multi-threading working on toy examples

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 18b12824a4c83e6ac8cc5a7f45fb7f6c14ff65be..b9bde44ebd4b6e28d03f909a2ee4c6cc586c43f1 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;
 
        /* 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': g_subsam = atof(optarg); break;
                case 'c': is_count = 1; break;
@@ -151,6 +151,7 @@ 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);
                }
        }
@@ -208,6 +209,7 @@ int main_samview(int argc, char *argv[])
                ret = 1;
                goto view_end;
        }
+       if (n_threads > 1) samthreads(out, n_threads, 16); 
        if (is_header_only) goto view_end; // no need to print alignments
 
        if (argc == optind + 1) { // convert/print the entire file