static void
tabix_dealloc(TabixObject *self)
{
free(self->fn);
ti_close(self->tb);
PyObject_Del(self);
}
void lineFileClose(struct lineFile **pLf)
/* Close up a line file. */
{
struct lineFile *lf;
if ((lf = *pLf) != NULL)
{
if (lf->pl != NULL)
{
pipelineWait(lf->pl);
pipelineFree(&lf->pl);
}
else if (lf->fd > 0 && lf->fd != fileno(stdin))
{
close(lf->fd);
freeMem(lf->buf);
}
#ifdef USE_TABIX
else if (lf->tabix != NULL)
{
if (lf->tabixIter != NULL)
ti_iter_destroy(lf->tabixIter);
ti_close(lf->tabix);
}
#endif // USE_TABIX
freeMem(lf->fileName);
metaDataFree(lf);
freez(pLf);
}
}
struct lineFile *lineFileTabixMayOpen(char *fileOrUrl, bool zTerm)
/* Wrap a line file around a data file that has been compressed and indexed
* by the tabix command line program. The index file <fileOrUrl>.tbi must be
* readable in addition to fileOrUrl. If there's a problem, warn & return NULL.
* This works only if kent/src has been compiled with USE_TABIX=1 and linked
* with the tabix C library. */
{
#ifdef USE_TABIX
int tbiNameSize = strlen(fileOrUrl) + strlen(".tbi") + 1;
char *tbiName = needMem(tbiNameSize);
safef(tbiName, tbiNameSize, "%s.tbi", fileOrUrl);
tabix_t *tabix = ti_open(fileOrUrl, tbiName);
if (tabix == NULL)
{
warn("Unable to open \"%s\"", fileOrUrl);
freez(&tbiName);
return NULL;
}
if ((tabix->idx = ti_index_load(tbiName)) == NULL)
{
warn("Unable to load tabix index from \"%s\"", tbiName);
ti_close(tabix);
tabix = NULL;
freez(&tbiName);
return NULL;
}
struct lineFile *lf = needMem(sizeof(struct lineFile));
lf->fileName = cloneString(fileOrUrl);
lf->fd = -1;
lf->bufSize = 64 * 1024;
lf->buf = needMem(lf->bufSize);
lf->zTerm = zTerm;
lf->tabix = tabix;
freez(&tbiName);
return lf;
#else // no USE_TABIX
warn(COMPILE_WITH_TABIX, "lineFileTabixMayOpen");
return NULL;
#endif // no USE_TABIX
}
bool
parse_tabix_region(const char* filename,
const char* region,
int& begin,
int& end) {
if (NULL == region) {
return false;
}
if (NULL == filename) {
throw blt_exception("vcf filename is null ptr");
}
if ('\0' == *filename) {
throw blt_exception("vcf filename is empty string");
}
enforce_tabix_index(filename);
tabix_t* _tfp = ti_open(filename, 0);
if (NULL == _tfp) {
log_os << "ERROR: Failed to open VCF file: '" << filename << "'\n";
exit(EXIT_FAILURE);
}
// read from a specific region:
if (ti_lazy_index_load(_tfp) < 0) {
log_os << "ERROR: Failed to load index for vcf file: '" << filename << "'\n";
exit(EXIT_FAILURE);
}
int tid;
const bool result(0 == ti_parse_region(_tfp->idx, region, &tid, &begin, &end));
ti_close(_tfp);
return result;
}
int main(int argc, char *argv[])
{
int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, bed_reg = 0;
ti_conf_t conf = ti_conf_gff;
const char *reheader = NULL;
while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhfBr:")) >= 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 = ti_conf_gff;
else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf = ti_conf_vcf;
else if (strcmp(optarg, "psltbl") == 0) conf = 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 'f': force = 1; break;
case 'r': reheader = optarg; break;
}
}
if (skip >= 0) conf.line_skip = skip;
if (meta >= 0) conf.meta_char = meta;
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 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 (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);
struct stat stat_tbi,stat_vcf;
char *fnidx = calloc(strlen(argv[optind]) + 5, 1);
strcat(strcpy(fnidx, argv[optind]), ".tbi");
if (optind + 1 == argc) {
if (force == 0) {
if (stat(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
stat(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_check_bgzf(argv[optind])!=1 )
{
fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);
free(fnidx);
return 1;
}
return ti_index_build(argv[optind], &conf);
}
{ // retrieve
tabix_t *t;
// Common source of errors: new VCF is used with an old index
stat(fnidx, &stat_tbi);
stat(argv[optind], &stat_vcf);
if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime )
{
fprintf(stderr, "[tabix] the index file is older than the vcf file. Please use '-f' to overwrite or 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 (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;
}
tabix_chrom_list::
~tabix_chrom_list() {
if (NULL != _tptr) free(_tptr);
if (NULL != _tfp) ti_close(_tfp);
}
tabix_header_streamer::
~tabix_header_streamer() {
if (NULL != _titer) ti_iter_destroy(_titer);
if (NULL != _tfp) ti_close(_tfp);
}
void closeTabixFile(BCFReaderData * data) {
ti_close(data->tabix_file);
gzclose(data->gz_file);
}