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 9610a2656031657b796abc68bf32c1b6f1564745..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;
@@ -188,6 +193,15 @@ bam_index_t *bam_index_core(bamFile fp)
                                        bam1_qname(b), last_coor, c->pos, c->tid+1);
                        return NULL;
                }
+               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
@@ -459,6 +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");
@@ -489,6 +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);