* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index c2056bafecf266904172ddf68f40266329ba8bea..105b532b4d562e04a652af43761a23a92572d06d 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -2,6 +2,7 @@
 #include <string.h>
 #include <stdio.h>
 #include <unistd.h>
+#include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"
 
@@ -17,7 +18,7 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
                if (s) {
                        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));
+                               const char *p = sam_tbl_get(h->rg2lib, (const char*)(s + 1));
                                return (p && strcmp(p, g_library) == 0)? 0 : 1;
                        } return 1;
                } else return 1;
@@ -77,9 +78,7 @@ int main_samview(int argc, char *argv[])
        if (argc == optind) return usage(is_long_help);
 
        // generate the fn_list if necessary
-       if (fn_list && fn_ref) {
-               fprintf(stderr, "[main_samview] both -t and -T are applied. -T is ignored.\n");
-       } else fn_list = samfaipath(fn_ref);
+       if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
        // open file handlers
        if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
                fprintf(stderr, "[main_samview] fail to open file for reading.\n");
@@ -142,7 +141,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -S       input is SAM\n");
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
-       fprintf(stderr, "         -X       output FLAG in stirng (samtools-C specific)\n");
+       fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\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");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");