typedef khash_t(rg) *rghash_t;
-rghash_t g_rghash = 0;
+static rghash_t g_rghash = 0;
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
static char *g_library, *g_rg;
static int g_sol2sanger_tbl[128];
+static void *g_bed;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
static void sol2sanger(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_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
+ return 1;
if (g_rg || g_rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
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, slx2sngr = 0, is_count = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
int of_type = BAM_OFDEC, is_long_help = 0;
int count = 0;
samfile_t *in = 0, *out = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
switch (c) {
case 'c': is_count = 1; break;
case 'C': slx2sngr = 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 'u': compress_level = 0; break;
+ case '1': compress_level = 1; break;
case 'l': g_library = strdup(optarg); break;
+ case 'L': g_bed = bed_read(optarg); break;
case 'r': g_rg = strdup(optarg); break;
case 'R': fn_rg = strdup(optarg); break;
case 'x': of_type = BAM_OFHEX; break;
default: return usage(is_long_help);
}
}
- if (is_uncompressed) is_bamout = 1;
+ if (compress_level >= 0) is_bamout = 1;
if (is_header_only) is_header = 1;
if (is_bamout) strcat(out_mode, "b");
else {
}
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
- if (is_uncompressed) strcat(out_mode, "u");
+ if (compress_level >= 0) {
+ char tmp[2];
+ tmp[0] = compress_level + '0'; tmp[1] = '\0';
+ strcat(out_mode, tmp);
+ }
if (argc == optind) return usage(is_long_help); // potential memory leak...
// read the list of read groups
}
// close files, free and return
free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+ if (g_bed) bed_destroy(g_bed);
if (g_rghash) {
khint_t k;
for (k = 0; k < kh_end(g_rghash); ++k)
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, " -1 fast compression (force -b)\n");
fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
fprintf(stderr, " -c print only the count of matching records\n");
+ fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\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");