typedef khash_t(rg) *rghash_t;
+// FIXME: we'd better use no global variables...
static rghash_t g_rghash = 0;
-static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0;
+static float g_subsam = -1;
static char *g_library, *g_rg;
static void *g_bed;
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
-static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
+static int process_aln(const bam_header_t *h, bam1_t *b)
{
+ if (g_qual_scale > 1) {
+ int i;
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i) {
+ int c = qual[i] * g_qual_scale;
+ qual[i] = c < 93? c : 93;
+ }
+ }
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_subsam > 0.) {
+ int x = (int)(g_subsam + .499);
+ uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
+ if (k%1024 / 1024.0 >= g_subsam - x) return 1;
+ }
if (g_rg || g_rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
// callback function for bam_fetch() that prints nonskipped records
static int view_func(const bam1_t *b, void *data)
{
- if (!__g_skip_aln(((samfile_t*)data)->header, b))
+ if (!process_aln(((samfile_t*)data)->header, (bam1_t*)b))
samwrite((samfile_t*)data, b);
return 0;
}
// callback function for bam_fetch() that counts nonskipped records
static int count_func(const bam1_t *b, void *data)
{
- if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+ if (!process_aln(((count_func_data_t*)data)->header, (bam1_t*)b)) {
(*((count_func_data_t*)data)->count)++;
}
return 0;
int main_samview(int argc, char *argv[])
{
int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
- int of_type = BAM_OFDEC, is_long_help = 0;
+ int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
int count = 0;
samfile_t *in = 0, *out = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:")) >= 0) {
+ while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:")) >= 0) {
switch (c) {
+ case 's': g_subsam = atof(optarg); break;
case 'c': is_count = 1; break;
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
case 'X': of_type = BAM_OFSTR; break;
case '?': is_long_help = 1; break;
case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+ case 'B': bam_no_B = 1; break;
+ case 'Q': g_qual_scale = atoi(optarg); break;
+ case '@': n_threads = strtol(optarg, 0, 0); break;
default: return usage(is_long_help);
}
}
ret = 1;
goto view_end;
}
+ if (n_threads > 1) samthreads(out, n_threads, 256);
if (is_header_only) goto view_end; // no need to print alignments
if (argc == optind + 1) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
- if (!__g_skip_aln(in->header, b)) {
+ if (!process_aln(in->header, b)) {
if (!is_count) samwrite(out, b); // write the alignment to `out'
count++;
}
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, " -B collapse the backward CIGAR operation\n");
+ fprintf(stderr, " -@ INT number of BAM compression threads [0]\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, " -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, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
fprintf(stderr, " -? longer help\n");
fprintf(stderr, "\n");
if (is_long_help)