* samtools-0.1.4-11 (r346)

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 95a52c82513c41349afbc86d89249c068b3d20c4..e96afeefcdd4bc957f2879ad3ba3001a55ad57a8 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -5,17 +5,20 @@
 #include "sam.h"
 
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
-static char *g_library;
+static char *g_library, *g_rg;
 
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
        if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
                return 1;
-       if (g_library) {
+       if (g_library || g_rg) {
                uint8_t *s = bam_aux_get(b, "RG");
                if (s) {
-                       const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
-                       return (p && strcmp(p, g_library) == 0)? 0 : 1;
+                       if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
+                       if (g_library) {
+                               const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
+                               return (p && strcmp(p, g_library) == 0)? 0 : 1;
+                       } return 1;
                } else return 1;
        } else return 0;
 }
@@ -38,7 +41,7 @@ int main_samview(int argc, char *argv[])
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:")) >= 0) {
                switch (c) {
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -51,6 +54,7 @@ int main_samview(int argc, char *argv[])
                case 'q': g_min_mapQ = atoi(optarg); break;
                case 'u': is_uncompressed = 1; break;
                case 'l': g_library = strdup(optarg); break;
+               case 'r': g_rg = strdup(optarg); break;
                default: return usage();
                }
        }
@@ -104,7 +108,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
        // close files, free and return
-       free(fn_list); free(fn_out); free(g_library);
+       free(fn_list); free(fn_out); free(g_library); free(g_rg);
        samclose(in);
        samclose(out);
        return ret;
@@ -124,6 +128,8 @@ static int usage()
        fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
        fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");
        fprintf(stderr, "         -q INT   minimum mapping quality [0]\n");
+       fprintf(stderr, "         -l STR   only output reads in library STR [null]\n");
+       fprintf(stderr, "         -r STR   only output reads in read group STR [null]\n");
        fprintf(stderr, "\n\
 Notes:\n\
 \n\