r199: support retrieving reads w/o coordinates

samtools · Aug 31, 2012 · c8bdd76 · c8bdd76
1 parent 0a200b4
commit c8bdd76
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Showing 2 changed files with 44 additions and 17 deletions.
diff --git a/htslib/hts.c b/htslib/hts.c
@@ -666,12 +666,28 @@ hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end)
  hts_itr_t *iter = 0;
 
  if (tid < 0) {
+ uint64_t off0 = (uint64_t)-1;
+ khint_t k;
  if (tid == HTS_IDX_START) {
+ if (idx->n > 0) {
+ bidx = idx->bidx[0];
+ k = kh_get(bin, bidx, idx->n_bins + 1);
+ if (k == kh_end(bidx)) return 0;
+ off0 = kh_val(bidx, k).list[0].u;
+ } else return 0;
+ } else if (tid == HTS_IDX_NOCOOR) {
+ if (idx->n > 0) {
+ bidx = idx->bidx[idx->n - 1];
+ k = kh_get(bin, bidx, idx->n_bins + 1);
+ if (k == kh_end(bidx)) return 0;
+ off0 = kh_val(bidx, k).list[0].v;
+ } else return 0;
+ } else off0 = 0;
+ if (off0 != (uint64_t)-1) {
  iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t));
- iter->from_first = 1;
+ iter->read_rest = 1;
+ iter->curr_off = off0;
  return iter;
- } else if (tid == HTS_IDX_NOCOOR) {
- return 0; // not implemented
  } else return 0;
  }
  if (beg < 0) beg = 0;
@@ -769,23 +785,33 @@ hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f g
 {
  int tid, beg, end;
  char *q, *tmp;
- q = (char*)hts_parse_reg(reg, &beg, &end);
- tmp = (char*)alloca(q - reg + 1);
- strncpy(tmp, reg, q - reg);
- tmp[q - reg] = 0;
- if ((tid = getid(hdr, tmp)) < 0)
- tid = getid(hdr, reg);
- if (tid < 0) return 0;
- return hts_itr_query(idx, tid, beg, end);
+ if (strcmp(reg, "*")) {
+ q = (char*)hts_parse_reg(reg, &beg, &end);
+ tmp = (char*)alloca(q - reg + 1);
+ strncpy(tmp, reg, q - reg);
+ tmp[q - reg] = 0;
+ if ((tid = getid(hdr, tmp)) < 0)
+ tid = getid(hdr, reg);
+ if (tid < 0) return 0;
+ return hts_itr_query(idx, tid, beg, end);
+ } else return hts_itr_query(idx, HTS_IDX_NOCOOR, 0, 0);
 }
 
 int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, hts_readrec_f readrec, void *hdr)
 {
- int ret;
+ int ret, tid, beg, end;
  if (iter && iter->finished) return -1;
+ if (iter->read_rest) {
+ if (iter->curr_off) { // seek to the start
+ bgzf_seek(fp, iter->curr_off, SEEK_SET);
+ iter->curr_off = 0; // only seek once
+ }
+ ret = readrec(fp, hdr, r, &tid, &beg, &end);
+ if (ret < 0) iter->finished = 1;
+ return ret;
+ }
  if (iter->off == 0) return -1;
  for (;;) {
- int tid, beg, end;
  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) { ret = -1; break; } // no more chunks
  if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek

diff --git a/htslib/hts.h b/htslib/hts.h
@@ -1,7 +1,7 @@
 #ifndef HTS_H
 #define HTS_H
 
-#define HTS_VERSION "r198"
+#define HTS_VERSION "r199"
 
 #include <stdint.h>
 #include "bgzf.h"
@@ -60,8 +60,9 @@ extern "C" {
  * Indexing *
  ************/
 
-#define HTS_IDX_NOCOOR (-1)
-#define HTS_IDX_START (-2)
+#define HTS_IDX_NOCOOR (-2)
+#define HTS_IDX_START (-3)
+#define HTS_IDX_REST (-4)
 
 #define HTS_FMT_CSI 0
 #define HTS_FMT_BAI 1
@@ -75,7 +76,7 @@ typedef struct {
 } hts_pair64_t;
 
 typedef struct {
- uint32_t from_first:1, finished:1, dummy:30;
+ uint32_t read_rest:1, finished:1, dummy:29;
  int tid, beg, end, n_off, i;
  uint64_t curr_off;
  hts_pair64_t *off;