+++ /dev/null
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <zlib.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;
-} tmp_stack_t;
-
-static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
-{
- if (stack->n == stack->max) {
- stack->max = stack->max? stack->max<<1 : 0x10000;
- stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
- }
- stack->a[stack->n++] = b;
-}
-
-static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
-{
- int i;
- for (i = 0; i != stack->n; ++i) {
- samwrite(out, stack->a[i]);
- bam_destroy1(stack->a[i]);
- }
- stack->n = 0;
-}
-
-static void clear_del_set(khash_t(name) *del_set)
-{
- khint_t k;
- for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
- if (kh_exist(del_set, k))
- free((char*)kh_key(del_set, k));
- kh_clear(name, del_set);
-}
-
-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)
-{
- bam1_t *b;
- int last_tid = -1, last_pos = -1;
- tmp_stack_t stack;
- khint_t k;
- khash_t(lib) *aux;
- khash_t(name) *del_set;
-
- aux = kh_init(lib);
- del_set = kh_init(name);
- b = bam_init1();
- memset(&stack, 0, sizeof(tmp_stack_t));
-
- kh_resize(name, del_set, 4 * BUFFER_SIZE);
- while (samread(in, b) >= 0) {
- bam1_core_t *c = &b->core;
- if (c->tid != last_tid || last_pos != c->pos) {
- dump_best(&stack, out); // write the result
- clear_best(aux, BUFFER_SIZE);
- if (c->tid != last_tid) {
- 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
- 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", in->header->target_name[c->tid]);
- }
- }
- if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
- 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;
- 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(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(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 samwrite(out, b);
- }
- last_pos = c->pos;
- }
-
- 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);
- free(stack.a);
- bam_destroy1(b);
-}
-
-void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
-
-int bam_rmdup(int argc, char *argv[])
-{
- 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 = 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;
- }
- if (is_se) bam_rmdupse_core(in, out, force_se);
- else bam_rmdup_core(in, out);
- samclose(in); samclose(out);
- return 0;
-}
projects / pysam.git / blobdiff