static void faidx1(const char *filename)
{
int n, n_exp = 0, n_fq_exp = 0;
char tmpfilename[FILENAME_MAX], line[500];
FILE *fin, *fout;
faidx_t *fai;
fin = fopen(filename, "rb");
if (fin == NULL) fail("can't open %s\n", filename);
sprintf(tmpfilename, "%s.tmp", filename);
fout = fopen(tmpfilename, "wb");
if (fout == NULL) fail("can't create temporary %s\n", tmpfilename);
while (fgets(line, sizeof line, fin)) {
if (line[0] == '>') n_exp++;
if (line[0] == '+' && line[1] == '\n') n_fq_exp++;
fputs(line, fout);
}
fclose(fin);
fclose(fout);
if (n_exp == 0 && n_fq_exp != 0) {
// probably a fastq file
n_exp = n_fq_exp;
}
if (fai_build(tmpfilename) < 0) fail("can't index %s", tmpfilename);
fai = fai_load(tmpfilename);
if (fai == NULL) { fail("can't load faidx file %s", tmpfilename); return; }
n = faidx_fetch_nseq(fai);
if (n != n_exp)
fail("%s: faidx_fetch_nseq returned %d, expected %d", filename, n, n_exp);
n = faidx_nseq(fai);
if (n != n_exp)
fail("%s: faidx_nseq returned %d, expected %d", filename, n, n_exp);
fai_destroy(fai);
}
int IndexedFastaReader::NumSequences(void) const
{
REQUIRE_FAIDX_LOADED;
return faidx_nseq(handle_);
}
