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yahs.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 *****************************
* *
* 22/06/21 - Chenxi Zhou: Created *
* *
*********************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include <ctype.h>
#include "ketopt.h"
#include "kvec.h"
#include "sdict.h"
#include "link.h"
#include "cov.h"
#include "graph.h"
#include "break.h"
#include "enzyme.h"
#include "telo.h"
#include "asset.h"
#include "version.h"
#undef DEBUG_ERROR_BREAK
#undef DEBUG_GRAPH_PRUNE
#undef DEBUG_OPTIONS
#undef DEBUG_RAM_USAGE
#undef DEBUG_QLF
#undef DEBUG_ENZ
#undef DEBUG_GT4G
#undef DEBUG_LINK
#define ENOMEM_ERR 15
#define ENOBND_ERR 14
#define GB 0x40000000
#define MAX_N_SEQ 45000
#ifndef DEBUG_GT4G
static int ec_min_window = 1000000;
static int ec_resolution = 10000;
static int ec_bin = 1000;
static int ec_move_avg = 0;
static int ec_merge_thresh = 10000;
static int ec_dual_break_thresh = 50000;
#else
static int ec_min_window = 5000000;
static int ec_resolution = 50000;
static int ec_bin = 5000;
static int ec_move_avg = 0;
static int ec_merge_thresh = 50000;
static int ec_dual_break_thresh = 250000;
#endif
static double ec_min_frac = .8;
static double ec_fold_thresh = .2;
static double max_noise_ratio = .1;
static int max_extra_try = 3;
static uint64_t n_stats[10];
static uint32_t l_stats[10];
double qbinom(double, double, double, int, int);
enum fileTypes{NOSET, BED, BAM, BIN, PA5};
int VERBOSE = 0;
static double ys_realtime0;
graph_t *build_graph_from_links(inter_link_mat_t *link_mat, asm_dict_t *dict, double min_norm, double la, int8_t *telo_ends)
{
int32_t i, j, n, c0, c1;
uint32_t v, w;
int8_t t;
double norm, qla;
inter_link_t *link;
graph_t *g;
graph_arc_t *arc;
g = graph_init();
g->sdict = dict;
// build graph
n = link_mat->n;
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
if (link->n == 0 || link->n0 == 0)
continue;
c0 = link->c0;
c1 = link->c1;
t = link->linkt;
if (!t)
continue;
qla = qbinom(.99, link->n0, la, 1, 0) / link->n0;
for (j = 0; j < 4; ++j) {
if (1 << j & t) {
norm = link->norms[j];
if (norm >= min_norm) {
if (norm < qla) {
#ifdef DEBUG_QLF
fprintf(stderr, "[DEBUG_QLF::%s] #Edge rejected by QL filter: %s %s %u %u %.3f (< %.3f)\n", __func__, dict->s[c0].name, dict->s[c1].name, j, link->n0, norm, qla);
#endif
continue;
}
v = c0<<1 | (j>>1);
w = c1<<1 | (j&1);
if (telo_ends[v^1] || telo_ends[w])
continue;
arc = graph_add_arc(g, v, w, -1, 0, norm);
graph_add_arc(g, w^1, v^1, arc->link_id, 0, norm);
}
}
}
}
graph_arc_sort(g);
graph_arc_index(g);
return g;
}
#define MAX_TELO_CLIP 50
int8_t *find_aseq_telos(asm_dict_t *dict, int8_t *telo_ends)
{
int i, n;
int8_t *telos;
sdict_t *sdict;
sd_aseq_t *aseq;
sd_seg_t *segs, *seg;
sdict = dict->sdict;
n = dict->n;
telos = (int8_t *) calloc(dict->n * 2, sizeof(int8_t));
segs = dict->seg;
for (i = 0; i < n; i++) {
aseq = &dict->s[i];
// first seg
seg = &segs[aseq->s];
if ((telo_ends[seg->c>>1<<1] && seg->x <= MAX_TELO_CLIP && (seg->c&1) == 0) ||
(telo_ends[seg->c>>1<<1|1] && (seg->x + seg->y + MAX_TELO_CLIP) >= sdict->s[seg->c>>1].len && (seg->c&1) == 1))
telos[i<<1] = 1;
// last seg
seg = &segs[aseq->s + aseq->n - 1];
if ((telo_ends[seg->c>>1<<1] && seg->x <= MAX_TELO_CLIP && (seg->c&1) == 1) ||
(telo_ends[seg->c>>1<<1|1] && (seg->x + seg->y + MAX_TELO_CLIP) >= sdict->s[seg->c>>1].len && (seg->c&1) == 0))
telos[i<<1|1] = 1;
}
return telos;
}
int run_scaffolding(char *fai, char *agp, char *link_file, cov_norm_t *cov_norm, uint32_t ml, uint8_t mq, re_cuts_t *re_cuts, int8_t *telo_ends, char *out, int resolution, double *noise, uint32_t d_min_cell, double d_mass_frac, long rss_limit, int no_mem_check)
{
//TODO: adjust wt thres by resolution
sdict_t *sdict = make_sdict_from_index(fai, ml);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
int i, re = 0;
uint64_t len = 0;
for (i = 0; i < dict->n; ++i)
len += dict->s[i].len;
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] #sequences loaded %d = %lubp\n", __func__, dict->n, len);
#endif
long rss_intra, rss_inter;
rss_intra = no_mem_check? 0 : estimate_intra_link_mat_init_rss(dict, resolution, 1);
if ((rss_limit >= 0 && rss_intra > rss_limit) || rss_intra < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try lower resolutions... End of scaffolding round.\n", __func__);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
fprintf(stderr, "[I::%s] RAM required: %.3fGB\n", __func__, (double) rss_intra / GB);
re = ENOMEM_ERR;
goto scaff_failed_0;
}
rss_limit -= rss_intra;
fprintf(stderr, "[I::%s] starting norm estimation...\n", __func__);
intra_link_mat_t *intra_link_mat = intra_link_mat_from_file(link_file, cov_norm, dict, re_cuts, resolution, 1, mq);
#ifdef DEBUG_RAM_USAGE
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM peak: %.3fGB\n", __func__, (double) peakrss() / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM intra: %.3fGB\n", __func__, (double) rss_intra / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM free: %.3fGB\n", __func__, (double) rss_limit / GB);
#endif
norm_t *norm = calc_norms(intra_link_mat, d_min_cell, d_mass_frac);
if (norm == 0) {
fprintf(stderr, "[W::%s] No enough bands for norm calculation... End of scaffolding round.\n", __func__);
re = ENOBND_ERR;
goto scaff_failed_1;
}
rss_inter = no_mem_check? 0 : estimate_inter_link_mat_init_rss(dict, resolution, norm->r);
if ((rss_limit >= 0 && rss_inter > rss_limit) || rss_inter < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try lower resolutions... End of scaffolding round.\n", __func__);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
fprintf(stderr, "[I::%s] RAM required: %.3fGB\n", __func__, (double) rss_inter / GB);
re = ENOMEM_ERR;
goto scaff_failed_1;
}
rss_limit -= rss_inter;
fprintf(stderr, "[I::%s] starting link estimation...\n", __func__);
inter_link_mat_t *inter_link_mat = inter_link_mat_from_file(link_file, cov_norm, dict, re_cuts, resolution, norm->r, mq);
#ifdef DEBUG_RAM_USAGE
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM peak: %.3fGB\n", __func__, (double) peakrss() / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM inter: %.3fGB\n", __func__, (double) rss_inter / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM free: %.3fGB\n", __func__, (double) rss_limit / GB);
#endif
*noise = inter_link_mat->noise / resolution / resolution;
double la;
re = inter_link_norms(inter_link_mat, norm, 1, max_noise_ratio, &la);
if (re) {
goto scaff_failed_2;
}
int8_t *directs = 0;
// directs = calc_link_directs_from_file(link_file, dict);
calc_link_directs(inter_link_mat, .1, dict, directs);
if(directs) free(directs);
#ifdef DEBUG_LINK
fprintf(stderr, "[DEBUG_LINK::%s] print_inter_link_norms\n", __func__);
print_inter_link_norms(stderr, inter_link_mat, dict);
#endif
int8_t *telos;
telos = find_aseq_telos(dict, telo_ends);
fprintf(stderr, "[I::%s] starting scaffolding graph contruction...\n", __func__);
graph_t *g = build_graph_from_links(inter_link_mat, dict, .1, la, telos);
free(telos);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (before pruning) in GV format\n", __func__);
graph_print_gv(g, stderr);
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (before pruning) in GFA format\n", __func__);
graph_print(g, stderr, 1);
#endif
uint64_t n_arc;
n_arc = g->n_arc;
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges before trimming: %ld\n", __func__, n_arc);
int round = 0;
#endif
while (1) {
trim_graph_simple_filter(g, .1, .7, .1, 0);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges after simple trimming round %d: %ld\n", __func__, round, g->n_arc);
graph_print_gv(g, stderr);
#endif
trim_graph_tips(g);
trim_graph_blunts(g);
trim_graph_repeats(g);
trim_graph_transitive_edges(g);
trim_graph_pop_bubbles(g);
trim_graph_pop_undirected(g);
trim_graph_weak_edges(g);
trim_graph_self_loops(g);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges after trimming round %d: %ld\n", __func__, ++round, g->n_arc);
graph_print_gv(g, stderr);
#endif
if (g->n_arc == n_arc)
break;
else
n_arc = g->n_arc;
}
trim_graph_ambiguous_edges(g);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (after pruning) in GV format\n", __func__);
graph_print_gv(g, stderr);
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (after pruning) in GFA format\n", __func__);
graph_print(g, stderr, 1);
#endif
asm_dict_t *d = make_asm_dict_from_graph(g, g->sdict);
// write scaffolds to AGP file
FILE *agp_out = NULL;
if (out) {
char *agp_out_name = (char *) malloc(strlen(out) + 5);
sprintf(agp_out_name, "%s.agp", out);
agp_out = fopen(agp_out_name, "w");
free(agp_out_name);
} else {
agp_out = fopen("scaffolds_FINAL.agp", "w");
}
if (agp_out == NULL) {
fprintf(stderr, "[E::%s] fail to open file to write\n", __func__);
re = 1;
} else {
write_asm_dict_to_agp(d, agp_out);
fclose(agp_out);
}
asm_destroy(d);
graph_destroy(g);
scaff_failed_2:
inter_link_mat_destroy(inter_link_mat);
scaff_failed_1:
norm_destroy(norm);
intra_link_mat_destroy(intra_link_mat);
scaff_failed_0:
asm_destroy(dict);
sd_destroy(sdict);
return re;
}
int contig_error_break(char *agp, char *fai, char *link_file, uint32_t ml, char *out)
{
uint32_t i, ec_round, err_no, bp_n;
sdict_t *sdict;
asm_dict_t *dict;
int dist_thres;
sdict = make_sdict_from_index(fai, ml);
dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
dist_thres = estimate_dist_thres_from_file(link_file, dict, ec_min_frac, ec_resolution, 0);
dist_thres = MAX(dist_thres, ec_min_window);
fprintf(stderr, "[I::%s] dist threshold for contig error break: %d\n", __func__, dist_thres);
char* out1 = (char *) malloc(strlen(out) + 35);
ec_round = err_no = 0;
while (1) {
if (ec_round) dict = make_asm_dict_from_agp(sdict, out1, 1);
link_mat_t *link_mat = link_mat_from_file(link_file, dict, dist_thres, ec_bin, .0, ec_move_avg, 0);
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] ec_round %u link matrix\n", __func__, ec_round);
print_link_mat(link_mat, dict, stderr);
#endif
bp_n = 0;
bp_t *breaks = detect_break_points(link_mat, ec_bin, ec_merge_thresh, ec_fold_thresh, ec_dual_break_thresh, &bp_n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] number contig breaks in round %u: %u\n", __func__, ec_round + 1, bp_n);
#endif
sprintf(out1, "%s_%02d.agp", out, ++ec_round);
FILE *agp_out = fopen(out1, "w");
write_break_agp(dict, breaks, bp_n, agp_out);
fclose(agp_out);
link_mat_destroy(link_mat);
asm_destroy(dict);
for (i = 0; i < bp_n; ++i)
free(breaks[i].p);
free(breaks);
err_no += bp_n;
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] bp_n %d\n", __func__, bp_n);
#endif
if (!bp_n)
break;
}
sd_destroy(sdict);
free(out1);
fprintf(stderr, "[I::%s] performed %u round assembly error correction. Made %u breaks \n", __func__, ec_round, err_no);
return ec_round;
}
int scaffold_error_break(char *fai, char *link_file, uint32_t ml, uint8_t mq, char *agp, int flank_size, double noise, char *out)
{
int dist_thres;
sdict_t *sdict = make_sdict_from_index(fai, ml);
asm_dict_t *dict = make_asm_dict_from_agp(sdict, agp, 1);
dist_thres = flank_size * 2;
//dist_thres = estimate_dist_thres_from_file(link_file, dict, ec_min_frac, ec_resolution);
//dist_thres = MAX(dist_thres, ec_min_window);
//fprintf(stderr, "[I::%s] dist threshold for scaffold error break: %d\n", __func__, dist_thres);
link_mat_t *link_mat = link_mat_from_file(link_file, dict, dist_thres, ec_bin, noise, ec_move_avg, mq);
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] link matrix\n", __func__);
print_link_mat(link_mat, dict, stderr);
#endif
uint32_t bp_n = 0;
bp_t *breaks = detect_break_points_local_joint(link_mat, ec_bin, ec_fold_thresh, flank_size, dict, &bp_n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] number scaffold breaks: %u\n", __func__, bp_n);
#endif
FILE *agp_out = fopen(out, "w");
write_break_agp(dict, breaks, bp_n, agp_out);
fclose(agp_out);
link_mat_destroy(link_mat);
asm_destroy(dict);
sd_destroy(sdict);
int i;
for (i = 0; i < bp_n; ++i)
free(breaks[i].p);
free(breaks);
return bp_n;
}
static void print_asm_stats(uint64_t *n_stats, uint32_t *l_stats, int all)
{
#ifdef DEBUG
int i;
fprintf(stderr, "[I::%s] assembly stats:\n", __func__);
for (i = 0; i < 10; ++i)
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, (i + 1) * 10, n_stats[i], l_stats[i]);
#else
fprintf(stderr, "[I::%s] assembly stats:\n", __func__);
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 50, n_stats[4], l_stats[4]);
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 90, n_stats[8], l_stats[8]);
if (all)
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 100, n_stats[9], l_stats[9]);
#endif
}
int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, char *out, int *resolutions, int nr, int rr, re_cuts_t *re_cuts, int8_t *telo_ends, uint32_t d_min_cell, double d_mass_frac, int no_contig_ec, int no_scaffold_ec, int no_mem_check)
{
int ec_round, resolution, re, r, rn, rc, ex;
uint64_t n50;
char *out_fn, *out_agp, *out_agp_break;
double noise;
FILE *fo;
sdict_t *sdict;
asm_dict_t *dict;
cov_norm_t *cov_norm;
long rss_total, rss_limit;
ram_limit(&rss_total, &rss_limit);
fprintf(stderr, "[I::%s] RAM total: %.3fGB\n", __func__, (double) rss_total / GB);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
if (no_mem_check)
fprintf(stderr, "[I::%s] RAM check disabled\n", __func__);
sdict = make_sdict_from_index(fai, ml);
out_fn = (char *) malloc(strlen(out) + 35);
out_agp = (char *) malloc(strlen(out) + 35);
out_agp_break = (char *) malloc(strlen(out) + 35);
if (no_contig_ec == 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] perform contig error break...\n", __func__);
#endif
sprintf(out_agp_break, "%s_inital_break", out);
ec_round = contig_error_break(agp, fai, link_file, ml, out_agp_break);
sprintf(out_agp_break, "%s_inital_break_%02d.agp", out, ec_round);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] contig error break done\n", __func__);
#endif
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] no contig error break...\n", __func__);
#endif
if (agp != 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] use input AGP file\n", __func__);
#endif
if (strlen(agp) > strlen(out)) {
free(out_agp_break);
out_agp_break = (char *) malloc(strlen(agp) + 35);
}
sprintf(out_agp_break, "%s", agp);
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] make AGP file from input FASTA file\n", __func__);
#endif
sprintf(out_agp_break, "%s_no_break.agp", out);
fo = fopen(out_agp_break, "w");
if (fo == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out_agp_break);
exit(EXIT_FAILURE);
}
write_sdict_to_agp(sdict, fo);
fclose(fo);
}
}
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
if (dict->n > MAX_N_SEQ) {
fprintf(stderr, "[E::%s] sequence number exceeds limit (%d > %d)\n", __func__, dict->n, MAX_N_SEQ);
fprintf(stderr, "[E::%s] consider removing short sequences before scaffolding, or\n", __func__);
fprintf(stderr, "[E::%s] running without error correction (--no-contig-ec) if due to excessive contig error breaks\n", __func__);
fprintf(stderr, "[E::%s] program halted...\n", __func__);
return 1;
}
asm_sd_stats(dict, n_stats, l_stats);
print_asm_stats(n_stats, l_stats, 1);
asm_destroy(dict);
cov_norm = cov_norm_from_file(link_file, sdict);
r = rc = 0;
rn = rr;
ex = max_extra_try;
while (r < nr) {
resolution = resolutions[r];
// dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
if (n_stats[4] < resolution * 10) {
if (!ex) {
fprintf(stderr, "[I::%s] assembly N50 (%lu) too small. End of scaffolding.\n", __func__, n_stats[4]);
fprintf(stderr, "[I::%s] consider running with increased memory limit if there was a memory issue.\n", __func__);
break;
} else {
if (r > 0)
resolution = resolutions[r - 1]; // use the previous resolution level
else {
resolution /= 10;
if (resolution < 1000)
resolution = 1000;
if (resolution > resolutions[0])
resolution = resolutions[0] / 2;
}
fprintf(stderr, "[I::%s] assembly N50 (%lu) too small.\n", __func__, n_stats[4]);
fprintf(stderr, "[I::%s] do an extra round scaffolding with resolution = %d\n", __func__, resolution);
ex--; // increase extra try number
}
} else {
rn--;
if (!rn || n_stats[8] > resolution * 10) {
r++; // move to the next resolution level
rn = rr;
}
ex = max_extra_try; // reset extra try number
}
rc++;
fprintf(stderr, "[I::%s] scaffolding round %d resolution = %d\n", __func__, rc, resolution);
sprintf(out_fn, "%s_r%02d", out, rc);
// noise per unit
re = run_scaffolding(fai, out_agp_break, link_file, cov_norm, ml, mq, re_cuts, telo_ends, out_fn, resolution,
&noise, d_min_cell, d_mass_frac, rss_limit, no_mem_check);
if (!re) {
sprintf(out_agp, "%s_r%02d.agp", out, rc);
if (no_scaffold_ec == 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] perform scaffold error break\n", __func__);
#endif
sprintf(out_agp_break, "%s_r%02d_break.agp", out, rc);
scaffold_error_break(fai, link_file, ml, mq, out_agp, resolution, noise, out_agp_break);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] scaffold error break done\n", __func__);
#endif
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] no scaffold error break\n", __func__);
#endif
sprintf(out_agp_break, "%s", out_agp);
}
}
// asm_destroy(dict);
fprintf(stderr, "[I::%s] scaffolding round %d done\n", __func__, rc);
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
n50 = n_stats[4]; // old n50
asm_sd_stats(dict, n_stats, l_stats);
// no improvements in a retry round
if (ex < max_extra_try && n50 == n_stats[4])
ex = 0;
print_asm_stats(n_stats, l_stats, 0);
asm_destroy(dict);
/***
if (re && re != ENOMEM_ERR) {
fprintf(stderr, "[I::%s] Reach data limit for HiC contact density estimation in lower resulutions. End of scaffolding.\n", __func__);
break;
}
**/
}
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] make final output...\n", __func__);
#endif
sprintf(out_agp, "%s_scaffolds_final.agp", out);
// output sorted agp by scaffold size instead of file copy
// file_copy(out_agp_break, out_agp);
if (ml > 0) {
// add short sequences to dict
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] add unused short sequences back...\n", __func__);
#endif
sd_destroy(sdict);
sdict = make_sdict_from_index(fai, 0);
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
add_unplaced_short_seqs(dict, ml);
} else {
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
}
fo = fopen(out_agp, "w");
if (fo == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out_agp);
exit(EXIT_FAILURE);
}
write_sorted_agp(dict, fo);
fclose(fo);
asm_destroy(dict);
sd_destroy(sdict);
cov_norm_destroy(cov_norm);
free(out_agp);
free(out_fn);
free(out_agp_break);
return 0;
}
#ifndef DEBUG_GT4G
static int default_resolutions[15] = {10000, 20000, 50000, 100000, 200000, 500000, 1000000, 2000000, 5000000, 10000000, 20000000, 50000000, 100000000, 200000000, 500000000};
#else
static int default_resolutions[13] = {50000, 100000, 250000, 500000, 1000000, 2500000, 5000000, 10000000, 25000000, 50000000, 100000000, 250000000, 500000000};
#endif
static int default_nr(char *fai, uint32_t ml)
{
int i, max_res, nr;
int64_t genome_size;
genome_size = 0;
sdict_t *sdict = make_sdict_from_index(fai, ml);
for (i = 0; i < sdict->n; ++i)
genome_size += sdict->s[i].len;
sd_destroy(sdict);
max_res = 0;
if (genome_size < 100000000)
max_res = 1000000;
else if (genome_size < 200000000)
max_res = 2000000;
else if (genome_size < 500000000)
max_res = 5000000;
else if (genome_size < 1000000000)
max_res = 10000000;
else if (genome_size < 2000000000)
max_res = 20000000;
else if (genome_size < 5000000000)
max_res = 50000000;
else if (genome_size < 10000000000)
max_res = 100000000;
else if (genome_size < 20000000000)
max_res = 200000000;
else
max_res = 500000000;
nr = 0;
while (nr < sizeof(default_resolutions) / sizeof(int) && default_resolutions[nr] <= max_res)
++nr;
return nr;
}
static void print_help(FILE *fp_help, int is_long_help)
{
fprintf(fp_help, "Usage: yahs [options] <contigs.fa> <hic.bed>|<hic.bam>|<hic.pa5>|<hic.bin>\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " -a FILE AGP file (for rescaffolding) [none]\n");
fprintf(fp_help, " -r INT[,INT,...] list of resolutions in ascending order [automate]\n");
fprintf(fp_help, " -R INT rounds to run at each resoultion level [1]\n");
fprintf(fp_help, " -e STR restriction enzyme cutting sites [none]\n");
fprintf(fp_help, " -l INT minimum length of a contig to scaffold [0]\n");
fprintf(fp_help, " -q INT minimum mapping quality [10]\n");
fprintf(fp_help, "\n");
fprintf(fp_help, " --no-contig-ec do not do contig error correction\n");
fprintf(fp_help, " --no-scaffold-ec do not do scaffold error correction\n");
fprintf(fp_help, " --no-mem-check do not do memory check at runtime\n");
fprintf(fp_help, " --file-type STR input file type BED|BAM|PA5|BIN, file name extension is ignored if set\n");
fprintf(fp_help, " --read-length read length (required for PA5 format input) [150]\n");
fprintf(fp_help, " --telo-motif STR telomeric sequence motif\n");
if (is_long_help) {
fprintf(fp_help, "\n");
fprintf(fp_help, " --D-min-cells INT minimum number of cells to calculate the distance threshold [30]\n");
fprintf(fp_help, " --D-mass-frac FLOAT fraction of HiC signals to calculate the distance threshold [0.99]\n");
fprintf(fp_help, "\n");
fprintf(fp_help, " --seq-ctype STR AGP output sequence component type [%s]\n", agp_component_type_val(DEFAULT_AGP_SEQ_COMPONENT_TYPE));
fprintf(fp_help, " --gap-ctype STR AGP output gap component type [%s]\n", agp_component_type_val(DEFAULT_AGP_GAP_COMPONENT_TYPE));
fprintf(fp_help, " --gap-link STR AGP output gap linkage evidence [%s]\n", agp_linkage_evidence_val(DEFAULT_AGP_LINKAGE_EVIDENCE));
fprintf(fp_help, " --gap-size INT AGP output gap size between sequence component [%d]\n", DEFAULT_AGP_GAP_SIZE);
fprintf(fp_help, "\n");
fprintf(fp_help, " --convert-to-binary make a binary ouput file from the input and exit\n");
fprintf(fp_help, " --print-telo-motifs print telomeric motifs in the database and exit\n");
fprintf(fp_help, " --search-telo-ends search telomeric ends in the sequences and exit\n");
}
fprintf(fp_help, "\n");
fprintf(fp_help, " -o STR prefix of output files [yahs.out]\n");
fprintf(fp_help, " -v INT verbose level [%d]\n", VERBOSE);
fprintf(fp_help, " -? print long help with extra option list\n");
fprintf(fp_help, " --version show version number\n");
}
static ko_longopt_t long_options[] = {
{ "no-contig-ec", ko_no_argument, 301 },
{ "no-scaffold-ec", ko_no_argument, 302 },
{ "no-mem-check", ko_no_argument, 303 },
{ "D-min-cells", ko_required_argument, 304 },
{ "D-mass-frac", ko_required_argument, 305 },
{ "file-type", ko_required_argument, 306 },
{ "seq-ctype", ko_required_argument, 307 },
{ "gap-ctype", ko_required_argument, 308 },
{ "gap-link", ko_required_argument, 309 },
{ "gap-size", ko_required_argument, 310 },
{ "read-length", ko_required_argument, 311 },
{ "telo-motif", ko_required_argument, 312 },
{ "print-telo-motifs", ko_no_argument, 313 },
{ "search-telo-ends", ko_no_argument, 314 },
{ "convert-to-binary", ko_no_argument, 315 },
{ "help", ko_no_argument, 'h' },
{ "version", ko_no_argument, 'V' },
{ 0, 0, 0 }
};
typedef struct {size_t n, m; char **a;} cstr_v;
int main(int argc, char *argv[])
{
if (argc < 2) {
print_help(stderr, 0);
return 1;
}
liftrlimit();
ys_realtime0 = realtime();
char *fa, *fai, *agp, *link_file, *out, *restr, *ecstr, *ext1, *ext2, *link_bin_file, *agp_final, *fa_final;
int *resolutions, nr, rr, mq, ml, rl;
int no_contig_ec, no_scaffold_ec, no_mem_check, d_min_cell, print_telomotifs, search_teloends, convert_binary;
int8_t *telo_ends;
double q_drop, d_mass_frac;
enum fileTypes f_type;
const char *opt_str = "a:e:r:R:o:l:q:Vv:h";
ketopt_t opt = KETOPT_INIT;
int c, ret, is_long_help;
FILE *fp_help = stderr;
fa = fai = agp = link_file = out = restr = link_bin_file = agp_final = fa_final = 0;
no_contig_ec = no_scaffold_ec = no_mem_check = 0;
rr = 1;
mq = 10;
ml = 0;
rl = 150;
ecstr = 0;
q_drop = 0.1;
d_min_cell = 30;
d_mass_frac = 0.99;
convert_binary = 0;
print_telomotifs = 0;
search_teloends = 0;
f_type = NOSET;
is_long_help = 0;
while ((c = ketopt(&opt, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'a') {
agp = opt.arg;
} else if (c == 'r') {
restr = opt.arg;
} else if (c == 'R') {
rr = atoi(opt.arg);
} else if (c == 'o') {
out = opt.arg;
} else if (c == 'l') {
ml = atoi(opt.arg);
} else if (c == 'q') {
mq = atoi(opt.arg);
} else if (c == 'e') {
// make a copy of ecstr to make sure the CMD correct
ecstr = strdup(opt.arg);
} else if (c == 301) {
no_contig_ec = 1;
} else if (c == 302) {
no_scaffold_ec = 1;
} else if (c == 303) {
no_mem_check = 1;
} else if (c == 304) {
d_min_cell = atoi(opt.arg);
} else if (c == 305) {
d_mass_frac = atof(opt.arg);
} else if (c == 306) {
if (strcasecmp(opt.arg, "BED") == 0)
f_type = BED;
else if (strcasecmp(opt.arg, "BAM") == 0)
f_type = BAM;
else if (strcasecmp(opt.arg, "BIN") == 0)
f_type = BIN;
else if (strcasecmp(opt.arg, "PA5") == 0)
f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown file type: \"%s\"\n", __func__, opt.arg);
return 1;
}
} else if (c == 307) {
DEFAULT_AGP_SEQ_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_N ||
DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_U)
fprintf(stderr, "[W::%s] a GAP component identifier will be used for sequences: %s\n",
__func__, opt.arg);
} else if (c == 308) {
DEFAULT_AGP_GAP_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_N &&
DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_U)
fprintf(stderr, "[W::%s] a SEQ component identifier will be used for gaps: %s\n",
__func__, opt.arg);
} else if (c == 309) {
DEFAULT_AGP_LINKAGE_EVIDENCE = agp_linkage_evidence_key(opt.arg);
} else if (c == 310) {
DEFAULT_AGP_GAP_SIZE = atoi(opt.arg);
} else if (c == 311) {
rl = atoi(opt.arg);
} else if (c == 312) {
telo_motif = opt.arg;
} else if (c == 313) {
print_telomotifs = 1;
} else if (c == 314) {
search_teloends = 1;
} else if (c == 315) {
convert_binary = 1;
} else if (c == 'v') {
VERBOSE = atoi(opt.arg);
} else if (c == 'V') {
puts(YAHS_VERSION);
return 0;
} else if (c == 'h') {
fp_help = stdout;
} else if (c == '?') {
if (argv[opt.i - 1][1] == '?') {
fp_help = stdout;
is_long_help = 1;
} else {
fprintf(stderr, "[E::%s] unknown option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
} else if (c == ':') {
fprintf(stderr, "[E::%s] missing option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
}
if (fp_help == stdout) {
print_help(stdout, is_long_help);
return 0;
}
if (print_telomotifs) {
fprintf(stderr, "[I::%s] telomeric motifs in the database:\n", __func__);
list_telo_motifs(stderr);
return 0;
}
if (search_teloends) {
if (argc - opt.ind < 1) {
fprintf(stderr, "[E::%s] missing input: need a FASTA file\n", __func__);
return 1;
}
fprintf(stderr, "[I::%s] search telomeric ends in the sequence:\n", __func__);
telo_ends = telo_finder(argv[opt.ind], 0);
if (telo_ends)
free(telo_ends);
return 0;
}
if (argc - opt.ind < 2) {
fprintf(stderr, "[E::%s] missing input: two positional options required\n", __func__);
print_help(stderr, is_long_help);
return 1;
}
if (mq < 0 || mq > 255) {
fprintf(stderr, "[E::%s] invalid mapping quality threshold: %d\n", __func__, mq);
return 1;
}
if (ml < 0) {
fprintf(stderr, "[E::%s] invalid contig length threshold: %d\n", __func__, ml);
return 1;
}
if (rl < 0) {
fprintf(stderr, "[E::%s] invalid read length: %d\n", __func__, rl);
return 1;
}
if (check_motif(telo_motif)) {
fprintf(stderr, "[E::%s] invalid telomeric motif string: %s\n", __func__, telo_motif);
return 1;
}
if (rr < 1) {
rr = 1;
fprintf(stderr, "[W::%s] set round number to %d\n", __func__, rr);
}
if (d_min_cell < 10) {
d_min_cell = 10;
fprintf(stderr, "[W::%s] using cell threshold for D: %d\n", __func__, d_min_cell);
}
if (d_mass_frac < 0.8) {
d_mass_frac = 0.8;
fprintf(stderr, "[W::%s] using mass fraction threshold for D: %.2f\n", __func__, d_mass_frac);
}
if (d_mass_frac > 1.0) {
d_mass_frac = 1.0;
fprintf(stderr, "[W::%s] using mass fraction threshold for D: %.2f\n", __func__, d_mass_frac);
}
if (DEFAULT_AGP_GAP_COMPONENT_TYPE == AGP_CT_U && DEFAULT_AGP_GAP_SIZE != DEFAULT_AGP_U_GAP_SIZE)
fprintf(stderr, "[W::%s] type 'U' gap size is not %d\n", __func__, DEFAULT_AGP_U_GAP_SIZE);
fa = argv[opt.ind];
link_file = argv[opt.ind + 1];
if (f_type == NOSET) {
ext1 = strlen(link_file) >= 4? (link_file + strlen(link_file) - 4) : NULL;
ext2 = strlen(link_file) >= 7? (link_file + strlen(link_file) - 7) : NULL;
if (ext1 && !strcasecmp(ext1, ".bam")) f_type = BAM;
else if (ext1 && !strcasecmp(ext1, ".bin")) f_type = BIN;
else if ((ext1 && !strcasecmp(ext1, ".bed")) || (ext2 && !strcasecmp(ext2, ".bed.gz"))) f_type = BED;
else if ((ext1 && !strcasecmp(ext1, ".pa5")) || (ext2 && !strcasecmp(ext2, ".pa5.gz"))) f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown link file format. File extension .bam, .bed, .pa5 or .bin or --file-type is expected\n", __func__);
exit(EXIT_FAILURE);
}
}
if (f_type == BIN && (strcmp(link_file, "-") == 0 || *link_file == '<')) {
fprintf(stderr, "[E::%s] BIN file format from STDIN is not supported\n", __func__);
exit(EXIT_FAILURE);
}
uint8_t mq8;
mq8 = (uint8_t) mq;
if (out == 0)
out = "yahs.out";
fai = (char *) malloc(strlen(fa) + 5);
sprintf(fai, "%s.fai", fa);
if (restr) {
// resolutions
int max_n_res = 128;
char *eptr, *fptr;
resolutions = (int *) malloc(max_n_res * sizeof(int));
nr = 0;
resolutions[nr++] = strtol(restr, &eptr, 10);
while (*eptr != '\0') {
if (nr == max_n_res) {
fprintf(stderr, "[E::%s] more than %d resolutions specified. Is that really necessary?\n", __func__, max_n_res);
exit(EXIT_FAILURE);
}
resolutions[nr++] = strtol(eptr + 1, &fptr, 10);
eptr = fptr;
}
} else {
resolutions = default_resolutions;
nr = default_nr(fai, ml);
}
re_cuts_t *re_cuts;
re_cuts = 0;
if (ecstr) {