index = idx->index[i];
for (k = kh_begin(index); k != kh_end(index); ++k) {
bam_binlist_t *p;
- if (!kh_exist(index, k)) continue;
+ if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue;
p = &kh_value(index, k);
m = 0;
for (l = 1; l < p->n; ++l) {
bam_index_t *idx;
bam_header_t *header;
bamFile fp;
- int i, no_stats = 0;
+ int i;
if (argc < 2) {
fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
return 1;
k = kh_get(i, h, BAM_MAX_BIN);
if (k != kh_end(h))
printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
- else no_stats = 1;
+ else printf("\t0\t0");
putchar('\n');
}
- printf("*\t0");
- if (!no_stats) printf("\t0\t%llu", (long long)idx->n_no_coor);
- putchar('\n');
+ printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
bam_header_destroy(header);
bam_index_destroy(idx);
return 0;
}
}
free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
{
- if (iter->finished) return -1;
- if (iter->from_first) {
- int ret = bam_read1(fp, b);
- if (ret < 0) iter->finished = 1;
+ int ret;
+ if (iter && iter->finished) return -1;
+ if (iter == 0 || iter->from_first) {
+ ret = bam_read1(fp, b);
+ if (ret < 0 && iter) iter->finished = 1;
return ret;
}
if (iter->off == 0) return -1;
for (;;) {
- 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 == iter->n_off - 1) { ret = -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
bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
}
++iter->i;
}
- if ((ret = bam_read1(fp, b)) > 0) {
+ if ((ret = bam_read1(fp, b)) >= 0) {
iter->curr_off = bam_tell(fp);
- if (b->core.tid != iter->tid || b->core.pos >= iter->end) break; // no need to proceed
+ if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
+ ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
+ break;
+ }
else if (is_overlap(iter->beg, iter->end, b)) return ret;
- } else break; // end of file
+ } else break; // end of file or error
}
iter->finished = 1;
- return -1;
+ return ret;
}
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
{
+ int ret;
bam_iter_t iter;
bam1_t *b;
b = bam_init1();
iter = bam_iter_query(idx, tid, beg, end);
- while (bam_iter_read(fp, iter, b) >= 0) func(b, data);
+ while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+ bam_iter_destroy(iter);
bam_destroy1(b);
- return 0;
+ return (ret == -1)? 0 : ret;
}