ti_lidx_t *index2;
};
+struct __ti_iter_t {
+ int from_first; // read from the first record; no random access
+ int tid, beg, end, n_off, i, finished;
+ uint64_t curr_off;
+ kstring_t str;
+ BGZF *fp;
+ const ti_index_t *idx;
+ pair64_t *off;
+};
+
typedef struct {
int tid, beg, end, bin;
} ti_intv_t;
index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
}
- for (i = beg + 1; i <= end; ++i)
- if (index2->offset[i] == 0) index2->offset[i] = offset;
- index2->n = end + 1;
+ if (beg == end) {
+ if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+ } else {
+ for (i = beg; i <= end; ++i)
+ if (index2->offset[i] == 0) index2->offset[i] = offset;
+ }
+ if (index2->n < end + 1) index2->n = end + 1;
}
static void merge_chunks(ti_index_t *idx)
last_tid = intv.tid;
last_bin = 0xffffffffu;
} else if (last_coor > intv.beg) {
- fprintf(stderr, "[ti_index_core] the file is not sorted at line %llu\n", (unsigned long long)lineno);
+ fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
exit(1);
}
- if (intv.bin < 4681) insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+ insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
if (intv.bin != last_bin) { // then possibly write the binning index
if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
free(fnidx); return 0;
}
-int ti_list_chromosomes(const char *fn)
+const char **ti_seqname(const ti_index_t *idx, int *n)
{
- ti_index_t *idx;
- char **names;
- int i;
+ const char **names;
khint_t k;
- idx = ti_index_load(fn);
+ *n = idx->n;
names = calloc(idx->n, sizeof(void*));
for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
if (kh_exist(idx->tname, k))
- names[kh_val(idx->tname, k)] = (char*)kh_key(idx->tname, k);
- for (i = 0; i < idx->n; ++i) printf("%s\n", names[i]);
- free(names);
- ti_index_destroy(idx);
- return 0;
+ names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
+ return names;
}
ti_index_t *ti_index_load(const char *fn)
return i;
}
-static inline int is_overlap(int32_t beg, int32_t end, int rbeg, int rend)
+ti_iter_t ti_first(BGZF *fp)
{
- return (rend > beg && rbeg < end);
+ ti_iter_t iter;
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->fp = fp; iter->from_first = 1;
+ return iter;
}
-// ti_fetch helper function retrieves
-pair64_t *get_chunk_coordinates(const ti_index_t *idx, int tid, int beg, int end, int* cnt_off)
+ti_iter_t ti_query(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end)
{
uint16_t *bins;
int i, n_bins, n_off;
khint_t k;
khash_t(i) *index;
uint64_t min_off;
+ ti_iter_t iter = 0;
+ // initialize the iterator
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->fp = fp; iter->idx = idx;
+ iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
+ // random access
bins = (uint16_t*)calloc(MAX_BIN, 2);
n_bins = reg2bins(beg, end, bins);
index = idx->index[tid];
- min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
- : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
+ if (idx->index2[tid].n > 0) {
+ min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+ : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
+ if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+ int n = beg>>TAD_LIDX_SHIFT;
+ if (n > idx->index2[tid].n) n = idx->index2[tid].n;
+ for (i = n - 1; i >= 0; --i)
+ if (idx->index2[tid].offset[i] != 0) break;
+ if (i >= 0) min_off = idx->index2[tid].offset[i];
+ }
+ } else min_off = 0; // tabix 0.1.2 may produce such index files
for (i = n_off = 0; i < n_bins; ++i) {
if ((k = kh_get(i, index, bins[i])) != kh_end(index))
n_off += kh_value(index, k).n;
}
if (n_off == 0) {
- free(bins); return 0;
+ free(bins); return iter;
}
off = (pair64_t*)calloc(n_off, 16);
for (i = n_off = 0; i < n_bins; ++i) {
n_off = l + 1;
}
}
- *cnt_off = n_off;
- return off;
+ iter->n_off = n_off; iter->off = off;
+ return iter;
}
-int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
+const char *ti_iter_read(ti_iter_t iter, int *len)
{
- int n_off;
- pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
- if (off == 0) return 0;
- {
- // retrive alignments
- uint64_t curr_off;
- int i, ret, n_seeks;
- kstring_t *str = calloc(1, sizeof(kstring_t));
- n_seeks = 0; i = -1; curr_off = 0;
- for (;;) {
- if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
- if (i == n_off - 1) break; // no more chunks
- if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
- if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
- bgzf_seek(fp, off[i+1].u, SEEK_SET);
- curr_off = bgzf_tell(fp);
- ++n_seeks;
- }
- ++i;
+ if (iter->finished) return 0;
+ if (iter->from_first) {
+ int ret;
+ if ((ret = ti_readline(iter->fp, &iter->str)) < 0) {
+ iter->finished = 1;
+ return 0;
+ } else {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ }
+ if (iter->n_off == 0) return 0;
+ while (1) {
+ int ret;
+ if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+ if (iter->i == iter->n_off - 1) break; // no more chunks
+ if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
+ if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+ bgzf_seek(iter->fp, iter->off[iter->i+1].u, SEEK_SET);
+ iter->curr_off = bgzf_tell(iter->fp);
}
- if ((ret = ti_readline(fp, str)) >= 0) {
- ti_intv_t intv;
- curr_off = bgzf_tell(fp);
- if (str->s[0] == idx->conf.meta_char) continue;
- get_intv((ti_index_t*)idx, str, &intv);
- if (intv.tid != tid || intv.beg >= end) break; // no need to proceed
- else if (is_overlap(beg, end, intv.beg, intv.end)) func(str->l, str->s, data);
- } else break; // end of file
+ ++iter->i;
}
-// fprintf(stderr, "[ti_fetch] # seek calls: %d\n", n_seeks);
- free(str->s); free(str);
+ if ((ret = ti_readline(iter->fp, &iter->str)) >= 0) {
+ ti_intv_t intv;
+ iter->curr_off = bgzf_tell(iter->fp);
+ if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
+ get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
+ if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
+ else if (intv.end > iter->beg && iter->end > intv.beg) {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ } else break; // end of file
+ }
+ iter->finished = 1;
+ return 0;
+}
+
+void ti_iter_destroy(ti_iter_t iter)
+{
+ if (iter) {
+ free(iter->str.s); free(iter->off);
+ free(iter);
}
- free(off);
+}
+
+int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
+{
+ ti_iter_t iter;
+ const char *s;
+ int len;
+ iter = ti_query(fp, idx, tid, beg, end);
+ while ((s = ti_iter_read(iter, &len)) != 0)
+ func(len, s, data);
+ ti_iter_destroy(iter);
return 0;
}
projects / tabix.git / blobdiff