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#include "pysam.h"
#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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "\n");
fprintf(pysamerr, "Usage: samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
fprintf(pysamerr, "Option: -s rmdup for SE reads\n");
fprintf(pysamerr, " -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(pysamerr, "[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;
}
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