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Return failure status for invalid SAF indexes #672

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Return failure status for invalid SAF indexes #672

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14 changes: 7 additions & 7 deletions misc/safreader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ int safversion(const char *fname)
gz = gzopen(fname,"r");
if(gz==Z_NULL){
fprintf(stderr,"\t-> Problem opening file: \'%s\'",fname);
exit(0);
exit(EXIT_FAILURE);
}
char buf[8];
gzread(gz,buf,8*sizeof(char));
Expand Down Expand Up @@ -92,14 +92,14 @@ persaf * persaf_init(char *fname, int verbose)
size_t clen;
if(!fexists(fname)){
fprintf(stderr, "[persaf::persaf_init] Problem opening file: \'%s\'\n", fname);
exit(0);
exit(EXIT_FAILURE);
}

FILE *fp = NULL;
fp=fopen(fname,"r");
if(fp==NULL){
fprintf(stderr, "[persaf::persaf_init] Problem opening file: \'%s\'\n", fname);
exit(0);
exit(EXIT_FAILURE);
}

char buf[8];
Expand All @@ -110,12 +110,12 @@ persaf * persaf_init(char *fname, int verbose)
fprintf(stderr, "[persaf::persaf_init] Version of %s is %d\n", fname, ret->version);
if(!(ret->version==2 || ret->version==3)){
fprintf(stderr,"[persaf::persaf_init] You are using a version of realSFS that is incompatible with the old binary output from ANGSD. Please recreate the SAF files.\n");
exit(0);
exit(EXIT_FAILURE);
}

if(1!=fread(&ret->nChr,sizeof(size_t),1,fp)){
fprintf(stderr,"[%s.%s():%d] Problem reading data: %s \n",__FILE__,__FUNCTION__,__LINE__,fname);
exit(0);
exit(EXIT_FAILURE);
}

ret->nSites = 0;
Expand Down Expand Up @@ -173,13 +173,13 @@ persaf * persaf_init(char *fname, int verbose)
ret->saf = bgzf_open(tmp2,"r");
if(!ret->saf){
fprintf(stderr,"[persaf::persaf_init] Problem opening file \'%s\', will exit.\n",tmp2);
exit(0);
exit(EXIT_FAILURE);
}
if(ret->saf)
my_bgzf_seek(ret->saf,8,SEEK_SET);
if(ret->saf && ret->version!=safversion(tmp2)){
fprintf(stderr,"[persaf::persaf_init] Version mismatch between %s and %s (%d and %d)\n",fname,tmp2,ret->version,safversion(tmp2));
exit(0);
exit(EXIT_FAILURE);
}

snprintf(tmp2,strlen(fname)+100,"%spos.gz",tmp);
Expand Down