int main(int argc, char *argv[])
{
struct lineFile *pf, *ef, *apf;
FILE *of, *nf, *enf=NULL;
char *efName=NULL, filename[256];
int verb = 0;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
{
fprintf(stderr, "USAGE: pslAnal [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
return 1;
}
verb = optionInt("verbose", 0);
verboseSetLevel(verb);
efName = optionVal("epcr", NULL);
pf = pslFileOpen(argv[1]);
apf = lineFileOpen(argv[2], TRUE);
of = mustOpen(argv[3], "w");
sprintf(filename, "%s.notfound.primers", argv[3]);
nf = mustOpen(filename, "w");
verbose(1, "Reading all.primers file\n");
readPrimerInfo(apf);
if (efName)
{
ef = lineFileOpen(efName, TRUE);
verbose(1, "Reading epcr file\n");
readEpcr(ef);
}
verbose(1, "Reading and processing isPCR file\n");
processPrimers(pf, of);
if (efName)
{
verbose(1, "Writing epcr.not.found file\n");
sprintf(filename, "epcr.not.found");
enf = mustOpen(filename, "w");
writeEpcrNotFound(enf);
}
verbose(1, "Writing out primers not found\n");
writePrimersNotFound(nf);
if (efName)
{
lineFileClose(&ef);
fclose(enf);
}
lineFileClose(&pf);
lineFileClose(&apf);
fclose(of);
fclose(nf);
return(0);
}
int main(int argc, char *argv[])
{
struct lineFile *pf, *ef, *apf;
FILE *of, *nf, *enf=NULL;
char *efName=NULL, filename[256], notFound[256];
int verb = 0;
verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
{
verbose(0, "usage: pslFilterPrimers [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
return 1;
}
verb = optionInt("verbose", 0);
verboseSetLevel(verb);
efName = optionVal("epcr", NULL);
pf = pslFileOpen(argv[1]);
apf = lineFileOpen(argv[2], TRUE);
of = mustOpen(argv[3], "w");
safef(notFound, sizeof(filename), "%s.notfound.primers", argv[3]);
nf = mustOpen(notFound, "w");
verbose(1, "Reading all primers file: '%s'\n", argv[2]);
readPrimerInfo(apf);
if (efName)
{
ef = lineFileOpen(efName, TRUE);
verbose(1, "Reading epcr file: '%s'\n", efName);
readEpcr(ef);
}
verbose(1, "Reading isPCR file: '%s' processing output to: '%s'\n", argv[1], argv[3]);
processPrimers(pf, of);
if (efName)
{
safef(filename, sizeof(filename), "epcr.not.found");
verbose(1, "Writing %s file\n", filename);
enf = mustOpen(filename, "w");
writeEpcrNotFound(enf);
}
verbose(1, "Writing primers not found to file: '%s'\n", notFound);
writePrimersNotFound(nf);
if (efName)
{
lineFileClose(&ef);
fclose(enf);
}
lineFileClose(&pf);
lineFileClose(&apf);
fclose(of);
fclose(nf);
return(0);
}