#include "sam.h"
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static char *g_library, *g_rg;
-#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))
+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 || g_rg) {
+ uint8_t *s = bam_aux_get(b, "RG");
+ 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));
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ } return 1;
+ } else return 1;
+ } else return 0;
+}
// callback function for bam_fetch()
static int view_func(const bam1_t *b, void *data)
{
- if (!__g_skip_aln(b)) samwrite((samfile_t*)data, b);
+ if (!__g_skip_aln(((samfile_t*)data)->header, 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, "Sbt:hHo:q:f:F:u")) >= 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;
case 'F': g_flag_off = strtol(optarg, 0, 0); break;
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();
}
}
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) // read one alignment from `in'
- if (!__g_skip_aln(b))
+ if (!__g_skip_aln(in->header, b))
samwrite(out, b); // write the alignment to `out'
if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
bam_destroy1(b);
view_end:
// close files, free and return
- free(fn_list); free(fn_out);
+ free(fn_list); free(fn_out); free(g_library); free(g_rg);
samclose(in);
samclose(out);
return ret;
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\
4. A region should be presented in one of the following formats:\n\
`chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
specified, the input alignment file must be an indexed BAM file.\n\
+\n\
+ 5. Option `-u' is preferred over `-b' when the output is piped to\n\
+ another samtools command.\n\
\n");
return 1;
}