Replacing P-> with P. Save before replacing *P) with P)

Author: alexdobin

source/BAMbinSortByCoordinate.cpp

@@ -3,7 +3,7 @@
 #include "serviceFuns.cpp"
 #include "BAMfunctions.h"
 
-void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, Parameters *P) {
+void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, Parameters &P) {
 
     if (binS==0) return; //nothing to do for empty bins
     //allocate arrays
@@ -30,7 +30,7 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st
         ostringstream errOut;
         errOut << "EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: ";
         errOut << binS <<"   "<< bamInBytes <<"   "<< iBin <<"\n";
-        exitWithError(errOut.str(),std::cerr, P->inOut->logMain, 1, *P);
+        exitWithError(errOut.str(),std::cerr, P.inOut->logMain, 1, *P);
     };
 
     //extract coordinates
@@ -48,8 +48,8 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st
     qsort((void*) startPos, binN, sizeof(uint)*3, funCompareArrays<uint,3>);
 
     BGZF *bgzfBin;
-    bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P->outBAMcompression)).c_str());
-    outBAMwriteHeader(bgzfBin,P->samHeaderSortedCoord,P->chrNameAll,P->chrLengthAll);
+    bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P.outBAMcompression)).c_str());
+    outBAMwriteHeader(bgzfBin,P.samHeaderSortedCoord,P.chrNameAll,P.chrLengthAll);
     //send ordered aligns to bgzf one-by-one
     for (uint ia=0;ia<binN;ia++) {
         char* ib=bamIn+startPos[ia*3+2];

source/BAMbinSortByCoordinate.h

@@ -4,6 +4,6 @@
 #include "Parameters.h"
 #include SAMTOOLS_BGZF_H
 
-void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, Parameters *P);
+void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, Parameters &P);
 
 #endif

source/BAMbinSortUnmapped.cpp

@@ -2,11 +2,11 @@
 #include "ErrorWarning.h"
 #include "BAMfunctions.h"
 
-void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) {
+void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters &P) {
 
     BGZF *bgzfBin;
-    bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P->outBAMcompression)).c_str());
-    outBAMwriteHeader(bgzfBin,P->samHeaderSortedCoord,P->chrNameAll,P->chrLengthAll);
+    bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P.outBAMcompression)).c_str());
+    outBAMwriteHeader(bgzfBin,P.samHeaderSortedCoord,P.chrNameAll,P.chrLengthAll);
 
 
     vector<string> bamInFile;

source/BAMbinSortUnmapped.h

@@ -4,6 +4,6 @@
 #include "Parameters.h"
 #include SAMTOOLS_BGZF_H
 
-void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P);
+void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters &P);
 
 #endif

source/BAMoutput.cpp

@@ -5,18 +5,18 @@
 #include "serviceFuns.cpp"
 #include "ThreadControl.h"
 
-BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters *Pin) {//allocate bam array
+BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters &Pin) {//allocate bam array
 
     P=Pin;
 
-    nBins=P->outBAMcoordNbins;
-    binSize=P->chunkOutBAMsizeBytes/nBins;
+    nBins=P.outBAMcoordNbins;
+    binSize=P.chunkOutBAMsizeBytes/nBins;
     bamArraySize=binSize*nBins;
     bamArray = new char [bamArraySize];
 
     bamDir=tmpDir+to_string((uint) iChunk);//local directory for this thread (iChunk)
 
-    mkdir(bamDir.c_str(),P->runDirPerm);
+    mkdir(bamDir.c_str(),P.runDirPerm);
     binStart=new char* [nBins];
     binBytes=new uint64 [nBins];
     binStream=new ofstream* [nBins];
@@ -34,11 +34,11 @@ BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters *Pin) {//allocate ba
     nBins=1;//start with one bin to estimate genomic bin sizes
 };
 
-BAMoutput::BAMoutput (BGZF *bgzfBAMin, Parameters *Pin) {//allocate BAM array with one bin, streamed directly into bgzf file
+BAMoutput::BAMoutput (BGZF *bgzfBAMin, Parameters &Pin) {//allocate BAM array with one bin, streamed directly into bgzf file
 
     P=Pin;
 
-    bamArraySize=P->chunkOutBAMsizeBytes;
+    bamArraySize=P.chunkOutBAMsizeBytes;
     bamArray = new char [bamArraySize];
     binBytes1=0;
     bgzfBAM=bgzfBAMin;
@@ -90,9 +90,9 @@ void BAMoutput::coordOneAlign (char *bamIn, uint bamSize, uint iRead) {
         bamIn32=(uint32*) bamIn;
         alignG=( ((uint) bamIn32[1]) << 32 ) | ( (uint)bamIn32[2] );
         if (bamIn32[1] == ((uint32) -1) ) {//unmapped
-            iBin=P->outBAMcoordNbins-1;
+            iBin=P.outBAMcoordNbins-1;
         } else if (nBins>1) {//bin starts have already been determined
-            iBin=binarySearch1a <uint64> (alignG, P->outBAMsortingBinStart, (int32) (nBins-1));
+            iBin=binarySearch1a <uint64> (alignG, P.outBAMsortingBinStart, (int32) (nBins-1));
         };
     };
 
@@ -104,7 +104,7 @@ void BAMoutput::coordOneAlign (char *bamIn, uint bamSize, uint iRead) {
 
     //write buffer is filled
     if (binBytes[iBin]+bamSize+sizeof(uint) > ( (iBin>0 || nBins>1) ? binSize : binSize1) ) {//write out this buffer
-        if ( nBins>1 || iBin==(P->outBAMcoordNbins-1) ) {//normal writing, bins have already been determined
+        if ( nBins>1 || iBin==(P.outBAMcoordNbins-1) ) {//normal writing, bins have already been determined
             binStream[iBin]->write(binStart[iBin],binBytes[iBin]);
             binBytes[iBin]=0;//rewind the buffer
         } else {//the first chunk of reads was written in one bin, need to determine bin sizes, and re-distribute reads into bins
@@ -125,11 +125,11 @@ void BAMoutput::coordOneAlign (char *bamIn, uint bamSize, uint iRead) {
 };
 
 void BAMoutput::coordBins() {//define genomic starts for bins
-    nBins=P->outBAMcoordNbins;//this is the true number of bins
+    nBins=P.outBAMcoordNbins;//this is the true number of bins
 
     //mutex here
-    if (P->runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexBAMsortBins);
-    if (P->outBAMsortingBinStart[0]!=0) {//it's set to 0 only after the bin sizes are determined
+    if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexBAMsortBins);
+    if (P.outBAMsortingBinStart[0]!=0) {//it's set to 0 only after the bin sizes are determined
         //extract coordinates and sort
         uint *startPos = new uint [binTotalN[0]];//array of aligns start positions
         for (uint ib=0,ia=0;ia<binTotalN[0];ia++) {
@@ -140,19 +140,19 @@ void BAMoutput::coordBins() {//define genomic starts for bins
         qsort((void*) startPos, binTotalN[0], sizeof(uint), funCompareUint1);
 
         //determine genomic starts of the bins
-        P->inOut->logMain << "BAM sorting: "<<binTotalN[0]<< " mapped reads\n";
-        P->inOut->logMain << "BAM sorting bins genomic start loci:\n";
+        P.inOut->logMain << "BAM sorting: "<<binTotalN[0]<< " mapped reads\n";
+        P.inOut->logMain << "BAM sorting bins genomic start loci:\n";
 
-        P->outBAMsortingBinStart[0]=0;
+        P.outBAMsortingBinStart[0]=0;
         for (uint32 ib=1; ib<(nBins-1); ib++) {
-            P->outBAMsortingBinStart[ib]=startPos[binTotalN[0]/(nBins-1)*ib];
-            P->inOut->logMain << ib <<"\t"<< (P->outBAMsortingBinStart[ib]>>32) << "\t" << ((P->outBAMsortingBinStart[ib]<<32)>>32) <<endl;
+            P.outBAMsortingBinStart[ib]=startPos[binTotalN[0]/(nBins-1)*ib];
+            P.inOut->logMain << ib <<"\t"<< (P.outBAMsortingBinStart[ib]>>32) << "\t" << ((P.outBAMsortingBinStart[ib]<<32)>>32) <<endl;
             //how to deal with equal boundaries???
         };
         delete [] startPos;
     };
     //mutex here
-    if (P->runThreadN>1) pthread_mutex_unlock(&g_threadChunks.mutexBAMsortBins);
+    if (P.runThreadN>1) pthread_mutex_unlock(&g_threadChunks.mutexBAMsortBins);
 
     //re-allocate binStart
     uint binTotalNold=binTotalN[0];
@@ -186,7 +186,7 @@ void BAMoutput::coordFlush () {//flush all alignments
 };
 
 void BAMoutput::coordUnmappedPrepareBySJout () {//flush all alignments
-    uint iBin=P->outBAMcoordNbins-1;
+    uint iBin=P.outBAMcoordNbins-1;
     binStream[iBin]->write(binStart[iBin],binBytes[iBin]);
     binStream[iBin]->flush();
     binBytes[iBin]=0;//rewind the buffer

source/BAMoutput.h

@@ -8,12 +8,12 @@
 class BAMoutput {//
 public:
     //sorted output
-    BAMoutput (int iChunk, string tmpDir, Parameters *Pin);
+    BAMoutput (int iChunk, string tmpDir, Parameters &Pin);
     void coordOneAlign (char *bamIn, uint bamSize, uint iRead);
     void coordBins ();
     void coordFlush ();
     //unsorted output
-    BAMoutput (BGZF *bgzfBAMin, Parameters *Pin);
+    BAMoutput (BGZF *bgzfBAMin, Parameters &Pin);
     void unsortedOneAlign (char *bamIn, uint bamSize, uint bamSize2);
     void unsortedFlush ();
     void coordUnmappedPrepareBySJout();
@@ -30,7 +30,7 @@ class BAMoutput {//
     uint64 *binBytes, binBytes1;//number of bytes currently written to each bin
     ofstream **binStream;//output streams for each bin
     BGZF *bgzfBAM;
-    Parameters *P;
+    Parameters &P;
     string bamDir;
 };
 

source/Chain.cpp

@@ -2,7 +2,7 @@
 #include "streamFuns.h"
 #include "serviceFuns.cpp"
 
-Chain::Chain(Parameters *Pin, string chainFileNameIn) : P(Pin), chainFileName(chainFileNameIn)
+Chain::Chain(Parameters &Pin, string chainFileNameIn) : P(Pin), chainFileName(chainFileNameIn)
 {
     chainLoad();
 };
@@ -74,7 +74,7 @@ void Chain::liftOverGTF(string gtfFileName, string outFileName)
             continue;//empty or comment line
 
         if (chrChains.count(chr1)==0)
-            exitWithError("GTF contains chromosome " + chr1 + " not present in the chain file " + chainFileName,std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
+            exitWithError("GTF contains chromosome " + chr1 + " not present in the chain file " + chainFileName,std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
 
         OneChain *ch1 = & chrChains[chr1];//the chain for the chr1
 
@@ -115,12 +115,12 @@ void Chain::liftOverGTF(string gtfFileName, string outFileName)
     streamOut.close();
 };
 
-//             if (P->chrNameIndex.count(oldname))
+//             if (P.chrNameIndex.count(oldname))
 //             {
 //                 ostringstream errOut;
 //                 errOut << "EXITING because of fatal INPUT file error: chain file contains chromosome (scaffold) not present in the genome " << oldname <<"\n";
 //                 errOut << ERROR_OUT << "\n";
-//                 exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
+//                 exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
 //             };            
-//             uint ichr=P->chrNameIndex[oldname];//chr index in the genome list
-//             bStart1[bN] += P->chrLength[ichr];//whole genome chain - shift by chr start
+//             uint ichr=P.chrNameIndex[oldname];//chr index in the genome list
+//             bStart1[bN] += P.chrLength[ichr];//whole genome chain - shift by chr start

source/Chain.h

@@ -18,10 +18,10 @@ class Chain {
 // //         uint bN;//number of blocks
 // //         vector <uint> bStart1, bStart2, bLen; //blocks starts in 1/2, lengths
 
-        Chain(Parameters *Pin, string chainFileNameIn);
+        Chain(Parameters &Pin, string chainFileNameIn);
         void liftOverGTF(string gtfFileName, string outFileName);
     private:
-        Parameters *P;
+        Parameters &P;
         string chainFileName;
         void chainLoad();
         std::map <string,OneChain> chrChains;