C++ (Cpp) fai_read Examples

Example #1

File: faidx.c Project: mtmorgan/Rhtslib

faidx_t *fai_load(const char *fn)
{
    char *str;
    FILE *fp;
    faidx_t *fai;
    str = (char*)calloc(strlen(fn) + 5, 1);
    sprintf(str, "%s.fai", fn);

#ifdef _USE_KNETFILE
    if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
    {
        fp = download_and_open(str);
        if ( !fp )
        {
            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
            free(str);
            return 0;
        }
    }
    else
#endif
        fp = fopen(str, "rb");
    if (fp == 0) {
        fprintf(stderr, "[fai_load] build FASTA index.\n");
        fai_build(fn);
        fp = fopen(str, "rb");
        if (fp == 0) {
            fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
            free(str);
            return 0;
        }
    }

    fai = fai_read(fp);
    fclose(fp);

    fai->bgzf = bgzf_open(fn, "rb");
    free(str);
    if (fai->bgzf == 0) {
        fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
        return 0;
    }
    if ( fai->bgzf->is_compressed==1 )
    {
        if ( bgzf_index_load(fai->bgzf, fn, ".gzi") < 0 )
        {
            fprintf(stderr, "[fai_load] failed to load .gzi index: %s[.gzi]\n", fn);
            fai_destroy(fai);
            return NULL;
        }
    }
    return fai;
}

Example #2

File: faidx.c Project: Griffan/FASTQuick

faidx_t *fai_load(const char *fn)
{
	char *str;
	FILE *fp;
	faidx_t *fai;
	str = (char*)calloc(strlen(fn) + 5, 1);
	sprintf(str, "%s.fai", fn);

#ifdef _USE_KNETFILE
    if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
    {
        fp = download_and_open(str);
        if ( !fp )
        {
            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
            free(str);
            return 0;
        }
    }
    else
#endif
        fp = fopen(str, "rb");
	if (fp == 0) {
		fprintf(stderr, "[fai_load] build FASTA index.\n");
		fai_build(fn);
		fp = fopen(str, "rb");
		if (fp == 0) {
			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
			free(str);
			return 0;
		}
	}

	fai = fai_read(fp);
	fclose(fp);

	fai->rz = razf_open(fn, "rb");
	free(str);
	if (fai->rz == 0) {
		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
		return 0;
	}
	return fai;
}