#include "sam.h"
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static char *g_library;
+
+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) {
+ uint8_t *s = bam_aux_get(b, "RG");
+ if (s) {
+ const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ } else return 1;
+ } else return 0;
+}
// 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(((samfile_t*)data)->header, b))
+ samwrite((samfile_t*)data, b);
return 0;
}
int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
samfile_t *in = 0, *out = 0;
- char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 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:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:")) >= 0) {
switch (c) {
case 'S': is_bamin = 0; break;
- case 'b': strcat(out_mode, "b"); break;
+ case 'b': is_bamout = 1; 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 '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;
+ case 'u': is_uncompressed = 1; break;
+ case 'l': g_library = strdup(optarg); break;
default: return usage();
}
}
+ if (is_uncompressed) is_bamout = 1;
if (is_header_only) is_header = 1;
+ if (is_bamout) strcat(out_mode, "b");
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();
// open file handlers
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(in->header, 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
view_end:
// close files, free and return
- free(fn_list); free(fn_out);
+ free(fn_list); free(fn_out); free(g_library);
samclose(in);
samclose(out);
return ret;
fprintf(stderr, " -h print header for the SAM output\n");
fprintf(stderr, " -H print header only (no alignments)\n");
fprintf(stderr, " -S input is SAM\n");
+ fprintf(stderr, " -u uncompressed BAM output (force -b)\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");