bcftools.1 and samtools.1 were merged in upstream release 0.1.17.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 94970b5f9e1c0f9ef76a73fcdda12e8a633a3ff2..abf8d4f6caf6dfeb25af423784934d78fe677478 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -71,6 +71,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
 #define MERGE_RG     1
 #define MERGE_UNCOMP 2
 #define MERGE_LEVEL1 4
+#define MERGE_FORCE  8
 
 /*!
   @abstract    Merge multiple sorted BAM.
@@ -203,7 +204,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                h->i = i;
                h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
                if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
-                       h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
+                       h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
                        h->idx = idx++;
                }
                else h->pos = HEAP_EMPTY;
@@ -228,7 +229,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                }
                bam_write1_core(fpout, &b->core, b->data_len, b->data);
                if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
-                       heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
+                       heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
                        heap->idx = idx++;
                } else if (j == -1) {
                        heap->pos = HEAP_EMPTY;
@@ -256,9 +257,10 @@ int bam_merge(int argc, char *argv[])
        int c, is_by_qname = 0, flag = 0, ret = 0;
        char *fn_headers = NULL, *reg = 0;
 
-       while ((c = getopt(argc, argv, "h:nru1R:")) >= 0) {
+       while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
                switch (c) {
                case 'r': flag |= MERGE_RG; break;
+               case 'f': flag |= MERGE_FORCE; break;
                case 'h': fn_headers = strdup(optarg); break;
                case 'n': is_by_qname = 1; break;
                case '1': flag |= MERGE_LEVEL1; break;
@@ -272,6 +274,7 @@ int bam_merge(int argc, char *argv[])
                fprintf(stderr, "Options: -n       sort by read names\n");
                fprintf(stderr, "         -r       attach RG tag (inferred from file names)\n");
                fprintf(stderr, "         -u       uncompressed BAM output\n");
+               fprintf(stderr, "         -f       overwrite the output BAM if exist\n");
                fprintf(stderr, "         -1       compress level 1\n");
                fprintf(stderr, "         -R STR   merge file in the specified region STR [all]\n");
                fprintf(stderr, "         -h FILE  copy the header in FILE to <out.bam> [in1.bam]\n\n");
@@ -280,6 +283,14 @@ int bam_merge(int argc, char *argv[])
                fprintf(stderr, "      the header dictionary in merging.\n\n");
                return 1;
        }
+       if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
+               FILE *fp = fopen(argv[optind], "rb");
+               if (fp != NULL) {
+                       fclose(fp);
+                       fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
+                       return 1;
+               }
+       }
        if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
        free(reg);
        free(fn_headers);
@@ -292,8 +303,8 @@ static inline int bam1_lt(const bam1_p a, const bam1_p b)
 {
        if (g_is_by_qname) {
                int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
-               return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos))));
-       } else return (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos));
+               return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
+       } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
 }
 KSORT_INIT(sort, bam1_p, bam1_lt)