#include <string.h>
#include <stdio.h>
#include <zlib.h>
-#include "bam.h"
+#include <unistd.h>
+#include "sam.h"
typedef bam1_t *bam1_p;
+
#include "khash.h"
KHASH_SET_INIT_STR(name)
KHASH_MAP_INIT_INT64(pos, bam1_p)
#define BUFFER_SIZE 0x40000
+typedef struct {
+ uint64_t n_checked, n_removed;
+ khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
typedef struct {
int n, max;
bam1_t **a;
stack->a[stack->n++] = b;
}
-static inline void dump_best(tmp_stack_t *stack, khash_t(pos) *best_hash, bamFile out)
+static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
{
int i;
for (i = 0; i != stack->n; ++i) {
- bam_write1(out, stack->a[i]);
+ samwrite(out, stack->a[i]);
bam_destroy1(stack->a[i]);
}
stack->n = 0;
- if (kh_size(best_hash) > BUFFER_SIZE) kh_clear(pos, best_hash);
}
static void clear_del_set(khash_t(name) *del_set)
kh_clear(name, del_set);
}
-void bam_rmdup_core(bamFile in, bamFile out)
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->n_checked = q->n_removed = 0;
+ q->best_hash = kh_init(pos);
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+ khint_t k;
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ if (kh_size(q->best_hash) >= max)
+ kh_clear(pos, q->best_hash);
+ }
+ }
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+void bam_rmdup_core(samfile_t *in, samfile_t *out)
{
- bam_header_t *header;
bam1_t *b;
int last_tid = -1, last_pos = -1;
- uint64_t n_checked = 0, n_removed = 0;
tmp_stack_t stack;
khint_t k;
- khash_t(pos) *best_hash;
+ khash_t(lib) *aux;
khash_t(name) *del_set;
-
- best_hash = kh_init(pos);
+
+ aux = kh_init(lib);
del_set = kh_init(name);
b = bam_init1();
memset(&stack, 0, sizeof(tmp_stack_t));
- header = bam_header_read(in);
- bam_header_write(out, header);
kh_resize(name, del_set, 4 * BUFFER_SIZE);
- kh_resize(pos, best_hash, 3 * BUFFER_SIZE);
- while (bam_read1(in, b) >= 0) {
+ while (samread(in, b) >= 0) {
bam1_core_t *c = &b->core;
if (c->tid != last_tid || last_pos != c->pos) {
- dump_best(&stack, best_hash, out); // write the result
+ dump_best(&stack, out); // write the result
+ clear_best(aux, BUFFER_SIZE);
if (c->tid != last_tid) {
- kh_clear(pos, best_hash);
+ clear_best(aux, 0);
if (kh_size(del_set)) { // check
fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
clear_del_set(del_set);
}
if ((int)c->tid == -1) { // append unmapped reads
- bam_write1(out, b);
- while (bam_read1(in, b) >= 0) bam_write1(out, b);
+ samwrite(out, b);
+ while (samread(in, b) >= 0) samwrite(out, b);
break;
}
last_tid = c->tid;
- fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
+ fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
}
}
if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
- bam_write1(out, b);
+ samwrite(out, b);
} else if (c->isize > 0) { // paired, head
uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+ const char *lib;
+ lib_aux_t *q;
int ret;
- ++n_checked;
- k = kh_put(pos, best_hash, key, &ret);
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ k = kh_put(pos, q->best_hash, key, &ret);
if (ret == 0) { // found in best_hash
- bam1_t *p = kh_val(best_hash, k);
- ++n_removed;
- if (p->core.qual < c->qual) { // the current alignment is better
+ bam1_t *p = kh_val(q->best_hash, k);
+ ++q->n_removed;
+ if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
bam_copy1(p, b); // replaced as b
} else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
if (ret == 0)
fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
} else { // not found in best_hash
- kh_val(best_hash, k) = bam_dup1(b);
- stack_insert(&stack, kh_val(best_hash, k));
+ kh_val(q->best_hash, k) = bam_dup1(b);
+ stack_insert(&stack, kh_val(q->best_hash, k));
}
} else { // paired, tail
k = kh_get(name, del_set, bam1_qname(b));
if (k != kh_end(del_set)) {
free((char*)kh_key(del_set, k));
kh_del(name, del_set, k);
- } else bam_write1(out, b);
+ } else samwrite(out, b);
}
last_pos = c->pos;
}
- dump_best(&stack, best_hash, out);
- bam_header_destroy(header);
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ dump_best(&stack, out);
+ fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(pos, q->best_hash);
+ free((char*)kh_key(aux, k));
+ }
+ }
+ kh_destroy(lib, aux);
+
clear_del_set(del_set);
kh_destroy(name, del_set);
- kh_destroy(pos, best_hash);
free(stack.a);
bam_destroy1(b);
- fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf\n", (long long)n_removed, (long long)n_checked,
- (double)n_removed/n_checked);
}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
+
int bam_rmdup(int argc, char *argv[])
{
- bamFile in, out;
- if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n");
+ int c, is_se = 0, force_se = 0;
+ samfile_t *in, *out;
+ while ((c = getopt(argc, argv, "sS")) >= 0) {
+ switch (c) {
+ case 's': is_se = 1; break;
+ case 'S': force_se = is_se = 1; break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+ fprintf(stderr, "Option: -s rmdup for SE reads\n");
+ fprintf(stderr, " -S treat PE reads as SE in rmdup (force -s)\n\n");
return 1;
}
- in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
- out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+ in = samopen(argv[optind], "rb", 0);
+ out = samopen(argv[optind+1], "wb", in->header);
if (in == 0 || out == 0) {
fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
return 1;
}
- bam_rmdup_core(in, out);
- bam_close(in);
- bam_close(out);
+ if (is_se) bam_rmdupse_core(in, out, force_se);
+ else bam_rmdup_core(in, out);
+ samclose(in); samclose(out);
return 0;
}
projects / samtools.git / blobdiff