1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
|
#include "pysam.h"
#include <math.h>
#include "sam.h"
#include "khash.h"
#include "klist.h"
#define QUEUE_CLEAR_SIZE 0x100000
#define MAX_POS 0x7fffffff
typedef struct {
int endpos;
uint32_t score:31, discarded:1;
bam1_t *b;
} elem_t, *elem_p;
#define __free_elem(p) bam_destroy1((p)->data.b)
KLIST_INIT(q, elem_t, __free_elem)
typedef klist_t(q) queue_t;
KHASH_MAP_INIT_INT(best, elem_p)
typedef khash_t(best) besthash_t;
typedef struct {
uint64_t n_checked, n_removed;
besthash_t *left, *rght;
} lib_aux_t;
KHASH_MAP_INIT_STR(lib, lib_aux_t)
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->left = kh_init(best);
q->rght = kh_init(best);
q->n_checked = q->n_removed = 0;
return q;
} else return &kh_val(aux, k);
}
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;
}
static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
{
elem_t *p = kl_pushp(q, queue);
p->discarded = 0;
p->endpos = endpos; p->score = score;
if (p->b == 0) p->b = bam_init1();
bam_copy1(p->b, b);
return p;
}
static void clear_besthash(besthash_t *h, int32_t pos)
{
khint_t k;
for (k = kh_begin(h); k != kh_end(h); ++k)
if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
kh_del(best, h, k);
}
static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
{
if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
khint_t k;
while (1) {
elem_t *q;
if (queue->head == queue->tail) break;
q = &kl_val(queue->head);
if (q->discarded) {
q->b->data_len = 0;
kl_shift(q, queue, 0);
continue;
}
if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
samwrite(out, q->b);
q->b->data_len = 0;
kl_shift(q, queue, 0);
}
for (k = kh_begin(h); k != kh_end(h); ++k) {
if (kh_exist(h, k)) {
clear_besthash(kh_val(h, k).left, pos);
clear_besthash(kh_val(h, k).rght, pos);
}
}
}
}
void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
{
bam1_t *b;
queue_t *queue;
khint_t k;
int last_tid = -2;
khash_t(lib) *aux;
aux = kh_init(lib);
b = bam_init1();
queue = kl_init(q);
while (samread(in, b) >= 0) {
bam1_core_t *c = &b->core;
int endpos = bam_calend(c, bam1_cigar(b));
int score = sum_qual(b);
if (last_tid != c->tid) {
if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
last_tid = c->tid;
} else dump_alignment(out, queue, c->pos, aux);
if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
push_queue(queue, b, endpos, score);
} else {
const char *lib;
lib_aux_t *q;
besthash_t *h;
uint32_t key;
int ret;
lib = bam_get_library(in->header, b);
q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
++q->n_checked;
h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
k = kh_put(best, h, key, &ret);
if (ret == 0) { // in the hash table
elem_t *p = kh_val(h, k);
++q->n_removed;
if (p->score < score) {
if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
p->discarded = 1;
kh_val(h, k) = push_queue(queue, b, endpos, score);
} else { // replace
p->score = score; p->endpos = endpos;
bam_copy1(p->b, b);
}
} // otherwise, discard the alignment
} else kh_val(h, k) = push_queue(queue, b, endpos, score);
}
}
dump_alignment(out, queue, MAX_POS, aux);
for (k = kh_begin(aux); k != kh_end(aux); ++k) {
if (kh_exist(aux, k)) {
lib_aux_t *q = &kh_val(aux, k);
fprintf(pysamerr, "[bam_rmdupse_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(best, q->left); kh_destroy(best, q->rght);
free((char*)kh_key(aux, k));
}
}
kh_destroy(lib, aux);
bam_destroy1(b);
kl_destroy(q, queue);
}
|
