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#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include "bam.h"
#include "ksort.h"
#define TV_GAP 2
typedef struct __freenode_t {
uint32_t level:28, cnt:4;
struct __freenode_t *next;
} freenode_t, *freenode_p;
#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
KSORT_INIT(node, freenode_p, freenode_lt)
/* Memory pool, similar to the one in bam_pileup.c */
typedef struct {
int cnt, n, max;
freenode_t **buf;
} mempool_t;
static mempool_t *mp_init()
{
return (mempool_t*)calloc(1, sizeof(mempool_t));
}
static void mp_destroy(mempool_t *mp)
{
int k;
for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
free(mp->buf); free(mp);
}
static inline freenode_t *mp_alloc(mempool_t *mp)
{
++mp->cnt;
if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
else return mp->buf[--mp->n];
}
static inline void mp_free(mempool_t *mp, freenode_t *p)
{
--mp->cnt; p->next = 0; p->cnt = TV_GAP;
if (mp->n == mp->max) {
mp->max = mp->max? mp->max<<1 : 256;
mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
}
mp->buf[mp->n++] = p;
}
/* core part */
struct __bam_lplbuf_t {
int max, n_cur, n_pre;
int max_level, *cur_level, *pre_level;
mempool_t *mp;
freenode_t **aux, *head, *tail;
int n_nodes, m_aux;
bam_pileup_f func;
void *user_data;
bam_plbuf_t *plbuf;
};
void bam_lplbuf_reset(bam_lplbuf_t *buf)
{
freenode_t *p, *q;
bam_plbuf_reset(buf->plbuf);
for (p = buf->head; p->next;) {
q = p->next;
mp_free(buf->mp, p);
p = q;
}
buf->head = buf->tail;
buf->max_level = 0;
buf->n_cur = buf->n_pre = 0;
buf->n_nodes = 0;
}
static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
freenode_t *p;
int i, l, max_level;
// allocate memory if necessary
if (tv->max < n) { // enlarge
tv->max = n;
kroundup32(tv->max);
tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
}
tv->n_cur = n;
// update cnt
for (p = tv->head; p->next; p = p->next)
if (p->cnt > 0) --p->cnt;
// calculate cur_level[]
max_level = 0;
for (i = l = 0; i < n; ++i) {
const bam_pileup1_t *p = pl + i;
if (p->is_head) {
if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
freenode_t *p = tv->head->next;
tv->cur_level[i] = tv->head->level;
mp_free(tv->mp, tv->head);
tv->head = p;
--tv->n_nodes;
} else tv->cur_level[i] = ++tv->max_level;
} else {
tv->cur_level[i] = tv->pre_level[l++];
if (p->is_tail) { // then return a free slot
tv->tail->level = tv->cur_level[i];
tv->tail->next = mp_alloc(tv->mp);
tv->tail = tv->tail->next;
++tv->n_nodes;
}
}
if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
((bam_pileup1_t*)p)->level = tv->cur_level[i];
}
assert(l == tv->n_pre);
tv->func(tid, pos, n, pl, tv->user_data);
// sort the linked list
if (tv->n_nodes) {
freenode_t *q;
if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
tv->m_aux = tv->n_nodes + 1;
kroundup32(tv->m_aux);
tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux);
}
for (p = tv->head, i = l = 0; p->next;) {
if (p->level > max_level) { // then discard this entry
q = p->next;
mp_free(tv->mp, p);
p = q;
} else {
tv->aux[i++] = p;
p = p->next;
}
}
tv->aux[i] = tv->tail; // add a proper tail for the loop below
tv->n_nodes = i;
if (tv->n_nodes) {
ks_introsort(node, tv->n_nodes, tv->aux);
for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
tv->head = tv->aux[0];
} else tv->head = tv->tail;
}
// clean up
tv->max_level = max_level;
memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
// squeeze out terminated levels
for (i = l = 0; i < n; ++i) {
const bam_pileup1_t *p = pl + i;
if (!p->is_tail)
tv->pre_level[l++] = tv->pre_level[i];
}
tv->n_pre = l;
/*
fprintf(stderr, "%d\t", pos+1);
for (i = 0; i < n; ++i) {
const bam_pileup1_t *p = pl + i;
if (p->is_head) fprintf(stderr, "^");
if (p->is_tail) fprintf(stderr, "$");
fprintf(stderr, "%d,", p->level);
}
fprintf(stderr, "\n");
*/
return 0;
}
bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
{
bam_lplbuf_t *tv;
tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
tv->mp = mp_init();
tv->head = tv->tail = mp_alloc(tv->mp);
tv->func = func;
tv->user_data = data;
tv->plbuf = bam_plbuf_init(tview_func, tv);
return (bam_lplbuf_t*)tv;
}
void bam_lplbuf_destroy(bam_lplbuf_t *tv)
{
freenode_t *p, *q;
free(tv->cur_level); free(tv->pre_level);
bam_plbuf_destroy(tv->plbuf);
free(tv->aux);
for (p = tv->head; p->next;) {
q = p->next;
mp_free(tv->mp, p); p = q;
}
mp_free(tv->mp, p);
assert(tv->mp->cnt == 0);
mp_destroy(tv->mp);
free(tv);
}
int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
{
return bam_plbuf_push(b, tv->plbuf);
}
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