Merge branch 'master' into mt

diff --cc sam_view.c
index b6896c908cb367c1083eb3fbe994fe3c83a753f4,ce1e1092b791386d27d8e88f61dee1ed8332dc3f..d1178ffd4dd36c8805ef00230c51ff161af226c6
--- 1/sam_view.c
--- 2/sam_view.c
+++ b/sam_view.c
@@@ -119,16 -119,22 +119,22 @@@ 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;
+       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': g_subsam = atof(optarg); break;
+               case 's':
+                       if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
+                               srand(g_subsam_seed);
+                               g_subsam_seed = rand();
+                       }
+                       g_subsam_frac = strtod(q, &q);
+                       break;
                case 'c': is_count = 1; break;
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;