From: Heng Li <lh3@me.com>
Date: Tue, 20 Mar 2012 15:49:52 +0000 (-0400)
Subject: Merge branch 'master' into mt
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=185e80bd42cead0e5af6ae0c54ebb6d0b66ca47c

Merge branch 'master' into mt
---

185e80bd42cead0e5af6ae0c54ebb6d0b66ca47c
diff --cc sam_view.c
index b6896c9,ce1e109..d1178ff
--- a/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;