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link.c
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link.c
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/*********************************************************************************
* MIT License *
* *
* Copyright (c) 2021 Chenxi Zhou <[email protected]> *
* *
* Permission is hereby granted, free of charge, to any person obtaining a copy *
* of this software and associated documentation files (the "Software"), to deal *
* in the Software without restriction, including without limitation the rights *
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell *
* copies of the Software, and to permit persons to whom the Software is *
* furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE *
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER *
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, *
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE *
* SOFTWARE. *
*********************************************************************************/
/********************************** Revision History *****************************
* *
* 23/06/21 - Chenxi Zhou: Created *
* *
*********************************************************************************/
#include <stdlib.h>
#include <stdint.h>
#include <stdio.h>
#include <math.h>
#include <assert.h>
#include <float.h>
#include "khash.h"
#include "kvec.h"
#include "bamlite.h"
#include "sdict.h"
#include "enzyme.h"
#include "link.h"
#include "cov.h"
#include "asset.h"
#undef DEBUG_NOISE
#undef DEBUG_ORIEN
#undef DEBUG_INTRA
#define USE_MEDIAN_NORM
#define MIN_RE_DENS .1
static uint32_t MAX_RADIUS = 100;
KHASH_SET_INIT_STR(str)
void intra_link_mat_destroy(intra_link_mat_t *link_mat)
{
if (!link_mat) return;
uint32_t i;
for (i = 0; i < link_mat->n; ++i)
if (link_mat->links[i].n)
free(link_mat->links[i].link);
if (link_mat->links)
free(link_mat->links);
free(link_mat);
}
void inter_link_mat_destroy(inter_link_mat_t *link_mat)
{
if (!link_mat) return;
uint32_t i, j;
for (i = 0; i < link_mat->n; ++i) {
if (link_mat->links[i].n) {
for (j = 0; j < 4; ++j) {
free(link_mat->links[i].link[j]);
free(link_mat->links[i].linkb[j]);
}
}
}
if (link_mat->links)
free(link_mat->links);
free(link_mat);
}
// index mapping (c0, c1) -> (i, j) -> (n * 2 - i - 3) * i / 2 + j - 1
// 0 (0, 1)
// 1 (0, 2) 5 (1, 2)
// 2 (0, 3) 6 (1, 3) 9 (2, 3)
// 3 (0, 4) 7 (1, 4) 10 (2, 4) 12 (3, 4)
// 4 (0, 5) 8 (1, 5) 11 (2, 5) 13 (3, 5) 14 (4, 5)
// number of cells
// (b0, b1, r) -> n -> MIN(b0, r) * MIN(b1, r)
// index mapping for cells
// (i, j, r) -> p -> MAX(0, i - 1) * b1 + j
// reverse index mapping for cells
// (p, r) -> (i, j) -> (p / b1, p % b1)
// # # # # # #
// o x x x x x
// o o x x x x
// b0 o o o x x x
// o o o o x x
// o o o o o x
// o o o o o o
// O o o o o o
// b1
// TODO improve memory efficiency
// number of cells
// (b0, b1, r) -> n
// for (k = 0; k < MIN(b0, r); ++k) p += MIN(b1, r - k)
// index mapping for cells
// (i, j, r) -> p
// for (k = 0; k < i; ++k) p += MIN(b1, r - k)
// p += j
// reverse index mapping for cells
// (p, r) -> (i, j)
// ???
// (1) radius [15] >= b0 + b1 [14] >= b0 [8] >= b1 [6]
// b0 * b1
// o o o o o o
// o o o o o o
// o o o o o o
// b0 o o o o o o
// o o o o o o
// o o o o o o
// o o o o o o
// O o o o o o
// b1
// (2) b0 + b1 [14] >= radius [10] >= b0 [8] >= b1 [6]
// k = (b0 + b1 - radius)
// b0 * b1 - k * (k - 1) / 2
// o o o # # #
// o o o o # #
// o o o o o #
// b0 o o o o o o
// o o o o o o
// o o o o o o
// o o o o o o
// O o o o o o
// b1
// (3) b0 [8] >= radius [7] >= b1 [6]
// (r - b1) *
// # # # # # #
// o # # # # #
// o o # # # #
// b0 o o o # # #
// o o o o # #
// o o o o o #
// o o o o o o
// O o o o o o
// b1
// (4) b0 [8] >= b1 [6] >= radius [4]
// # # # # # #
// # # # # # #
// # # # # # #
// b0 # # # # # #
// o # # # # #
// o o # # # #
// o o o # # #
// O o o o # #
// b1
//
inter_link_mat_t *inter_link_mat_init(asm_dict_t *dict, uint32_t resolution, uint32_t radius)
{
inter_link_mat_t *link_mat;
inter_link_t *link;
uint32_t i, j, k, b0, b1, n, m, p, r2;
n = dict->n;
m = (long) n * (n - 1) / 2;
r2 = resolution * 2;
link_mat = (inter_link_mat_t *) malloc(sizeof(inter_link_mat_t));
link_mat->n = m;
link_mat->r = radius;
link_mat->links = (inter_link_t *) malloc(m * sizeof(inter_link_t));
for (i = 0; i < n; ++i) {
if (dict->s[i].len < r2) {
for (j = i + 1; j < n; ++j)
link_mat->links[(long) (n * 2 - i - 3) * i / 2 + j - 1].n = 0;
continue;
}
b0 = MIN(radius, div_ceil(dict->s[i].len, r2));
for (j = i + 1; j < n; ++j) {
link = &link_mat->links[(long) (n * 2 - i - 3) * i / 2 + j - 1];
if (dict->s[j].len < r2) {
link->n = 0;
continue;
}
b1 = MIN(radius, div_ceil(dict->s[j].len, r2));
p = b0 * b1;
link->c0 = i;
link->c1 = j;
link->b0 = b0;
link->b1 = b1;
link->r = MIN(radius, (uint32_t) (b0 + b1 - 1));
link->n = p;
link->n0 = 0;
link->linkt = 0;
assert(p == (long) b0 * b1);
for (k = 0; k < 4; ++k) {
link->link[k] = (double *) calloc(p, sizeof(double));
link->linkb[k] = (double *) calloc(link->r, sizeof(double));
if (!link->link[k] || !link->linkb[k]) {
fprintf(stderr, "[E::%s] memory allocation failure\n", __func__);
exit(EXIT_FAILURE);
}
}
memset(link->norms, 0, sizeof(link->norms));
}
}
return link_mat;
}
long estimate_inter_link_mat_init_rss(asm_dict_t *dict, uint32_t resolution, uint32_t radius)
{
long bytes, p, m;
uint32_t i, j, b0, b1, n, r, r2;
n = dict->n;
m = (long) n * (n - 1) / 2;
if (m > UINT32_MAX)
return -1;
r2 = resolution * 2;
bytes = 0;
bytes += sizeof(inter_link_mat_t);
bytes += m * sizeof(inter_link_t);
for (i = 0; i < n; ++i) {
if (dict->s[i].len < r2)
continue;
b0 = MIN(radius, div_ceil(dict->s[i].len, r2));
for (j = i + 1; j < n; ++j) {
if (dict->s[j].len < r2)
continue;
b1 = MIN(radius, div_ceil(dict->s[j].len, r2));
p = b0 * b1;
if (p > UINT32_MAX)
return -1;
r = MIN(radius, (uint32_t) (b0 + b1 - 1));
bytes += (p + r) * 4 * sizeof(double);
}
}
return bytes;
}
// index mapping (i, j) -> ([n - (j - i)] + [n - 1]) / 2 * (j - i) + j -> (n * 2 - j + i - 1) * (j - i) / 2 + j
// distance k [0 ... n-1] start from (n * 2 - k - 1) * k / 2 + k
// 0 (0,0)
// 7 (0,1) 1 (1,1)
// 13 (0,2) 8 (1,2) 2 (2,2)
// 18 (0,3) 14 (1,3) 9 (2,3) 3 (3,3)
// 22 (0,4) 19 (1,4) 15 (2,4) 10 (3,4) 4 (4,4)
// 25 (0,5) 23 (1,5) 20 (2,5) 16 (3,5) 11 (4,5) 5 (5,5)
// 27 (0,6) 26 (1,6) 24 (2,6) 21 (3,6) 17 (4,6) 12 (5,6) 6 (6,6)
intra_link_mat_t *intra_link_mat_init(void *dict, uint32_t resolution, int use_gap_seq)
{
intra_link_mat_t *link_mat;
intra_link_t *link;
uint32_t i, n, b, p;
uint64_t len;
n = use_gap_seq? ((asm_dict_t *) dict)->n : ((sdict_t *) dict)->n;
link_mat = (intra_link_mat_t *) malloc(sizeof(intra_link_mat_t));
link_mat->n = n;
link_mat->links = (intra_link_t *) calloc(n, sizeof(intra_link_t));
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
link->c = i;
len = use_gap_seq? ((asm_dict_t *) dict)->s[i].len : ((sdict_t *) dict)->s[i].len;
if (len < resolution) {
link->n = 0;
continue;
}
b = div_ceil(len, resolution);
link->n = b;
p = (long) b * (b + 1) / 2;
link->link = (double *) calloc(p, sizeof(double));
if (!link->link) {
fprintf(stderr, "[E::%s] memory allocation failure\n", __func__);
exit(EXIT_FAILURE);
}
#ifdef DEBUG_INTRA
fprintf(stderr, "[DEBUG_INTRA::%s] %s bins: %d\n", __func__, use_gap_seq? ((asm_dict_t *) dict)->s[i].name : ((sdict_t *) dict)->s[i].name, link->n);
#endif
}
return link_mat;
}
long estimate_intra_link_mat_init_rss(void *dict, uint32_t resolution, int use_gap_seq)
{
long bytes, p;
uint32_t i, n, b;
uint64_t len;
n = use_gap_seq? ((asm_dict_t *) dict)->n : ((sdict_t *) dict)->n;
bytes = 0;
bytes += sizeof(intra_link_mat_t);
bytes += n * sizeof(intra_link_t);
for (i = 0; i < n; ++i) {
len = use_gap_seq? ((asm_dict_t *) dict)->s[i].len : ((sdict_t *) dict)->s[i].len;
if (len < resolution)
continue;
b = div_ceil(len, resolution);
p = (long) b * (b + 1) / 2;
if (p > UINT32_MAX)
return -1;
bytes += p * sizeof(double);
}
return bytes;
}
static void intra_link_mat_normalise(intra_link_mat_t *link_mat, void *dict, re_cuts_t *re_cuts, uint32_t resolution, int use_gap_seq)
{
intra_link_t *link;
uint32_t i, j, k, n, b;
uint64_t len;
double a, a0, a1, s;
double **re_dens;
n = use_gap_seq? ((asm_dict_t *) dict)->n : ((sdict_t *) dict)->n;
re_dens = use_gap_seq? calc_re_cuts_density1(re_cuts, resolution, dict) : calc_re_cuts_density(re_cuts, resolution);
for (i = 0; i < n; ++i) {
len = use_gap_seq? ((asm_dict_t *) dict)->s[i].len : ((sdict_t *) dict)->s[i].len;
if (len < resolution) continue;
link = &link_mat->links[i];
b = link->n;
// relative size of the last cell
a = ((double) len - (double) (b - 1) * resolution) / resolution;
for (j = 0; j < b; ++j) {
a0 = j < b-1? 1. : a;
for (k = j; k < b; ++k) {
a1 = k < b-1? 1. : a;
a1 *= a0;
a1 = a1 < .5? .0 : a1;
s = re_dens? re_dens[i][j] * re_dens[i][k] : 1.;
s = s < MIN_RE_DENS? .0 : s;
s *= a1;
if (s < FLT_EPSILON)
link->link[(long) (b * 2 - k + j - 1) * (k - j) / 2 + k] = -DBL_MAX;
else
link->link[(long) (b * 2 - k + j - 1) * (k - j) / 2 + k] /= s;
}
}
}
if (re_dens) {
for (i = 0; i < n; ++i)
free(re_dens[i]);
free(re_dens);
}
}
intra_link_mat_t *intra_link_mat_from_file(const char *f, cov_norm_t *cov_norm, asm_dict_t *dict, re_cuts_t *re_cuts, uint32_t resolution, int use_gap_seq, uint8_t mq)
{
uint32_t i, k, m, i0, i1, b0, b1;
uint64_t p0, p1, pair_n, pair_c, intra_c;
int64_t magic_number;
uint8_t buffer[BUFF_SIZE * 17];
intra_link_mat_t *link_mat;
intra_link_t *link;
FILE *fp;
fp = fopen(f, "r");
if (fp == NULL)
return 0;
m = fread(&magic_number, sizeof(int64_t), 1, fp);
if (m != 1) bin_fread_error();
if (!is_valid_bin_header(magic_number)) {
fprintf(stderr, "[E::%s] not a valid BIN file\n", __func__);
return 0;
}
file_seek_skip_sdict(fp);
m = fread(&pair_n, sizeof(uint64_t), 1, fp);
if (m != 1) bin_fread_error();
link_mat = use_gap_seq? intra_link_mat_init(dict, resolution, use_gap_seq) : intra_link_mat_init(dict->sdict, resolution, use_gap_seq);
pair_c = 0;
intra_c = 0;
while (pair_c < pair_n) {
m = fread(buffer, sizeof(uint8_t), BUFF_SIZE * 17, fp);
for (i = 0; i < m && pair_c < pair_n; i += 17, ++pair_c) {
if (*(uint8_t *) (buffer + i + 16) < mq)
continue;
if (use_gap_seq) {
sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i), *(uint32_t *) (buffer + i + 4), &i0, &p0, 0);
sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i + 8), *(uint32_t *) (buffer + i + 12), &i1, &p1, 0);
b0 = p0 / resolution;
b1 = p1 / resolution;
} else {
i0 = *(uint32_t *) (buffer + i);
i1 = *(uint32_t *) (buffer + i + 8);
b0 = *(uint32_t *) (buffer + i + 4) / resolution;
b1 = *(uint32_t *) (buffer + i + 12) / resolution;
}
if (i0 == i1 && i0 != UINT32_MAX) {
link = &link_mat->links[i0];
if (link->n) {
if (b0 > b1)
SWAP(uint32_t, b0, b1);
k = (long) (link->n * 2 - b1 + b0 - 3) * (b1 - b0) / 2 + b1;
// link->link[k] += 1.;
link->link[k] += cov_norm->norm[*(uint32_t *) (buffer + i)][*(uint32_t *) (buffer + i + 4) / cov_norm->w] *
cov_norm->norm[*(uint32_t *) (buffer + i + 8)][*(uint32_t *) (buffer + i + 12) / cov_norm->w];
}
++intra_c;
}
}
}
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] %lu read pairs processed, %lu intra links \n", __func__, pair_c, intra_c);
#endif
fclose(fp);
// TODO normalise links by cell size
if (use_gap_seq)
intra_link_mat_normalise(link_mat, dict, re_cuts, resolution, use_gap_seq);
else
intra_link_mat_normalise(link_mat, dict->sdict, re_cuts, resolution, use_gap_seq);
return link_mat;
}
static void inter_link_mat_normalise(inter_link_mat_t *link_mat, asm_dict_t *dict, re_cuts_t *re_cuts, uint32_t resolution, uint32_t radius)
{
inter_link_t *link;
uint32_t i, j, k, l, b0, b1, n, p, r2;
double a0, a1, a;
double **re_dens, re;
n = dict->n;
r2 = resolution * 2;
re_dens = calc_re_cuts_density2(re_cuts, resolution, dict);
for (i = 0; i < n; ++i) {
if (dict->s[i].len < r2) continue;
b0 = MIN(radius, div_ceil(dict->s[i].len, r2));
// relative size of the last cell
a0 = MIN(1., (dict->s[i].len / 2. - (double) (b0 - 1) * resolution) / resolution);
for (j = i + 1; j < n; ++j) {
if (dict->s[j].len < r2) continue;
b1 = MIN(radius, div_ceil(dict->s[j].len, r2));
// relative size of the last cell
a1 = MIN(1., (dict->s[j].len / 2. - (double) (b1 - 1) * resolution) / resolution);
link = &link_mat->links[(long) (n * 2 - i - 3) * i / 2 + j - 1];
p = link->n;
// calculate relative areas for each cell
for (l = 0; l < p; ++l) {
a = 1.;
if (l / b1 == b0 - 1)
a *= a0;
if (l % b1 == b1 - 1)
a *= a1;
if (a < .5)
a = .0;
re = re_dens? re_dens[i][l / b1] * re_dens[j][l % b1] : 1.;
a *= re < MIN_RE_DENS? .0 : re;
if (a < FLT_EPSILON)
for (k = 0; k < 4; ++k) link->link[k][l] = -DBL_MAX;
else
for (k = 0; k < 4; ++k) link->link[k][l] /= a;
}
}
}
if (re_dens) {
for (i = 0; i < n; ++i)
free(re_dens[i]);
free(re_dens);
}
}
inter_link_mat_t *inter_link_mat_from_file(const char *f, cov_norm_t *cov_norm, asm_dict_t *dict, re_cuts_t *re_cuts, uint32_t resolution, uint32_t radius, uint8_t mq)
{
uint32_t i, j, k, m, n, i0, i1, b0, b1;
uint64_t p0, p1, pair_n, pair_c, inter_c, radius_c, noise_c;
int64_t magic_number;
uint8_t buffer[BUFF_SIZE * 17];
double l0, l1, c, a, na[4], nc[4];
inter_link_mat_t *link_mat;
inter_link_t *link;
FILE *fp;
fp = fopen(f, "r");
if (fp == NULL)
return 0;
m = fread(&magic_number, sizeof(int64_t), 1, fp);
if (m != 1) bin_fread_error();
if (!is_valid_bin_header(magic_number)) {
fprintf(stderr, "[E::%s] not a valid BIN file\n", __func__);
return 0;
}
file_seek_skip_sdict(fp);
m = fread(&pair_n, sizeof(uint64_t), 1, fp);
if (m != 1) bin_fread_error();
n = dict->n;
link_mat = inter_link_mat_init(dict, resolution, radius);
pair_c = inter_c = radius_c = 0;
while (pair_c < pair_n) {
m = fread(buffer, sizeof(uint8_t), BUFF_SIZE * 17, fp);
for (i = 0; i < m && pair_c < pair_n; i += 17, ++pair_c) {
if (*(uint8_t *) (buffer + i + 16) < mq)
continue;
sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i), *(uint32_t *) (buffer + i + 4), &i0, &p0, 0);
sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i + 8), *(uint32_t *) (buffer + i + 12), &i1, &p1, 0);
if (i0 != i1 && i0 != UINT32_MAX) {
c = cov_norm->norm[*(uint32_t *) (buffer + i)][*(uint32_t *) (buffer + i + 4) / cov_norm->w] *
cov_norm->norm[*(uint32_t *) (buffer + i + 8)][*(uint32_t *) (buffer + i + 12) / cov_norm->w];
if (i0 > i1) {
SWAP(uint32_t, i0, i1);
SWAP(uint64_t, p0, p1);
}
link = &link_mat->links[(long) (n * 2 - i0 - 3) * i0 / 2 + i1 - 1];
if (link->n == 0)
continue;
l0 = dict->s[i0].len / 2.;
l1 = dict->s[i1].len / 2.;
if (p0 >= l0 && p1 < l1) {
// i0(-) -> i1(+)
b0 = (uint32_t) ((2 * l0 - p0) / resolution);
b1 = (uint32_t) ((double) p1 / resolution);
if (b0 < link->b0 && b1 < link->b1 && b0 + b1 < radius) {
k = (long) (MAX(1, b0) - 1) * link->b1 + b1;
// link->link[0][k] += 1.;
link->link[0][k] += c;
++radius_c;
}
} else if(p0 >= l0 && p1 >= l1) {
// i0(-) -> i1(-)
b0 = (uint32_t) ((2 * l0 - p0) / resolution);
b1 = (uint32_t) ((2 * l1 - p1) / resolution);
if (b0 < link->b0 && b1 < link->b1 && b0 + b1 < radius) {
k = (long) (MAX(1, b0) - 1) * link->b1 + b1;
// link->link[1][k] += 1.;
link->link[1][k] += c;
++radius_c;
}
} else if(p0 < l0 && p1 < l1) {
// i0(+) -> i1(+)
b0 = (uint32_t) ((double) p0 / resolution);
b1 = (uint32_t) ((double) p1 / resolution);
if (b0 < link->b0 && b1 < link->b1 && b0 + b1 < radius) {
k = (long) (MAX(1, b0) - 1) * link->b1 + b1;
// link->link[2][k] += 1.;
link->link[2][k] += c;
++radius_c;
}
} else if(p0 < l0 && p1 >= l1) {
// i0(+) -> i1(-)
b0 = (uint32_t) ((double) p0 / resolution);
b1 = (uint32_t) ((2 * l1 - p1) / resolution);
if (b0 < link->b0 && b1 < link->b1 && b0 + b1 < radius) {
k = (long) (MAX(1, b0) - 1) * link->b1 + b1;
// link->link[3][k] += 1.;
link->link[3][k] += c;
++radius_c;
}
}
++inter_c;
}
}
}
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] %lu read pairs processed, %lu inter links \n", __func__, pair_c, inter_c);
fprintf(stderr, "[DEBUG::%s] within radius %d: %lu\n", __func__, radius, radius_c);
#endif
fclose(fp);
// TODO normalise links by cell size
inter_link_mat_normalise(link_mat, dict, re_cuts, resolution, radius);
// calculate noise level
noise_c = a = 0;
for (i = 0; i < link_mat->n; ++i) {
memset(nc, 0, sizeof(nc));
memset(na, 0, sizeof(na));
link = &link_mat->links[i];
for (j = 0; j < link->n; ++j) {
for (k = 0; k < 4; ++k) {
if (link->link[k][j] >= 0) {
nc[k] += link->link[k][j];
na[k] += 1.;
}
}
}
j = 0;
for (k = 1; k < 4; ++k)
if (nc[k] < nc[j])
j = k;
noise_c += nc[j];
a += na[j];
}
link_mat->noise = a > 0? noise_c / a : 0;
#ifdef DEBUG_NOISE
fprintf(stderr, "[DEBUG_NOISE::%s] noise links: %lu; area: %.12f; noise estimation: %.12f\n", __func__, noise_c, a, link_mat->noise);
#endif
return link_mat;
}
cov_norm_t *cov_norm_from_file(const char *f, sdict_t *dict)
{
uint32_t i;
uint64_t m, n;
double *norm_a, **norm;
int64_t magic_number;
cov_norm_t *cov_norm;
FILE *fp;
fp = fopen(f, "r");
if (fp == NULL)
return 0;
m = fread(&magic_number, sizeof(int64_t), 1, fp);
if (m != 1) bin_fread_error();
if (!is_valid_bin_header(magic_number)) {
fprintf(stderr, "[E::%s] not a valid BIN file\n", __func__);
fclose(fp);
return 0;
}
file_seek_skip_sdict(fp);
m = fread(&n, sizeof(uint64_t), 1, fp);
if (m != 1) bin_fread_error();
fseek(fp, n * 17, SEEK_CUR);
m = fread(&n, sizeof(uint64_t), 1, fp);
if (m != 1) bin_fread_error();
norm_a = (double *) malloc(sizeof(double) * n);
m = fread(norm_a, sizeof(double), n, fp);
if (m != n) bin_fread_error();
norm = (double **) malloc(sizeof(double *) * dict->n);
norm[0] = norm_a;
for (i = 1; i < dict->n; ++i)
norm[i] = norm[i-1] + div_ceil(dict->s[i-1].len, COV_NORM_WINDOW);
fclose(fp);
cov_norm = (cov_norm_t *) malloc(sizeof(cov_norm_t));
cov_norm->n = n;
cov_norm->w = COV_NORM_WINDOW;
cov_norm->norm = norm;
return cov_norm;
}
void norm_destroy(norm_t *norm)
{
if (!norm) return;
//uint32_t i;
free(norm->bs);
//for (i = 0; i < norm->n; ++i)
// free(norm->link[i]);
//free(norm->link);
free(norm->linkc);
free(norm->norms);
free(norm);
}
int dcmp (const void *a, const void *b) {
double cmp = *(double *) a - *(double *) b;
return cmp > 0? 1 : ( cmp < 0? -1 : 0);
}
norm_t *calc_norms(intra_link_mat_t *link_mat, uint32_t d_min_cell, double d_mass_frac)
{
uint32_t i, j, n, b, r, r0, t;
uint32_t *bs;
double intra_c, tmp_c;
double *norms, *link, *linkc;
norm_t *norm;
// find maximum numebr of bands
n = 0;
for (i = 0; i < link_mat->n; ++i)
n = MAX(link_mat->links[i].n, n);
if (n <= 1) {
fprintf(stderr, "[E::%s] no bands for norm calculation, try a higher resolution\n", __func__);
return 0;
}
n -= 1; // do not use the last one as it might be an incomplete cell
// calculate number of cells for each band
bs = (uint32_t *) calloc(n, sizeof(uint32_t));
for (i = 0; i < link_mat->n; ++i) {
if (link_mat->links[i].n) {
b = link_mat->links[i].n - 1;
for (j = 0; j < b; ++j)
bs[j] += b - j;
}
}
r0 = 0;
while (bs[r0] >= d_min_cell)
++r0;
if (r0 < 10) {
fprintf(stderr, "[E::%s] no enough bands (%d) for norm calculation, try a higher resolution\n", __func__, r0);
free(bs);
return 0;
}
// caluclate links in each band and radius
// calculate norms - using median or mean?
norms = (double *) malloc(n * sizeof(double));
linkc = (double *) malloc(n * sizeof(double));
intra_c = .0;
for (i = 0; i < n; ++i) {
link = (double *) malloc(bs[i] * sizeof(double));
t = 0;
for (j = 0; j < link_mat->n; ++j) {
b = link_mat->links[j].n;
if (b > i + 1) {
memcpy(link + t, link_mat->links[j].link + (long) (b * 2 - i - 1) * i / 2 + i, (b - 1 - i) * sizeof(double));
t += b - 1 - i;
}
}
tmp_c = .0;
for (j = 0; j < bs[i]; ++j)
tmp_c += link[j];
linkc[i] = tmp_c;
intra_c += tmp_c;
#ifdef USE_MEDIAN_NORM
qsort(link, bs[i], sizeof(double), dcmp);
norms[i] = bs[i] & 1? link[bs[i] / 2] : (link[bs[i] / 2] + link[bs[i] / 2 - 1]) / 2;
#else
norms[i] = MAX(linkc[i], 1.) / bs[i];
#endif
free(link);
}
intra_c -= linkc[0];
tmp_c = .0;
for (r = 1; r < n; ++r) {
tmp_c += linkc[r];
if (tmp_c / intra_c >= d_mass_frac)
break;
}
r = MIN(MIN(r, r0), MAX_RADIUS);
#ifdef USE_MEDIAN_NORM
// adjust radius by norms
// change radius if norm drops to zero before reaching r
// find the first position with 10 consective zeros
int zeros = 0;
int p = -1;
for (i = 0; i < n; ++i) {
if (norms[i] < 1) {
++zeros;
if (zeros >= 10) {
p = i - 9;
break;
}
} else {
zeros = 0;
}
}
if (p >= 0 && p < r)
r = p;
for (i = 0; i <= r; ++i) {
if(norms[i] < 1)
norms[i] = 1;
}
#endif
norm = (norm_t *) malloc(sizeof(norm_t));
norm->n = n;
norm->r = r;
norm->bs = bs;
//norm->link = link;
norm->linkc = linkc;
norm->norms = norms;
return norm;
}
void print_inter_link_norms(FILE *fp, inter_link_mat_t *link_mat, asm_dict_t *dict)
{
uint32_t i, n;
inter_link_t *link;
n = link_mat->n;
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
if (link->n)
fprintf(fp, "NORM: %s %s (%u) [%.3f %.3f %.3f %.3f]\n", dict->s[link->c0].name, dict->s[link->c1].name, link->n0, link->norms[0], link->norms[1], link->norms[2], link->norms[3]);
}
}
void print_inter_link_bands(FILE *fp, inter_link_mat_t *link_mat, asm_dict_t *dict)
{
uint32_t i, j, k, n;
inter_link_t *link;
n = link_mat->n;
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
if (link->n) {
for (j = 0; j < 4; ++j) {
fprintf(fp, "BAND [%u %u]: %s%s %s%s (%u, %u) [%.3f]", i, j, dict->s[link->c0].name, j < 2? "-" : "+", dict->s[link->c1].name, j & 1? "-" : "+", link->n0, link->r, link->norms[j]);
for (k = 0; k < link->r; ++k)
fprintf(fp, " %.0f", link->linkb[j][k]);
fprintf(fp, "\n");
}
}
}
}
double *get_max_inter_norms(inter_link_mat_t *link_mat, asm_dict_t *dict)
{
uint32_t i, j, n, c0, c1;
double *max_norms;
inter_link_t *link;
n = link_mat->n;
max_norms = (double *) calloc(dict->n, sizeof(double));
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
if (link->n) {
c0 = link->c0;
c1 = link->c1;
for (j = 0; j < 4; ++j) {
max_norms[c0] = MAX(max_norms[c0], link->norms[j]);
max_norms[c1] = MAX(max_norms[c1], link->norms[j]);
}
}
}
return max_norms;
}
void print_norms(FILE *fp, norm_t *norm)
{
uint32_t i/**, j, n**/;
//uint64_t link_count;
//double *link;
//link_count = 0;
fprintf(fp, "norms:");
for (i = 0; i < norm->n; ++i)
fprintf(fp, " %.1f", norm->norms[i]);
fprintf(fp, "\n");
fprintf(fp, "links:");
for (i = 0; i < norm->n; ++i)
fprintf(fp, " %.0f", norm->linkc[i]);
fprintf(fp, "\n");
/***
for (i = 0; i < norm->n; ++i) {
fprintf(fp, "band %d:", i);
n = norm->bs[i];
link = norm->link[i];
for (j = 0; j < n; ++j) {
link_count += link[j];
fprintf(fp, " %.0f", link[j]);
}
fprintf(fp, "\n");
}
**/
}
int estimate_noise(inter_link_mat_t *link_mat)
{
uint32_t i, j, k, n;
uint32_t bin, *hist;
uint64_t total;
double l;
inter_link_t *inter_link;
bin = 4096;
hist = (uint32_t *) calloc(bin, sizeof(uint32_t));
for (i = 0; i < link_mat->n; ++i) {
inter_link = &link_mat->links[i];
n = inter_link->n;
for (j = 0; j < n; ++j) {
for (k = 0; k < 4; ++k) {
l = inter_link->link[k][j];
if (l < .0)
continue;
++hist[MIN(bin - 1, (int) l)];
}
}
}
hist[0] = 0;
total = 0;
for (i = 0; i < bin; ++i)
total += hist[i];
total >>= 1;
#ifdef DEBUG_NOISE
for (i = 0; i < bin; ++i)
fprintf(stderr, "[DEBUG_NOISE::%s] noise bin %d %d\n", __func__, i, hist[i]);
#endif
n = 0;
while (hist[n] < total) {
++n;
if (n == bin)
break;
hist[n] += hist[n - 1];
}
if (n == 4096)
fprintf(stderr, "[W::%s] noise esimation might be incorrect %d\n", __func__, n);
free(hist);
return n;
}
int inter_link_norms(inter_link_mat_t *link_mat, norm_t *norm, int use_estimated_noise, double max_noise_ratio, double *la)
{
uint32_t i, j, k, b, b1, r, n, n0;
uint32_t *fn;
int8_t bl;
double l, *norms, *fr, noise;
double c, c0, t;
inter_link_t *inter_link;
noise = .0;
if (use_estimated_noise) {
// noise = estimate_noise(link_mat);
noise = link_mat->noise;
fprintf(stderr, "[I::%s] using noise level %.3f\n", __func__, noise);
}
r = link_mat->r;
norms = (double *) calloc(r + 1, sizeof(double));
for (i = 0; i <= r; ++i) {
if (norm->norms[i] * max_noise_ratio > noise) {
norms[i] = norm->norms[i] - noise;
} else {
fprintf(stderr, "[I::%s] using new radius %u (%u) as noise ratio exceeds threshold %.3f\n", __func__, i, r, max_noise_ratio);
r = i;
break;
}
}
if (r <= 1) return 1;
/***
// no weighting
c = c0 = 0;
for (i = 0; i < link_mat->n; ++i) {
inter_link = &link_mat->links[i];
n = inter_link->n;
if (n == 0)
continue;
r = inter_link->r;
b1 = inter_link->b1;
n0 = 0;
for (j = 0; j < n; ++j) {
b = j / b1 + j % b1;