added mt comression to merge

diff --git a/bam_sort.c b/bam_sort.c
index 2c2b83d20d41047d3680a243762d0f1b95a0509d..f436fb9d80bcbe9227bddf14f75dc5b1660898bf 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -89,8 +89,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
   @discussion Padding information may NOT correctly maintained. This
   function is NOT thread safe.
  */
-int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
-                                       int flag, const char *reg)
+int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads)
 {
        bamFile fpout, *fp;
        heap1_t *heap;
@@ -222,6 +221,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
        }
        bam_header_write(fpout, hout);
        bam_header_destroy(hout);
+       if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);
 
        ks_heapmake(heap, n, heap);
        while (heap->pos != HEAP_EMPTY) {
@@ -256,12 +256,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
        return 0;
 }
 
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
+{
+       return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0);
+}
+
 int bam_merge(int argc, char *argv[])
 {
-       int c, is_by_qname = 0, flag = 0, ret = 0;
+       int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0;
        char *fn_headers = NULL, *reg = 0;
 
-       while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
+       while ((c = getopt(argc, argv, "h:nru1R:f@:")) >= 0) {
                switch (c) {
                case 'r': flag |= MERGE_RG; break;
                case 'f': flag |= MERGE_FORCE; break;
@@ -270,6 +275,7 @@ int bam_merge(int argc, char *argv[])
                case '1': flag |= MERGE_LEVEL1; break;
                case 'u': flag |= MERGE_UNCOMP; break;
                case 'R': reg = strdup(optarg); break;
+               case '@': n_threads = atoi(optarg); break;
                }
        }
        if (optind + 2 >= argc) {
@@ -280,6 +286,7 @@ int bam_merge(int argc, char *argv[])
                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, "         -@ INT   number of BAM compression threads [0]\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");
                fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
@@ -295,7 +302,7 @@ int bam_merge(int argc, char *argv[])
                        return 1;
                }
        }
-       if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
+       if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads) < 0) ret = 1;
        free(reg);
        free(fn_headers);
        return ret;

diff --git a/sam_view.c b/sam_view.c
index f198591e9aabbe44f67ee35c1497d2e73d0a3d7d..b6896c908cb367c1083eb3fbe994fe3c83a753f4 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -290,6 +290,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
        fprintf(stderr, "         -c       print only the count of matching records\n");
        fprintf(stderr, "         -B       collapse the backward CIGAR operation\n");
+       fprintf(stderr, "         -@ INT   number of BAM compression threads [0]\n");
        fprintf(stderr, "         -L FILE  output alignments overlapping the input BED FILE [null]\n");
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");