New upstream release.

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index f60a6f874b106f03c655d1207dddf21c4df7fc48..9610a2656031657b796abc68bf32c1b6f1564745 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -172,19 +172,23 @@ bam_index_t *bam_index_core(bamFile fp)
 
        save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
        save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
-    n_mapped = n_unmapped = n_no_coor = off_end = 0;
+       n_mapped = n_unmapped = n_no_coor = off_end = 0;
        off_beg = off_end = bam_tell(fp);
        while ((ret = bam_read1(fp, b)) >= 0) {
                if (c->tid < 0) ++n_no_coor;
-               if (last_tid != c->tid) { // change of chromosomes
+               if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
                        last_tid = c->tid;
                        last_bin = 0xffffffffu;
-               } else if (last_coor > c->pos) {
+               } else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+                       fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+                                       bam1_qname(b), last_tid+1, c->tid+1);
+                       return NULL;
+               } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
                        fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
                                        bam1_qname(b), last_coor, c->pos, c->tid+1);
-                       exit(1);
+                       return NULL;
                }
-               if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+               if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
                if (c->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);
@@ -203,7 +207,7 @@ bam_index_t *bam_index_core(bamFile fp)
                if (bam_tell(fp) <= last_off) {
                        fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
                                        (unsigned long long)bam_tell(fp), (unsigned long long)last_off);
-                       exit(1);
+                       return NULL;
                }
                if (c->flag & BAM_FUNMAP) ++n_unmapped;
                else ++n_mapped;
@@ -212,13 +216,20 @@ 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));
-               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);
-       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");
+                               return NULL;
+                       }
+               }
+       }
        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;
@@ -466,6 +477,10 @@ int bam_index_build2(const char *fn, const char *_fnidx)
        }
        idx = bam_index_core(fp);
        bam_close(fp);
+       if(idx == 0) {
+               fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+               return -1;
+       }
        if (_fnidx == 0) {
                fnidx = (char*)calloc(strlen(fn) + 5, 1);
                strcpy(fnidx, fn); strcat(fnidx, ".bai");
@@ -698,6 +713,7 @@ 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);
+       bam_iter_destroy(iter);
        bam_destroy1(b);
        return (ret == -1)? 0 : ret;
 }