         int degree,int intercept,bool logLogNorm,float minExpectedGC,float maxExpectedGC,float knownContamination,float breakPointThreshold,int breakPointType,int minCNAlength,
         int teloCentroFlanks, vector<double> & RSS, vector<double> &percentage_GenExpl,bool contaminationAdjustment,vector<double> &contamination, ThreadPool * thrPool,
-        ThreadPoolManager * thrPoolManager, string makePileup, float seekSubclones, std::string outputDir, vector<int> &unexplainedChromosomes, bool CompleteGenomicsData) {
+        ThreadPoolManager * thrPoolManager, string makePileup, float seekSubclones, std::string myName, vector<int> &unexplainedChromosomes, bool CompleteGenomicsData) {
         //NORMALIZE READ COUNT:
         sampleCopyNumber.setPloidy(ploidy);
         sampleCopyNumber.setNormalContamination(knownContamination);
@@ -1181,7 +1187,7 @@ void runWithDefinedPloidy(int ploidy, GenomeCopyNumber & sampleCopyNumber, Genom
         if (seekSubclones < 100 && seekSubclones>0)
             {
             cout << "Seeking eventual subclones...";
-            SeekSubclones subc(sampleCopyNumber, ploidy, outputDir, seekSubclones);
+            SeekSubclones subc(sampleCopyNumber, ploidy, myName, seekSubclones);
             cout << "-> Done!\n";
             }
              //Calculate RSS score

diff --git a/src/version.h b/src/version.h
@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 9.9;
+const double FREEC_VERSION = 10.0;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif