Merge branch 'master' into mt

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index ce1e1092b791386d27d8e88f61dee1ed8332dc3f..d1178ffd4dd36c8805ef00230c51ff161af226c6 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -119,14 +119,14 @@ static int usage(int is_long_help);
 int main_samview(int argc, char *argv[])
 {
        int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
-       int of_type = BAM_OFDEC, is_long_help = 0;
+       int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
        int count = 0;
        samfile_t *in = 0, *out = 0;
        char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:")) >= 0) {
+       while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:")) >= 0) {
                switch (c) {
                case 's':
                        if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
@@ -157,6 +157,7 @@ int main_samview(int argc, char *argv[])
                case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
                case 'B': bam_no_B = 1; break;
                case 'Q': g_qual_scale = atoi(optarg); break;
+               case '@': n_threads = strtol(optarg, 0, 0); break;
                default: return usage(is_long_help);
                }
        }
@@ -214,6 +215,7 @@ int main_samview(int argc, char *argv[])
                ret = 1;
                goto view_end;
        }
+       if (n_threads > 1) samthreads(out, n_threads, 256); 
        if (is_header_only) goto view_end; // no need to print alignments
 
        if (argc == optind + 1) { // convert/print the entire file
@@ -294,6 +296,7 @@ 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");