#include <string.h>
#include <stdio.h>
#include <unistd.h>
+#include "sam_header.h"
#include "sam.h"
#include "faidx.h"
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;
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");
goto view_end;
}
if (in->header == 0) {
- fprintf(stderr, "[main_samview] fail to read SAM header.\n");
+ fprintf(stderr, "[main_samview] fail to read the header.\n");
goto view_end;
}
if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
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");