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Imported Upstream version 0.1.13
[samtools.git]
/
bam_index.c
diff --git
a/bam_index.c
b/bam_index.c
index 1ad2e93e5051972b084513d5d7391c45c6cf7bf2..51c27014da0f9f010b563db92112f71d7ad6bdd6 100644
(file)
--- a/
bam_index.c
+++ b/
bam_index.c
@@
-212,13
+212,20
@@
bam_index_t *bam_index_core(bamFile fp)
}
if (save_tid >= 0) {
insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
}
if (save_tid >= 0) {
insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
- insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg,
off_end
);
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg,
bam_tell(fp)
);
insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
}
merge_chunks(idx);
fill_missing(idx);
insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
}
merge_chunks(idx);
fill_missing(idx);
- if (ret >= 0)
- while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+ if (ret >= 0) {
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ ++n_no_coor;
+ if (c->tid >= 0 && n_no_coor) {
+ fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+ exit(1);
+ }
+ }
+ }
if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
free(b->data); free(b);
idx->n_no_coor = n_no_coor;
if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
free(b->data); free(b);
idx->n_no_coor = n_no_coor;
@@
-608,6
+615,9
@@
bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
}
}
free(bins);
}
}
free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
@@
-695,6
+705,7
@@
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
b = bam_init1();
iter = bam_iter_query(idx, tid, beg, end);
while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
b = bam_init1();
iter = bam_iter_query(idx, tid, beg, end);
while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+ bam_iter_destroy(iter);
bam_destroy1(b);
return (ret == -1)? 0 : ret;
}
bam_destroy1(b);
return (ret == -1)? 0 : ret;
}