static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+#define __g_skip_aln(b) (((b)->core.qual < g_min_mapQ) || ((b->core.flag & g_flag_on) != g_flag_on) \
+ || (b->core.flag & g_flag_off))
+
// callback function for bam_fetch()
static int view_func(const bam1_t *b, void *data)
{
- if (b->core.qual < g_min_mapQ) return 0;
- if (g_flag_on && (b->core.flag & g_flag_on) == 0) return 0;
- if (b->core.flag & g_flag_off) return 0;
- samwrite((samfile_t*)data, b);
+ if (!__g_skip_aln(b)) samwrite((samfile_t*)data, b);
return 0;
}
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "bt:hHo:q:f:F:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:")) >= 0) {
switch (c) {
+ case 'S': is_bamin = 0; break;
case 'b': strcat(out_mode, "b"); break;
case 't': fn_list = strdup(optarg); is_bamin = 0; break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'f': g_flag_on = strtol(optarg, 0, 0); break;
- case 'F': g_flag_on = strtol(optarg, 0, 0); break;
+ case 'F': g_flag_off = strtol(optarg, 0, 0); break;
case 'q': g_min_mapQ = atoi(optarg); break;
default: return usage();
}
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) // read one alignment from `in'
- samwrite(out, b); // write the alignment to `out'
+ if (!__g_skip_aln(b))
+ samwrite(out, b); // write the alignment to `out'
if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
bam_destroy1(b);
} else { // retrieve alignments in specified regions
fprintf(stderr, "Options: -b output BAM\n");
fprintf(stderr, " -h print header for the SAM output\n");
fprintf(stderr, " -H print header only (no alignments)\n");
- fprintf(stderr, " -t FILE list of reference names and lengths, assuming SAM input [null]\n");
+ fprintf(stderr, " -S input is SAM\n");
+ fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");