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Fix segfault #38

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Merged
ANGSD merged 1 commit into from
Jun 26, 2025
Merged

Fix segfault #38

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34 changes: 18 additions & 16 deletions misc/extract_reads.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ char2int getkeys(const char *key,int value,int nospace){

if(((fp=fopen(key,"rb")))==NULL){
fprintf(stderr,"\t-> Problem opening file: %s\n",key);
exit(0);
exit(-1);
}
char buf[4096];
while(fgets(buf,4096,fp)){
Expand All @@ -103,7 +103,7 @@ int2int getkeysint(const char *key,int value){

if(((fp=fopen(key,"rb")))==NULL){
fprintf(stderr,"\t-> Problem opening file: %s\n",key);
exit(0);
exit(-1);
}
char buf[4096];
while(fgets(buf,4096,fp)){
Expand Down Expand Up @@ -158,7 +158,7 @@ void runextract_int2int(int2int &keeplist,samFile *htsfp,bam_hdr_t *hdr,const ch
samFile *outhts = NULL;
if ((outhts = sam_open_format(outname,out_mode, &fmt)) == NULL) {
fprintf(stderr,"Error opening file for writing: %s\n",outname);
exit(0);
exit(-1);
}

queue *myq = init_queue(5000);//very large, should be enough.
Expand Down Expand Up @@ -201,7 +201,7 @@ void runextract_readid(char2int &keeplist,samFile *htsfp,bam_hdr_t *hdr,const ch
samFile *outhts = NULL;
if ((outhts = sam_open_format(outname,out_mode, dingding2)) == 0) {
fprintf(stderr,"Error opening file for writing: %s\n",outname);
exit(0);
exit(-1);
}

if (sam_hdr_write(outhts, hdr) < 0)
Expand Down Expand Up @@ -396,7 +396,7 @@ int main_bytaxid(int argc,char**argv){
++argv;
}

fprintf(stderr,"\t-> key: %s \n\t-> hts: %s \n\t-> nodefile: %s \n\t-> acc2tax: %s \n\t-> taxid: %s\n\t-> taxnames: %s \n\t-> strict: %d \n\t-> type: %s \n\t-> outfile: %s\n\t-> forcedump:%d\n\t-> accout:%s names: %s\n",keyfile,hts,nodefile, acc2tax, taxid,taxnames,strict,type,outfile,forcedump,accout,names);
fprintf(stderr,"\t-> key: %s \n\t-> hts: %s \n\t-> nodefile: %s \n\t-> acc2tax: %s \n\t-> taxid: %s\n\t-> taxnames: %s \n\t-> strict: %d \n\t-> type: %s \n\t-> outfile: %s\n\t-> forcedump:%d\n\t-> accout:%s\n\t-> names: %s\n",keyfile,hts,nodefile, acc2tax, taxid,taxnames,strict,type,outfile,forcedump,accout,names);

if(taxid ==NULL&&taxnames==NULL){
fprintf(stderr,"\t-> Need to supply -taxid and/or -taxnames\n");
Expand All @@ -407,14 +407,16 @@ int main_bytaxid(int argc,char**argv){
return 0;
}
int2int taxids;
if(!fexists(taxid)) {
char *tok = strtok(taxid, ",");
while (tok != NULL) {
taxids[atoi(tok)] = 1;
tok = strtok(NULL, ",");
if(taxid!=NULL) {
if(!fexists(taxid)) {
char *tok = strtok(taxid, ",");
while (tok != NULL) {
taxids[atoi(tok)] = 1;
tok = strtok(NULL, ",");
}
} else {
taxids = getkeysint(taxid,0);
}
} else {
taxids = getkeysint(taxid,0);
}

//open inputfile and parse header
Expand All @@ -432,15 +434,15 @@ int main_bytaxid(int argc,char**argv){
if(taxnames!=NULL){
if(names==NULL){
fprintf(stderr,"\t-> if taxnames is defined then names should also be defined\n");
exit(0);
exit(-1);
}
int2char nammap = parse_names(names);
char2int mapnam;
for(auto it=nammap.begin();it!=nammap.end();it++){
auto it2=mapnam.find(it->second);
if(it2!=mapnam.end()){
fprintf(stderr,"\t-> Problem with duplicate name in name map: key %d val: %s\n",it->first,it->second);
exit(0);
exit(-1);
}
mapnam[it->second] = it->first;
}
Expand All @@ -450,7 +452,7 @@ int main_bytaxid(int argc,char**argv){
auto it = mapnam.find(tok);
if(it==mapnam.end()){
fprintf(stderr,"\t-> Problem finding taxname: %s\n",tok);
exit(0);
exit(-1);
}
taxids[it->second] = 1;
tok = strtok(NULL, ",");
Expand All @@ -461,7 +463,7 @@ int main_bytaxid(int argc,char**argv){
auto it2 = mapnam.find(it->first);
if(it2==mapnam.end()){
fprintf(stderr,"\t-> Problem finding taxname: %s\n",it->first);
exit(0);
exit(-1);
}
taxids[it2->second] = 1;
}
Expand Down
2 changes: 1 addition & 1 deletion shared.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ BGZF *getbgzf4(const char *str1, const char *str2, const char *str3, const char
}

int fexists(const char *str) { ///@param str Filename given as a string.
fprintf(stderr, "\t-> Checking if exits: \'%s\'\n", str);
fprintf(stderr, "\t-> Checking if exists: \'%s\'\n", str);
struct stat buffer;
return (stat(str, &buffer) == 0); /// @return Function returns 1 if file exists.
}
Expand Down