[style] Fixed a bunch of compilerwarnings

Changed a number of strcpy strncpy

abcFreq.cpp

@@ -82,7 +82,7 @@ void abcFreq::printArg(FILE *argFile){
   fprintf(argFile,"\t-minMaf  \t%f\t(Remove sites with MAF below)\n",minMaf);
   fprintf(argFile,"\t-SNP_pval\t%f\t(Remove sites with a pvalue larger)\n",SNP_pval);
   fprintf(argFile,"\t-rmTriallelic\t%f\t(Remove sites with a pvalue lower)\n",rmTriallelic);
-  fprintf(argFile,"\t-forceMaf\t%f\t(Write .mafs file when running -doAsso (by default does not output .mafs file with -doAsso))\n",forceMaf);
+  fprintf(argFile,"\t-forceMaf\t%d\t(Write .mafs file when running -doAsso (by default does not output .mafs file with -doAsso))\n",forceMaf);
   fprintf(argFile,"\t-skipMissing\t%d\t(Set post to 0.33 if missing (do not use freq as prior))\n",skipMissing);
   fprintf(argFile,"Extras:\n");
   fprintf(argFile,"\t-ref\t%s\t(Filename for fasta reference)\n",refName);

abcScounts.cpp

@@ -33,8 +33,8 @@ aMap readvcf(const char *fname){
     if(4!=sscanf(buf,"%s\t%d\t%c\t%c\n",chr,&pos,&al1,&al2)){
       fprintf(stderr,"\t-> problem parsing line: %d which looks like: %s\n",at,buf);
     }
-    char tmpnam[1024];
-    sprintf(tmpnam,"%s %d",chr,pos);
+    char tmpnam[2048];
+    snprintf(tmpnam,2048,"%s %d",chr,pos);
     aMap::iterator it=am.find(tmpnam);
     if(it!=am.end()){
       fprintf(stderr,"\t-> Problem with duplicate positions: %s \n",tmpnam);

abcTemplate.cpp

@@ -478,7 +478,8 @@ void abcTemplate::run(funkyPars *pars){
 
 	// Reference base:
 	int refB = -1;
-	if (pars->ref == 0) fprintf(outfile,"  Warning: Ref not defined! %s \n", pars->ref);
+	if (pars->ref == NULL)
+	  fprintf(outfile,"\t-> Warning: Ref not defined!  \n");
 	else refB = refToInt[pars->ref[s]];
 
 

abcWriteBcf.cpp

@@ -144,7 +144,7 @@ void abcWriteBcf::print(funkyPars *pars){
     rec->rid = bcf_hdr_name2id(hdr,header->target_name[pars->refId]);
     rec->pos = pars->posi[s];//<- maybe one index?
     //    bcf_update_id(hdr, rec, "rs6054257");
-    if(domcall!=NULL){
+    if(domcall>0&&mcall!=NULL){
       // 
       char alleles[16];
       int goa =0;

aio.cpp

@@ -19,7 +19,7 @@ FILE *aio::openFile(const char* a,const char* b){
     fprintf(stderr,"[%s] %s %s",__FUNCTION__,a,b);
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   dumpedFiles.push_back(strdup(c));
   FILE *fp = NULL;
@@ -36,7 +36,7 @@ BGZF *aio::openFileBG(const char* a,const char* b){
 
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   dumpedFiles.push_back(strdup(c));
   BGZF *fp = bgzf_open(c,"w6h");
   delete [] c;
@@ -47,7 +47,7 @@ htsFile *aio::openFileHts(const char* a,const char* b){
 
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   dumpedFiles.push_back(strdup(c));
   htsFile *fp = hts_open(c,"w");
   delete [] c;
@@ -58,7 +58,7 @@ htsFile *aio::openFileHtsBcf(const char* a,const char* b){
 
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   dumpedFiles.push_back(strdup(c));
   htsFile *fp = hts_open(c,"wb");
   delete [] c;

bgenReader.cpp

@@ -137,7 +137,7 @@ bgenLine *bgenReader::parseline(FILE *fp,header *hd){
   unsigned short Lchr_l;
   assert(fread(&Lchr_l,sizeof(unsigned short),1,fp)==1);
   bgen->Lchr =(char*) calloc(Lchr_l+1,sizeof(char));
-  fread(bgen->Lchr,sizeof(char),Lchr_l,fp);
+  assert(fread(bgen->Lchr,sizeof(char),Lchr_l,fp)==Lchr_l);
 
   assert(fread(&bgen->vpos,sizeof(unsigned),1,fp)==1);
   assert(fread(&bgen->nal,sizeof(unsigned short),1,fp)==1);

makeReadPool.cpp

@@ -260,7 +260,7 @@ void read_reads_noStop(htsFile *fp,int nReads,int &isEof,readPool &ret,int refTo
       rdObjRegionDone =1;
       break;
     }else if(ret.first[ret.l+i-1]>b->core.pos){
-      fprintf(stderr,"[%s] unsorted file detected will exit new(-1)=%d new=%lld,ret.l=%d i=%d\n",__FUNCTION__,ret.first[ret.l+i-1],b->core.pos,ret.l,i);
+      fprintf(stderr,"[%s] unsorted file detected will exit new(-1)=%d new=%ld,ret.l=%d i=%d\n",__FUNCTION__,ret.first[ret.l+i-1],b->core.pos,ret.l,i);
       exit(0);
     }
 

misc/fstreader.cpp

@@ -110,7 +110,7 @@ perfst * perfst_init(char *fname){
 #endif
   fclose(fp);
   char *tmp =(char*)calloc(strlen(fname)+100,1);//that should do it
-  tmp=strncpy(tmp,fname,strlen(fname)-3);
+  memcpy(tmp,fname,strlen(fname)-3);
   // fprintf(stderr,"tmp:%s\n",tmp);
 
   char *tmp2 = (char*)calloc(strlen(fname)+100,1);//that should do it

misc/header.cpp

@@ -28,7 +28,7 @@ BGZF *openFileBG(const char* a,const char* b){
 
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   BGZF *fp = bgzf_open(c,"wb");
   delete [] c;
   return fp;
@@ -38,7 +38,7 @@ FILE *openFile(const char* a,const char* b){
     fprintf(stderr,"[%s] %s %s",__FUNCTION__,a,b);
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   FILE *fp = fopen(c,"w");
   delete [] c;
   return fp;

misc/ibs.cpp

@@ -78,7 +78,7 @@ std::vector<char *> dumpedFiles;
 FILE *openFile(const char* a,const char* b){
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   fprintf(stderr,"\t-> Dumping file: %s\n",c);
 
   dumpedFiles.push_back(strdup(c));

misc/msHOT2glf.c

@@ -53,7 +53,7 @@ FILE *openFile(const char* a,const char* b){
   //  char *c = new char[strlen(a)+strlen(b)+1];
   char *c = malloc(strlen(a)+strlen(b)+1);
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   FILE *fp = getFILE(c,"w");
   free(c);
@@ -83,7 +83,7 @@ BGZF *openFileGz(const char* a,const char* b,const char *mode){
   //  char *c = new char[strlen(a)+strlen(b)+1];
   char *c = malloc(strlen(a)+strlen(b)+1);
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   BGZF *fp = getGz(c,mode);
   //delete [] c;
@@ -494,7 +494,7 @@ int main(int argc,char **argv){
   char *pch = strstr(line,"msHOT-lite");
   while(1){
     char *tmppch=strstr(pch+1,"msHOT-lite");
-    if(tmppch=='\0')
+    if(tmppch[0]=='\0')
       break;
     pch=tmppch;
   }

misc/msToGlf.c

@@ -603,7 +603,7 @@ FILE *openFile(const char* a,const char* b){
   //  char *c = new char[strlen(a)+strlen(b)+1];
   char *c = malloc(strlen(a)+strlen(b)+1);
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   FILE *fp = getFILE(c,"w");
   free(c);
@@ -633,7 +633,7 @@ BGZF* openFileGz(const char* a,const char* b,const char *mode){
   //  char *c = new char[strlen(a)+strlen(b)+1];
   char *c = malloc(strlen(a)+strlen(b)+1);
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   BGZF *fp = getGz(c,mode);
   //delete [] c;

misc/ngsadmix32.cpp

@@ -420,7 +420,7 @@ FILE *openFile(const char* a,const char* b){
     fprintf(stderr,"[%s] %s %s",__FUNCTION__,a,b);
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //fprintf(stderr,"\t-> Dumping file: %s\n",c);
   if(0&&fexists(c)){//ANDERS DAEMON DRAGON HATES THIS
     fprintf(stderr,"File: %s exists will exist\n",c);
@@ -438,7 +438,7 @@ gzFile openFileGz(const char* a,const char* b){
     fprintf(stderr,"[%s] %s %s",__FUNCTION__,a,b);
   char *c = new char[strlen(a)+strlen(b)+1];
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   //  fprintf(stderr,"\t-> Dumping file: %s\n",c);
   if(0&&fexists(c)){//ANDERS DAEMON DRAGON HATES THIS
     fprintf(stderr,"File: %s exists will exist\n",c);

misc/psmcreader.cpp

@@ -119,7 +119,7 @@ perpsmc * perpsmc_init(char *fname){
   }
   fclose(fp);
   char *tmp =(char*)calloc(strlen(fname)+100,1);//that should do it
-  tmp=strncpy(tmp,fname,strlen(fname)-3);
+  memcpy(tmp,fname,strlen(fname)-3);
   //  fprintf(stderr,"tmp:%s\n",tmp);
 
   char *tmp2 = (char*)calloc(strlen(fname)+100,1);//that should do it

misc/realSFS.cpp

@@ -254,7 +254,7 @@ int printMulti(args *arg){
     for(int i=0;i<saf.size();i++){
       size_t newlen = strlen(saf[i]->fname)+100;
       char *tmp =(char*) calloc(newlen,sizeof(char));
-      tmp = strncpy(tmp,saf[i]->fname,strlen(saf[i]->fname)-4);
+      memcpy(tmp,saf[i]->fname,strlen(saf[i]->fname)-4);
       fprintf(stderr,"\t-> Generating outputfile: %s\n",tmp);
       oldfp[i] = fopen(tmp,"wb");
       free(tmp);

misc/safreader.cpp

@@ -132,8 +132,8 @@ persaf * persaf_init(char *fname,int verbose){
     }
   }
   fclose(fp);
-  char *tmp =(char*)calloc(strlen(fname)+100,1);//that should do it
-  tmp=strncpy(tmp,fname,strlen(fname)-3);
+  char *tmp =(char*)calloc(strlen(fname)+100,sizeof(char));//that should do it
+  memcpy(tmp,fname,strlen(fname)-3);
   //  fprintf(stderr,"tmp:%s\n",tmp);
 
   char *tmp2 = (char*)calloc(strlen(fname)+100,1);//that should do it

misc/smartCount.c

@@ -478,7 +478,7 @@ int treemixer(int argc,char **argv){
     }
     ++argv;
   }
-  fprintf(stderr,"reg:%s flis:%s\n",reg,flis );
+  //  fprintf(stderr,"reg:%s flis:%s\n",reg,flis );
   if(!flis){
     fprintf(stderr,"Must supply -bin/idx or bam\n");
     return 0;

misc/supersim.cpp

@@ -312,7 +312,7 @@ double simfreqBN(double F, double p_anc) {
 char *append(const char* a,const char *b){
   char *c =(char *) malloc((strlen(a)+strlen(b)+1)*sizeof(char));
   strcpy(c,a);
-  strncat(c,b,strlen(b));
+  strcat(c,b);
   return c;
 }