void bcf_file::open()
{
int ret;
if (filename.substr(filename.size()-4) == ".vcf")
LOG.error("Filename ends in '.vcf'. Shouldn't you be using --vcf?\n");
if (filename.substr(filename.size()-7) == ".vcf.gz")
LOG.error("Filename ends in '.vcf.gz'. Shouldn't you be using --gzvcf?\n");
ret = bgzf_is_bgzf(filename.c_str());
if (ret == 1)
is_BGZF = true;
else
is_BGZF = false;
if (is_BGZF)
open_gz();
else
{
file_tmp.open(filename.c_str(), ios::in);
if (!file_tmp.is_open())
LOG.error("Could not open VCF file: " + filename, 0);
file_in = &file_tmp;
}
}
Tabix::Tabix(string& file) {
has_jumped = false;
filename = file;
const char* cfilename = file.c_str();
struct stat stat_tbi,stat_vcf;
char *fnidx = (char*) calloc(strlen(cfilename) + 5, 1);
strcat(strcpy(fnidx, cfilename), ".tbi");
if ( bgzf_is_bgzf(cfilename)!=1 )
{
cerr << "[tabix++] was bgzip used to compress this file? " << file << endl;
free(fnidx);
exit(1);
}
// Common source of errors: new VCF is used with an old index
stat(fnidx, &stat_tbi);
stat(cfilename, &stat_vcf);
if ( stat_vcf.st_mtime > stat_tbi.st_mtime )
{
cerr << "[tabix++] the index file is older than the vcf file. Please use '-f' to overwrite or reindex." << endl;
free(fnidx);
exit(1);
}
free(fnidx);
if ((fn = hts_open(cfilename, "r")) == 0) {
cerr << "[tabix++] fail to open the data file." << endl;
exit(1);
}
if ((tbx = tbx_index_load(cfilename)) == NULL) {
cerr << "[tabix++] failed to load the index file." << endl;
exit(1);
}
int nseq;
const char** seq = tbx_seqnames(tbx, &nseq);
for (int i=0; i<nseq; i++) {
chroms.push_back(seq[i]);
}
free(seq);
idxconf = &tbx_conf_vcf;
// set up the iterator, defaults to the beginning
if (nseq == 0){
// the vcf file contains only the header according
// to the index
iter = NULL;
current_chrom = chroms.end();
}else{
current_chrom = chroms.begin();
iter = tbx_itr_querys(tbx, current_chrom->c_str());
}
}
int goonindex(int argc, char *argv[])
{
struct option opts[] = {
{"seqkey", required_argument, NULL, 's'},
{"startkey", required_argument, NULL, 'b'},
{"endkey", required_argument, NULL, 'e'},
{"zerobased", no_argument, NULL, '0'},
{"rightopen", no_argument, NULL, 'r'},
{"help", no_argument, NULL, 'h'},
{NULL, 0, NULL, 0}
};
struct stat f_stat;
int c;
ti_conf_t conf;
if (argc == 1) {
USAGE;
return -1;
}
INIT_CONF(&conf);
while ((c = getopt_long(argc,
argv,
"s:b:e:0rh",
opts,
NULL)) != -1) {
switch (c) {
case 'h': USAGE;
return -1;
case 's': if (store_key(optarg, conf.sk) != 0) {
fprintf(stderr, "could not store key\n");
return -1;
}
break;
case 'b': if (store_key(optarg, conf.bk) != 0) {
fprintf(stderr, "could not store key\n");
return -1;
}
break;
case 'e': if (store_key(optarg, conf.ek) != 0) {
fprintf(stderr, "could not store key\n");
return -1;
}
break;
case '0': conf.zerobased = 1;
break;
case 'r': conf.rightopen = 1;
break;
default: return -1;
}
}
if (conf.sk[0] == '\0' || conf.bk[0] == '\0') {
fprintf(stderr, "error: missing mandatory argument\n");
return -1;
}
if (conf.ek[0] == '\0' && conf.rightopen) {
fprintf(stderr, "error: options `rightopen` not allowed with single "
"position\n");
return -1;
}
if (optind == argc) {
fprintf(stderr, "error: missing file name\n");
return -1;
}
if (stat(argv[optind], &f_stat) != 0) {
fprintf(stderr, "error: input file does not exist\n");
return -1;
}
if (bgzf_is_bgzf(argv[optind]) != 1) {
fprintf(stderr, "error: input file is not in bgzip format\n");
return -1;
}
return build_gn_index(argv[optind], &conf);
}
int main(int argc, char *argv[])
{
int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, print_only_header = 0, bed_reg = 0;
ti_conf_t conf = ti_conf_gff, *conf_ptr = NULL;
const char *reheader = NULL;
struct __stat64 stat_tbi,stat_vcf;
char *fnidx;
while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhHfBr:")) >= 0) {
switch (c) {
case 'B': bed_reg = 1; break;
case '0': conf.preset |= TI_FLAG_UCSC; break;
case 'S': skip = atoi(optarg); break;
case 'c': meta = optarg[0]; break;
case 'p':
if (strcmp(optarg, "gff") == 0) conf_ptr = &ti_conf_gff;
else if (strcmp(optarg, "bed") == 0) conf_ptr = &ti_conf_bed;
else if (strcmp(optarg, "sam") == 0) conf_ptr = &ti_conf_sam;
else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf_ptr = &ti_conf_vcf;
else if (strcmp(optarg, "psltbl") == 0) conf_ptr = &ti_conf_psltbl;
else {
fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);
return 1;
}
break;
case 's': conf.sc = atoi(optarg); break;
case 'b': conf.bc = atoi(optarg); break;
case 'e': conf.ec = atoi(optarg); break;
case 'l': list_chrms = 1; break;
case 'h': print_header = 1; break;
case 'H': print_only_header = 1; break;
case 'f': force = 1; break;
case 'r': reheader = optarg; break;
}
}
if (optind == argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");
fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
fprintf(stderr, "Usage: tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n");
fprintf(stderr, "Options: -p STR preset: gff, bed, sam, vcf, psltbl [gff]\n");
fprintf(stderr, " -s INT sequence name column [1]\n");
fprintf(stderr, " -b INT start column [4]\n");
fprintf(stderr, " -e INT end column; can be identical to '-b' [5]\n");
fprintf(stderr, " -S INT skip first INT lines [0]\n");
fprintf(stderr, " -c CHAR symbol for comment/meta lines [#]\n");
fprintf(stderr, " -r FILE replace the header with the content of FILE [null]\n");
fprintf(stderr, " -B region1 is a BED file (entire file will be read)\n");
fprintf(stderr, " -0 zero-based coordinate\n");
fprintf(stderr, " -h print also the header lines\n");
fprintf(stderr, " -H print only the header lines\n");
fprintf(stderr, " -l list chromosome names\n");
fprintf(stderr, " -f force to overwrite the index\n");
fprintf(stderr, "\n");
return 1;
}
if ( !conf_ptr )
{
int l = strlen(argv[optind]);
//int strcasecmp(const char *s1, const char *s2);
if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf_ptr = &ti_conf_gff;
else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf_ptr = &ti_conf_bed;
else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf_ptr = &ti_conf_sam;
else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf_ptr = &ti_conf_vcf;
else if (l>=10 && strcasecmp(argv[optind]+l-10, ".psltbl.gz") == 0) conf_ptr = &ti_conf_psltbl;
}
if ( conf_ptr )
conf = *conf_ptr;
if (skip >= 0) conf.line_skip = skip;
if (meta >= 0) conf.meta_char = meta;
if (list_chrms) {
ti_index_t *idx;
int i, n;
const char **names;
idx = ti_index_load(argv[optind]);
if (idx == 0) {
fprintf(stderr, "[main] fail to load the index file.\n");
return 1;
}
names = ti_seqname(idx, &n);
for (i = 0; i < n; ++i) printf("%s\n", names[i]);
free(names);
ti_index_destroy(idx);
return 0;
}
if (reheader)
return reheader_file(reheader,argv[optind],conf.meta_char);
fnidx = calloc(strlen(argv[optind]) + 5, 1);
strcat(strcpy(fnidx, argv[optind]), ".tbi");
if (optind + 1 == argc && !print_only_header) {
if (force == 0) {
if (_stat64(fnidx, &stat_tbi) == 0)
{
// Before complaining, check if the VCF file isn't newer. This is a common source of errors,
// people tend not to notice that tabix failed
_stat64(argv[optind], &stat_vcf);
if ( stat_vcf.st_mtime <= stat_tbi.st_mtime )
{
fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n");
free(fnidx);
return 1;
}
}
}
if ( bgzf_is_bgzf(argv[optind])!=1 )
{
fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);
free(fnidx);
return 1;
}
if ( !conf_ptr )
{
// Building the index but the file type was neither recognised nor given. If no custom change
// has been made, warn the user that GFF is used
if ( conf.preset==ti_conf_gff.preset
&& conf.sc==ti_conf_gff.sc
&& conf.bc==ti_conf_gff.bc
&& conf.ec==ti_conf_gff.ec
&& conf.meta_char==ti_conf_gff.meta_char
&& conf.line_skip==ti_conf_gff.line_skip )
fprintf(stderr,"[tabix] The file type not recognised and -p not given, using the preset [gff].\n");
}
return ti_index_build(argv[optind], &conf);
}
{ // retrieve
tabix_t *t;
// On some systems, stat on non-existent files returns undefined value for sm_mtime, the user had to use -f
int is_remote = (strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx) ? 1 : 0;
if ( !is_remote )
{
// Common source of errors: new VCF is used with an old index
_stat64(fnidx, &stat_tbi);
_stat64(argv[optind], &stat_vcf);
if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime )
{
fprintf(stderr, "[tabix] the index file either does not exist or is older than the vcf file. Please reindex.\n");
free(fnidx);
return 1;
}
}
free(fnidx);
if ((t = ti_open(argv[optind], 0)) == 0) {
fprintf(stderr, "[main] fail to open the data file.\n");
return 1;
}
if ( print_only_header )
{
ti_iter_t iter;
const char *s;
int len;
const ti_conf_t *idxconf;
if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {
fprintf(stderr,"[tabix] failed to load the index file.\n");
return 1;
}
idxconf = ti_get_conf(t->idx);
iter = ti_query(t, 0, 0, 0);
while ((s = ti_read(t, iter, &len)) != 0) {
if ((int)(*s) != idxconf->meta_char) break;
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
return 0;
}
if (strcmp(argv[optind+1], ".") == 0) { // retrieve all
ti_iter_t iter;
const char *s;
int len;
iter = ti_query(t, 0, 0, 0);
while ((s = ti_read(t, iter, &len)) != 0) {
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
} else { // retrieve from specified regions
int i, len;
ti_iter_t iter;
const char *s;
const ti_conf_t *idxconf;
if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {
fprintf(stderr,"[tabix] failed to load the index file.\n");
return 1;
}
idxconf = ti_get_conf(t->idx);
if ( print_header )
{
// If requested, print the header lines here
iter = ti_query(t, 0, 0, 0);
while ((s = ti_read(t, iter, &len)) != 0) {
if ((int)(*s) != idxconf->meta_char) break;
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
}
if (bed_reg) {
extern int bed_overlap(const void *_h, const char *chr, int beg, int end);
extern void *bed_read(const char *fn);
extern void bed_destroy(void *_h);
const ti_conf_t *conf_ = idxconf? idxconf : &conf; // use the index file if available
void *bed = bed_read(argv[optind+1]); // load the BED file
ti_interval_t intv;
if (bed == 0) {
fprintf(stderr, "[main] fail to read the BED file.\n");
return 1;
}
iter = ti_query(t, 0, 0, 0);
while ((s = ti_read(t, iter, &len)) != 0) {
int c;
ti_get_intv(conf_, len, (char*)s, &intv);
c = *intv.se; *intv.se = '\0';
if (bed_overlap(bed, intv.ss, intv.beg, intv.end)) {
*intv.se = c;
puts(s);
}
*intv.se = c;
}
ti_iter_destroy(iter);
bed_destroy(bed);
} else {
for (i = optind + 1; i < argc; ++i) {
int tid, beg, end;
if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) {
iter = ti_queryi(t, tid, beg, end);
while ((s = ti_read(t, iter, &len)) != 0) {
fputs(s, stdout); fputc('\n', stdout);
}
ti_iter_destroy(iter);
}
// else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
}
}
}
ti_close(t);
}
return 0;
}
