[Genabel-commits] r1401 - in pkg/GenABEL/src: GAlib ITERlib
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 19 19:17:39 CET 2013
Author: maksim
Date: 2013-11-19 19:17:38 +0100 (Tue, 19 Nov 2013)
New Revision: 1401
Modified:
pkg/GenABEL/src/GAlib/Chip.cpp
pkg/GenABEL/src/GAlib/convert.snp.affymetrix.cpp
pkg/GenABEL/src/GAlib/convert_snp_illumina.cpp
pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
pkg/GenABEL/src/GAlib/convert_snp_tped.cpp
pkg/GenABEL/src/GAlib/export_plink.cpp
pkg/GenABEL/src/GAlib/gtps_container.cpp
pkg/GenABEL/src/GAlib/gwaa.c
pkg/GenABEL/src/GAlib/gwaa_cpp.cpp
pkg/GenABEL/src/GAlib/interactions_rare_recesive_alleles.cpp
pkg/GenABEL/src/GAlib/mematrix.h
pkg/GenABEL/src/GAlib/reg1.h
pkg/GenABEL/src/GAlib/reg1data.h
pkg/GenABEL/src/ITERlib/iterator_functions.cpp
Log:
Fixed most of the issues reported by Mr. Jenkins: mostly unused variables, memory leak, and style.
Modified: pkg/GenABEL/src/GAlib/Chip.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/Chip.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/Chip.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -77,7 +77,7 @@
file.close();
-delete buf;
+delete[] buf;
}
//__________________________________________________________
@@ -277,7 +277,7 @@
file.close();
-delete buf;
+delete[] buf;
}
//__________________________________________________________
Modified: pkg/GenABEL/src/GAlib/convert.snp.affymetrix.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert.snp.affymetrix.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/convert.snp.affymetrix.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -229,8 +229,8 @@
outfile<<"\n";
}
-delete gtps_for_one_snp;
-delete rearrangement_array;
+delete[] gtps_for_one_snp;
+delete[] rearrangement_array;
Rprintf("%i SNPs excluded bacause of absent in annotation\n", snp_excludet_from_output_data);
Rprintf("Total %i SNPs are written into output file\n", snp_amount-snp_excludet_from_output_data);
Modified: pkg/GenABEL/src/GAlib/convert_snp_illumina.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_illumina.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/convert_snp_illumina.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -43,7 +43,7 @@
long unsigned int bcast = *Bcast;
bool loud = TRUE;
- if (bcast <= 0) loud = FALSE;
+ //if (bcast <= 0) loud = FALSE;
long unsigned int nsnps=0;
long unsigned int nids=0;
@@ -100,13 +100,14 @@
//
//Processing rest of the file
//
+
+ char gdata;
while (getline(illfile,data)) {
nsnps++;
istringstream datas (data);
- char gdata;
if (!(datas >> tmp_snpnam >> tmp_chrom >> tmp_map))
error("First three fields are missing in line %i!\n",(nsnps+1));
@@ -238,7 +239,12 @@
lasti += 1;
}
+ delete [] gnum;
+ delete [] tmp_gtype;
}
+
+
+
}
const ios_base::fmtflags hex = ios_base::hex;
@@ -294,13 +300,12 @@
}
outfile << endl;
- delete [] tmp_gtype;
}
if (loud) {
Rprintf("... done.\n");
}
-
+ delete [] chgt;
}
}
Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -422,10 +422,12 @@
}
outfile << endl;
- delete [] tmp_gtype;
}
- if (verbose) {
+ delete [] gnum;
+ delete [] tmp_gtype;
+
+ if (verbose) {
Rprintf("... done.\n");
}
Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -435,8 +435,10 @@
}
outfile << endl;
- delete [] tmp_gtype;
}
+
+ delete [] tmp_gtype;
+ delete [] gnum;
if (verbose) {
Rprintf("... done.\n");
Modified: pkg/GenABEL/src/GAlib/convert_snp_tped.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_tped.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/convert_snp_tped.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -291,10 +291,12 @@
}
outfile << endl;
- delete [] tmp_gtype;
// gtype.pop_front();
} //while (!gtype.empty());
+
+ delete [] tmp_gtype;
+ delete [] gnum;
if (verbose) {
Rprintf("... done.\n");
Modified: pkg/GenABEL/src/GAlib/export_plink.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/export_plink.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/export_plink.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -212,6 +212,7 @@
}
}
fileWoA << "\n";
+ delete [] Genotype;
//Rprintf("\n");
}
//Rprintf("B\n");
@@ -237,7 +238,6 @@
//for (int i=0; i<10; i++) Rprintf("%d ",sex[i]);
//Rprintf("oooo!\n" );
- delete [] Genotype;
delete [] gtint;
return R_NilValue;
Modified: pkg/GenABEL/src/GAlib/gtps_container.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/gtps_container.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/gtps_container.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -33,8 +33,11 @@
+local_person_number = 0; // Mr. Jenkins likes when everything is initilized in constructor
+our_byte_number = 1;
+
gtps_array = gtps_array_;
strand_array = strand_array_;
coding_array = coding_array_;
@@ -60,9 +63,11 @@
rearrangement_array[3] = 0;
+local_person_number = 0; // Mr. Jenkins likes when everything is initilized in constructor
+strand_array = NULL;
+our_byte_number = 1;
+coding_array = NULL;
-
-
gtps_array = gtps_array_;
id_numbers = id_numbers_;
snp_numbers = snp_numbers_;
Modified: pkg/GenABEL/src/GAlib/gwaa.c
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa.c 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/gwaa.c 2013-11-19 18:17:38 UTC (rev 1401)
@@ -364,7 +364,7 @@
unsigned int nids = (*Nids);
unsigned int nsnps = (*Nsnps);
unsigned int gt[nids];
- unsigned int count[2][4],R,S,N,r1,r2,n1,n2;
+ unsigned int count[2][4],R,N,r1,r2,n1,n2;//,S;
double mul, a, b, c, den;
char str;
unsigned int nbytes;
@@ -389,7 +389,7 @@
r1 = count[1][2]; r2 = count[1][3];
n1 = r1 + count[0][2]; n2 = r2 + count[0][3];
R = r1 + r2 + count[1][1];
- S = count[0][1]+count[0][2]+count[0][3];
+ //S = count[0][1]+count[0][2]+count[0][3];
if (N>0 && R>0 && R<N) {
mul = (1.*N)/(1.*R*(N-R));
a = 1.*(n1+2.*n2);
@@ -513,7 +513,7 @@
int nbytes;
double Ttotg, mx, bb, dgt, totg[nstra], x2[nstra], sumx[nstra];
double Tsg1, Tsg2, sg1[nstra], sg2[nstra], xg1[nstra], xg2[nstra];
- double det, u, v, u1, u2, v11, v12, v22;
+ double u, v, u1, u2, v11, v12, v22,det;
if ((nids % 4) == 0) nbytes = nids/4; else nbytes = ceil(1.*nids/4.);
// char chgt[nbytes];
@@ -1028,7 +1028,7 @@
double sumOmegaJ[nids];
double YiSumOmegaij[nids];
double sumOmega = 0.;
- double sumYiSumOmegaij = 0.;
+// double sumYiSumOmegaij = 0.;
for (i=0;i<nids;i++) {
sumOmegaJ[i] = 0.;
YiSumOmegaij[i] = 0.;
@@ -1040,7 +1040,7 @@
}
sumOmega += sumOmegaJ[i];
YiSumOmegaij[j] = pheno[i]*sumOmegaJ[i];
- sumYiSumOmegaij += YiSumOmegaij[j];
+// sumYiSumOmegaij += YiSumOmegaij[j];
ePH[j] = sph[j]/nIndividuals[j];
}
@@ -1074,8 +1074,8 @@
}
double sumYSumGOmega = 0.;
double sumGSumGOmega = 0.;
- double sumGSumOmega = 0.;
- double SumSumGOmega = 0.;
+// double sumGSumOmega = 0.;
+// double SumSumGOmega = 0.;
double summand2y, summand3y, summand2g, summand3g, summand4;
summand2y = summand3y = summand2g = summand3g = summand4 = 0.;
for (i=0;i<nids;i++) {
@@ -1086,8 +1086,8 @@
}
sumYSumGOmega += pheno[i]*svec[i];
sumGSumGOmega += gtctr[i]*svec[i];
- sumGSumOmega += gtctr[i]*sumOmegaJ[i];
- SumSumGOmega += svec[i];
+// sumGSumOmega += gtctr[i]*sumOmegaJ[i];
+// SumSumGOmega += svec[i];
summand2y += eG[cstr]*YiSumOmegaij[i];
summand2g += eG[cstr]*gtctr[i]*sumOmegaJ[i];
summand3y += ePH[cstr]*svec[i];
@@ -1130,7 +1130,7 @@
int gt[nids];
int i, j, igt, i1=1;
int nbytes;
- double Ttotg,dgt,svec[nids],gtctr[nids];
+ double Ttotg,svec[nids],gtctr[nids];//,dgt;
double Tsg;
double u, v;
if ((nids % 4) == 0) nbytes = nids/4; else nbytes = ceil(1.*nids/4.);
@@ -1184,8 +1184,8 @@
double SumSumGOmega = 0.;
double summand2y, summand3y, summand2g, summand3g, summand4;
summand2y = summand3y = summand2g = summand3g = summand4 = 0.;
- int gtOffs[4];
- gtOffs[0]=0;gtOffs[1]=nids*nids;gtOffs[2]=nids*nids*2;gtOffs[3]=nids*nids*3;
+// int gtOffs[4];
+// gtOffs[0]=0;gtOffs[1]=nids*nids;gtOffs[2]=nids*nids*2;gtOffs[3]=nids*nids*3;
for (i=0;i<nids;i++) {
svec[i] = 0.;
// double * offS = &invS[nids*i];
@@ -1350,7 +1350,8 @@
unsigned int useFreq = (*UseFreq);
unsigned int gt[nids];
unsigned int count[4],sumgt=0.;
- double varhomweight[4] = {0.,1.,1.,1.}, centgt[4], homweight[4] = {0.,1.,0.,1.},p0=0.,q0=0.,maf=0.;
+ double centgt[4], homweight[4] = {0.,1.,0.,1.},p0=0.,q0=0.,maf=0.;
+// double varhomweight[4] = {0.,1.,1.,1.}, centgt[4], homweight[4] = {0.,1.,0.,1.},p0=0.,q0=0.,maf=0.;
double den, fel;
char str;
unsigned int nbytes;
@@ -1631,7 +1632,7 @@
void comp_qval(double *p, int *Length, double *out) {
int length = (*Length);
int i;
- double sum,max=-1,min,minvec[length];
+ double sum,max=-1,minvec[length];//,min;
for (i=0;i<length;i++) out[i]=0.;
for (i=0;i<length;i++) {
sum = i+1;
@@ -1643,7 +1644,7 @@
if (out[i] < minvec[i+1]) minvec[i]=out[i]; else minvec[i]=minvec[i+1];
}
for (i=0;i<length;i++) {
- min = max;
+ //min = max;
if (out[i]<minvec[i]) out[i]=out[i]; else out[i]=minvec[i];
}
}
@@ -1653,7 +1654,7 @@
void r2new(char *indata, unsigned int *Nids, unsigned int *Nsnps, unsigned int *Nsnps1, unsigned int *snps1, unsigned int *Nsnps2, unsigned int *snps2, double *out) {
unsigned int i,j,m1,m2,idx;
unsigned int nids = (*Nids);
- unsigned int nsnps = (*Nsnps);
+// unsigned int nsnps = (*Nsnps);
unsigned int nsnps1 = (*Nsnps1);
unsigned int nsnps2 = (*Nsnps2);
unsigned int gt[2][nids],cgt[4][4],nAA,nAB,nBA,nBB,nDH;
Modified: pkg/GenABEL/src/GAlib/gwaa_cpp.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/gwaa_cpp.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/gwaa_cpp.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -154,7 +154,7 @@
//unsigned int nids = (*Nids);
//char str;
unsigned int count[3];
- double meaids,p,pmax,qmax,maf,fmax,loglik0,loglik1,chi2lrt;
+ double meaids,p;
count[0]=count[1]=count[2]=0;
p = 0.;
for (i=0;i<9;i++) out[i] = 0.;
@@ -175,6 +175,7 @@
out[4] = count[1];
out[5] = count[2];
if (meaids>0) {
+ double qmax, maf, pmax, loglik0, loglik1, chi2lrt, fmax;
out[6] = SNPHWE(count[1],count[0],count[2]);
pmax = out[2];
qmax = 1.-pmax;
Modified: pkg/GenABEL/src/GAlib/interactions_rare_recesive_alleles.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/interactions_rare_recesive_alleles.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/interactions_rare_recesive_alleles.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -106,8 +106,8 @@
window_current = snp_number - central_snp_position;
if(window_current > window) window_current=window;
-if(central_snp_position >= snp_number || central_snp_position <0) {Rprintf("snp_snp_interaction_results::push_chi2: error: central_snp_position is out of bound"); return -1;}
-if(window_snp_position > window_current || window_snp_position<0) {Rprintf("snp_snp_interaction_results::push_chi2: error: window is out of bound"); return -1;}
+if(central_snp_position >= snp_number) {Rprintf("snp_snp_interaction_results::push_chi2: error: central_snp_position is out of bound"); return -1;}
+if(window_snp_position > window_current) {Rprintf("snp_snp_interaction_results::push_chi2: error: window is out of bound"); return -1;}
chi2_results[central_snp_position][window_snp_position] = chi2;
//std::cout<<"snp_snp_interaction_results::push_chi2 end\n";
return 0;
@@ -618,8 +618,8 @@
UNPROTECT(1);
-delete snp1;
-delete snp2;
+delete [] snp1;
+delete [] snp2;
return(results_R);
} //end of interaction_rare_recesive_allele_C_
Modified: pkg/GenABEL/src/GAlib/mematrix.h
===================================================================
--- pkg/GenABEL/src/GAlib/mematrix.h 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/mematrix.h 2013-11-19 18:17:38 UTC (rev 1401)
@@ -11,7 +11,7 @@
int nelements;
DT * data;
- mematrix() {nrow=ncol=nelements=0;}
+ mematrix() {nrow=ncol=nelements=0;data=NULL;}
mematrix(int nr, int nc);
mematrix(const mematrix &M);
~mematrix() {if (nelements>0) delete [] data;}
Modified: pkg/GenABEL/src/GAlib/reg1.h
===================================================================
--- pkg/GenABEL/src/GAlib/reg1.h 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/reg1.h 2013-11-19 18:17:38 UTC (rev 1401)
@@ -152,6 +152,7 @@
double sigma2;
coxph_reg(coxph_data cdata, int maxiter, double eps, double tol_chol)
{
+ sigma2 = 0;
beta.reinit(cdata.X.nrow,1);
sebeta.reinit(cdata.X.nrow,1);
mematrix<double> newoffset = cdata.offset;
Modified: pkg/GenABEL/src/GAlib/reg1data.h
===================================================================
--- pkg/GenABEL/src/GAlib/reg1data.h 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/GAlib/reg1data.h 2013-11-19 18:17:38 UTC (rev 1401)
@@ -82,6 +82,7 @@
coxph_data(regdata regdat)
{
+ maxiter = 0;
nids = regdat.nids;
ncov = regdat.ncov;
if (regdat.noutcomes != 2)
Modified: pkg/GenABEL/src/ITERlib/iterator_functions.cpp
===================================================================
--- pkg/GenABEL/src/ITERlib/iterator_functions.cpp 2013-11-19 16:01:40 UTC (rev 1400)
+++ pkg/GenABEL/src/ITERlib/iterator_functions.cpp 2013-11-19 18:17:38 UTC (rev 1401)
@@ -276,6 +276,8 @@
delete [] xg1;
delete [] xg2;
+
+
}
#ifdef __cplusplus
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