Update 'samtools depad' help text regarding FASTA reference file

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 51c27014da0f9f010b563db92112f71d7ad6bdd6..35fb5b666e6d748804091d979342d1b67566412e 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -154,14 +154,19 @@ bam_index_t *bam_index_core(bamFile fp)
        bam_header_t *h;
        int i, ret;
        bam_index_t *idx;
-       uint32_t last_bin, save_bin;
+       uint32_t last_bin, save_bin, recalculated_bin;
        int32_t last_coor, last_tid, save_tid;
        bam1_core_t *c;
        uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
+       h = bam_header_read(fp);
+       if(h == 0) {
+           fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+           return NULL;
+       }
+
        idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
        b = (bam1_t*)calloc(1, sizeof(bam1_t));
-       h = bam_header_read(fp);
        c = &b->core;
 
        idx->n = h->n_targets;
@@ -172,19 +177,32 @@ 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) {
+                       recalculated_bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+                       if (c->bin != recalculated_bin) {
+                               fprintf(stderr, "[bam_index_core] read '%s' mapped at POS %d has BIN %d but should be %d\n",
+                                       bam1_qname(b), c->pos + 1, c->bin, recalculated_bin);
+                               fprintf(stderr, "[bam_index_core] Fix it by using BAM->SAM->BAM to force a recalculation of the BIN field\n");
+                               return NULL;
+                       }
+               }
+               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 +221,7 @@ 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;
@@ -222,7 +240,7 @@ bam_index_t *bam_index_core(bamFile fp)
                        ++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);
+                               return NULL;
                        }
                }
        }
@@ -455,6 +473,7 @@ bam_index_t *bam_index_load(const char *fn)
                strcat(strcpy(fnidx, fn), ".bai");
                fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
                download_from_remote(fnidx);
+        free(fnidx);
                idx = bam_index_load_local(fn);
        }
        if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
@@ -473,6 +492,10 @@ 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");
@@ -481,6 +504,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
        if (fpidx == 0) {
                fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
                free(fnidx);
+        bam_index_destroy(idx);
                return -1;
        }
        bam_index_save(idx, fpidx);