* commented out above. */
int ti_readline(BGZF *fp, kstring_t *str)
{
- int l, state = 0;
- unsigned char *buf = (unsigned char*)fp->uncompressed_block;
- str->l = 0;
- do {
- if (fp->block_offset >= fp->block_length) {
- if (bgzf_read_block(fp) != 0) { state = -2; break; }
- if (fp->block_length == 0) { state = -1; break; }
- }
- for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
- if (l < fp->block_length) state = 1;
- l -= fp->block_offset;
- if (str->l + l + 1 >= str->m) {
- str->m = str->l + l + 2;
- kroundup32(str->m);
- str->s = (char*)realloc(str->s, str->m);
- }
- memcpy(str->s + str->l, buf + fp->block_offset, l);
- str->l += l;
- fp->block_offset += l + 1;
- if (fp->block_offset >= fp->block_length) {
-#ifdef _USE_KNETFILE
- fp->block_address = knet_tell(fp->x.fpr);
-#else
- fp->block_address = ftello(fp->file);
-#endif
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- } while (state == 0);
- if (str->l == 0 && state < 0) return state;
- str->s[str->l] = 0;
- return str->l;
+ return bgzf_getline(fp, '\n', str);
}
/*************************************
return tid;
}
-static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
{
- int i, b = 0, id = 1;
+ int i, b = 0, id = 1, ncols = 0;
char *s;
- intv->tid = intv->beg = intv->end = intv->bin = -1;
- for (i = 0; i <= str->l; ++i) {
- if (str->s[i] == '\t' || str->s[i] == 0) {
- if (id == idx->conf.sc) {
- str->s[i] = 0;
- intv->tid = get_tid(idx, str->s + b);
- if (i != str->l) str->s[i] = '\t';
- } else if (id == idx->conf.bc) {
+ intv->ss = intv->se = 0; intv->beg = intv->end = -1;
+ for (i = 0; i <= len; ++i) {
+ if (line[i] == '\t' || line[i] == 0) {
+ ++ncols;
+ if (id == conf->sc) {
+ intv->ss = line + b; intv->se = line + i;
+ } else if (id == conf->bc) {
// here ->beg is 0-based.
- intv->beg = intv->end = strtol(str->s + b, &s, 0);
- if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
+ intv->beg = intv->end = strtol(line + b, &s, 0);
+ if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg;
else ++intv->end;
if (intv->beg < 0) intv->beg = 0;
if (intv->end < 1) intv->end = 1;
} else {
- if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
- if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_SAM) {
+ if ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
+ if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
+ } else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
if (id == 6) { // CIGAR
int l = 0, op;
char *t;
- for (s = str->s + b; s < str->s + i;) {
+ for (s = line + b; s < line + i;) {
long x = strtol(s, &t, 10);
op = toupper(*t);
if (op == 'M' || op == 'D' || op == 'N') l += x;
if (l == 0) l = 1;
intv->end = intv->beg + l;
}
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
+ } else if ((conf->preset&0xffff) == TI_PRESET_VCF) {
// FIXME: the following is NOT tested and is likely to be buggy
if (id == 4) {
if (b < i) intv->end = intv->beg + (i - b);
} else if (id == 8) { // look for "END="
- int c = str->s[i];
- str->s[i] = 0;
- s = strstr(str->s + b, "END=");
- if (s == str->s + b) s += 4;
+ int c = line[i];
+ line[i] = 0;
+ s = strstr(line + b, "END=");
+ if (s == line + b) s += 4;
else if (s) {
- s = strstr(str->s + b, ";END=");
+ s = strstr(line + b, ";END=");
if (s) s += 5;
}
if (s) intv->end = strtol(s, &s, 0);
- str->s[i] = c;
+ line[i] = c;
}
}
}
++id;
}
}
- if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
- intv->bin = ti_reg2bin(intv->beg, intv->end);
+/*
+ if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
+ if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
+ else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
+ exit(1);
+ }
+*/
+ if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
return 0;
}
+static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+{
+ ti_interval_t x;
+ intv->tid = intv->beg = intv->end = intv->bin = -1;
+ if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
+ int c = *x.se;
+ *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
+ intv->beg = x.beg; intv->end = x.end;
+ intv->bin = ti_reg2bin(intv->beg, intv->end);
+ return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
+ } else {
+ fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
+ return -1;
+ }
+}
+
/************
* indexing *
************/
continue;
}
get_intv(idx, str, &intv);
+ if ( intv.beg<0 || intv.end<0 )
+ {
+ fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n");
+ exit(1);
+ }
if (last_tid != intv.tid) { // change of chromosomes
if (last_tid>intv.tid )
{
- fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted?\n",(unsigned long long)lineno);
+ fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1);
exit(1);
}
last_tid = intv.tid;
return 0;
}
+const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
+
/*******************
* High-level APIs *
*******************/
projects / tabix.git / blobdiff