return 0;
}
-static int usage(void);
+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, is_uncompressed = 0, is_bamout = 0;
- int of_type = BAM_OFDEC;
+ int of_type = BAM_OFDEC, is_long_help = 0;
samfile_t *in = 0, *out = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?")) >= 0) {
switch (c) {
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
case 'r': g_rg = strdup(optarg); break;
case 'x': of_type = BAM_OFHEX; break;
case 'X': of_type = BAM_OFSTR; break;
- default: return usage();
+ case '?': is_long_help = 1; break;
+ default: return usage(is_long_help);
}
}
if (is_uncompressed) is_bamout = 1;
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
if (is_uncompressed) strcat(out_mode, "u");
- if (argc == optind) return usage();
+ if (argc == optind) return usage(is_long_help);
// open file handlers
if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
return ret;
}
-static int usage()
+static int usage(int is_long_help)
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\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\
+ fprintf(stderr, " -? longer help\n");
+ fprintf(stderr, "\n");
+ if (is_long_help)
+ fprintf(stderr, "Notes:\n\
\n\
1. By default, this command assumes the file on the command line is in\n\
the BAM format and it prints the alignments in SAM. If `-t' is\n\
\n\
5. Option `-u' is preferred over `-b' when the output is piped to\n\
another samtools command.\n\
+\n\
+ 6. In a string FLAG, each character represents one bit with\n\
+ p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
+ U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
+ 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
+ f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
+ `-X' are samtools-C specific. Picard and older samtools do not\n\
+ support HEX or string flags.\n\
\n");
return 1;
}