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wgsim-trans.c
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/* The MIT License
Copyright (c) 2008 Genome Research Ltd (GRL).
2011 Heng Li <[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.
*/
/* This program is separated from maq's read simulator with Colin
* Hercus' modification to allow longer indels. */
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <assert.h>
#include <stdio.h>
#include <unistd.h>
#include <stdint.h>
#include <ctype.h>
#include <string.h>
#include <zlib.h>
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
#define PACKAGE_VERSION "0.3.1-r13-trans-Nov2016"
const uint8_t nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
static unsigned int DEBUG = 0;
/* Simple normal random number generator, copied from genran.c */
double ran_normal()
{
static int iset = 0;
static double gset;
double fac, rsq, v1, v2;
if (iset == 0) {
do {
v1 = 2.0 * drand48() - 1.0;
v2 = 2.0 * drand48() - 1.0;
rsq = v1 * v1 + v2 * v2;
} while (rsq >= 1.0 || rsq == 0.0);
fac = sqrt(-2.0 * log(rsq) / rsq);
gset = v1 * fac;
iset = 1;
return v2 * fac;
} else {
iset = 0;
return gset;
}
}
/* wgsim */
enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};
typedef unsigned short mut_t;
static mut_t mutmsk = (mut_t)0xf000;
typedef struct {
int l, m; /* length and maximum buffer size */
mut_t *s; /* sequence */
} mutseq_t;
static double ERR_RATE = 0.02;
static double MUT_RATE = 0.001;
static double INDEL_FRAC = 0.15;
static double INDEL_EXTEND = 0.3;
static double MAX_N_RATIO = 0.05;
void wgsim_mut_diref(const kseq_t *ks, int is_hap, mutseq_t *hap1, mutseq_t *hap2)
{
int i, deleting = 0;
mutseq_t *ret[2];
ret[0] = hap1; ret[1] = hap2;
ret[0]->l = ks->seq.l; ret[1]->l = ks->seq.l;
ret[0]->m = ks->seq.m; ret[1]->m = ks->seq.m;
ret[0]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
ret[1]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
for (i = 0; i != ks->seq.l; ++i) {
int c;
c = ret[0]->s[i] = ret[1]->s[i] = (mut_t)nst_nt4_table[(int)ks->seq.s[i]];
if (deleting) {
if (drand48() < INDEL_EXTEND) {
if (deleting & 1) ret[0]->s[i] |= DELETE;
if (deleting & 2) ret[1]->s[i] |= DELETE;
continue;
} else deleting = 0;
}
if (c < 4 && drand48() < MUT_RATE) { // mutation
if (drand48() >= INDEL_FRAC) { // substitution
double r = drand48();
c = (c + (int)(r * 3.0 + 1)) & 3;
if (is_hap || drand48() < 0.333333) { // hom
ret[0]->s[i] = ret[1]->s[i] = SUBSTITUTE|c;
} else { // het
ret[drand48()<0.5?0:1]->s[i] = SUBSTITUTE|c;
}
} else { // indel
if (drand48() < 0.5) { // deletion
if (is_hap || drand48() < 0.333333) { // hom-del
ret[0]->s[i] = ret[1]->s[i] = DELETE;
deleting = 3;
} else { // het-del
deleting = drand48()<0.5?1:2;
ret[deleting-1]->s[i] = DELETE;
}
} else { // insertion
int num_ins = 0, ins = 0;
do {
num_ins++;
ins = (ins << 2) | (int)(drand48() * 4.0);
} while (num_ins < 4 && drand48() < INDEL_EXTEND);
if (is_hap || drand48() < 0.333333) { // hom-ins
ret[0]->s[i] = ret[1]->s[i] = (num_ins << 12) | (ins << 4) | c;
} else { // het-ins
ret[drand48()<0.5?0:1]->s[i] = (num_ins << 12) | (ins << 4) | c;
}
}
}
}
}
}
void wgsim_print_mutref(const char *name, const kseq_t *ks, mutseq_t *hap1, mutseq_t *hap2)
{
int i, j = 0; // j keeps the end of the last deletion
for (i = 0; i != ks->seq.l; ++i) {
int c[3];
c[0] = nst_nt4_table[(int)ks->seq.s[i]];
c[1] = hap1->s[i]; c[2] = hap2->s[i];
if (c[0] >= 4) continue;
if ((c[1] & mutmsk) != NOCHANGE || (c[2] & mutmsk) != NOCHANGE) {
if (c[1] == c[2]) { // hom
if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
printf("%s\t%d\t%c\t%c\t-\n", name, i+1, "ACGTN"[c[0]], "ACGTN"[c[1]&0xf]);
} else if ((c[1]&mutmsk) == DELETE) { // del
if (i >= j) {
printf("%s\t%d\t", name, i+1);
for (j = i; j < ks->seq.l && hap1->s[j] == hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
printf("\t-\t-\n");
}
} else if (((c[1] & mutmsk) >> 12) <= 4) { // ins
printf("%s\t%d\t-\t", name, i+1);
int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
while (n > 0) {
putchar("ACGTN"[ins & 0x3]);
ins >>= 2;
n--;
}
printf("\t-\n");
} // else: deleted base in a long deletion
} else { // het
if ((c[1]&mutmsk) == SUBSTITUTE || (c[2]&mutmsk) == SUBSTITUTE) { // substitution
printf("%s\t%d\t%c\t%c\t+\n", name, i+1, "ACGTN"[c[0]], "XACMGRSVTWYHKDBN"[1<<(c[1]&0x3)|1<<(c[2]&0x3)]);
} else if ((c[1]&mutmsk) == DELETE) {
if (i >= j) {
printf("%s\t%d\t", name, i+1);
for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
printf("\t-\t-\n");
}
} else if ((c[2]&mutmsk) == DELETE) {
if (i >= j) {
printf("%s\t%d\t", name, i+1);
for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap2->s[j]&mutmsk) == DELETE; ++j)
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
printf("\t-\t-\n");
}
} else if (((c[1] & mutmsk) >> 12) <= 4 && ((c[1] & mutmsk) >> 12) > 0) { // ins1
printf("%s\t%d\t-\t", name, i+1);
int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
while (n > 0) {
putchar("ACGTN"[ins & 0x3]);
ins >>= 2;
n--;
}
printf("\t+\n");
} else if (((c[2] & mutmsk) >> 12) <= 4 || ((c[2] & mutmsk) >> 12) > 0) { // ins2
printf("%s\t%d\t-\t", name, i+1);
int n = (c[2]&mutmsk) >> 12, ins = c[2] >> 4;
while (n > 0) {
putchar("ACGTN"[ins & 0x3]);
ins >>= 2;
n--;
}
printf("\t+\n");
} // else: deleted base in a long deletion
}
}
}
}
void wgsim_core(FILE *fpout1, FILE *fpout2, const char *fn, int is_hap, uint64_t N, int dist, int std_dev, int size_l, int size_r, int strand_specific_mode)
{
kseq_t *ks;
mutseq_t rseq[2];
gzFile fp_fa;
uint64_t tot_len, ii;
int i, l, n_ref;
char *qstr;
int size[2], Q, max_size;
uint8_t *tmp_seq[2];
mut_t *target;
l = size_l > size_r? size_l : size_r;
qstr = (char*)calloc(l+1, 1);
tmp_seq[0] = (uint8_t*)calloc(l+2, 1);
tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
size[0] = size_l; size[1] = size_r;
max_size = size_l > size_r? size_l : size_r;
Q = (ERR_RATE == 0.0)? 'I' : (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;
fp_fa = gzopen(fn, "r");
ks = kseq_init(fp_fa);
tot_len = n_ref = 0;
fprintf(stderr, "[%s] calculating the total length of the reference sequence...\n", __func__);
while ((l = kseq_read(ks)) >= 0) {
tot_len += l;
++n_ref;
}
fprintf(stderr, "[%s] %d sequences, total length: %llu\n", __func__, n_ref, (long long)tot_len);
kseq_destroy(ks);
gzclose(fp_fa);
fp_fa = gzopen(fn, "r");
ks = kseq_init(fp_fa);
int max_tries = 50;
int num_tries = 0;
while ((l = kseq_read(ks)) >= 0) {
uint64_t n_pairs = (uint64_t)((long double)l / tot_len * N + 0.5);
/*
if (num_tries > max_tries) {
fprintf(stderr, "ERROR, too many failed attempts to simulate reads");
exit(3);
}
*/
//
//if (l < dist + 3 * std_dev) {
// fprintf(stderr, "[%s] skip sequence '%s' as it is shorter than %d!\n", __func__, ks->name.s, dist + 3 * std_dev);
// continue;
//}
if (ks->seq.l < max_size) {
fprintf(stderr, "[%s] skip sequence '%s' as it is shorter than max read length: %d!\n", __func__, ks->name.s, max_size);
continue;
}
// generate mutations and print them out
wgsim_mut_diref(ks, is_hap, rseq, rseq+1);
wgsim_print_mutref(ks->name.s, ks, rseq, rseq+1);
for (ii = 0; ii != n_pairs; ++ii) { // the core loop
double ran;
int d, pos, s[2], is_flip = 0;
int n_sub[2], n_indel[2], n_err[2], ext_coor[2], j, k;
FILE *fpo[2];
// compute a random fragment size according to avg and stdev for frag len dist.
ran = ran_normal();
ran = ran * std_dev + dist;
// ensure frag length is at least the size of the longest read
d = (int)(ran + 0.5);
d = d > max_size? d : max_size;
// determine random starting point for fragment
pos = (int)((l - d + 1) * drand48());
if (DEBUG)
fprintf(stderr, "seqLength:[%zu], ii:[%zu], ran:[%f], d=[%d], pos:[%d]\n", ks->seq.l, ii, ran, d, pos);
// flip or not
if (strand_specific_mode > 0) {
if (strand_specific_mode == 1) {
fpo[0] = fpout1; fpo[1] = fpout2;
s[0] = size[0]; s[1] = size[1];
} else {
fpo[1] = fpout1; fpo[0] = fpout2;
s[1] = size[0]; s[0] = size[1];
is_flip = 1;
}
}
else {
// randomly flip
if (drand48() < 0.5) {
fpo[0] = fpout1; fpo[1] = fpout2;
s[0] = size[0]; s[1] = size[1];
} else {
fpo[1] = fpout1; fpo[0] = fpout2;
s[1] = size[0]; s[0] = size[1];
is_flip = 1;
}
}
// generate the read sequences
target = rseq[drand48()<0.5?0:1].s; // haplotype from which the reads are generated
n_sub[0] = n_sub[1] = n_indel[0] = n_indel[1] = n_err[0] = n_err[1] = 0;
#define __gen_read(x, start, iter) do { \
for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \
int c = target[i], mut_type = c & mutmsk; \
if (ext_coor[x] < 0) { \
if (mut_type != NOCHANGE && mut_type != SUBSTITUTE) continue; \
ext_coor[x] = i; \
} \
if (mut_type == DELETE) ++n_indel[x]; \
else if (mut_type == NOCHANGE || mut_type == SUBSTITUTE) { \
tmp_seq[x][k++] = c & 0xf; \
if (mut_type == SUBSTITUTE) ++n_sub[x]; \
} else { \
int n, ins; \
++n_indel[x]; \
tmp_seq[x][k++] = c & 0xf; \
for (n = mut_type>>12, ins = c>>4; n > 0 && k < s[x]; --n, ins >>= 2) \
tmp_seq[x][k++] = ins & 0x3; \
} \
} \
if (k != s[x]) ext_coor[x] = -10; \
} while (0)
// simulate the read sequences
__gen_read(0, pos, ++i);
__gen_read(1, pos + d - 1, --i);
for (k = 0; k < s[1]; ++k) tmp_seq[1][k] = tmp_seq[1][k] < 4? 3 - tmp_seq[1][k] : 4; // complement
if (ext_coor[0] < 0 || ext_coor[1] < 0) { // fail to generate the read(s)
--ii;
if (DEBUG)
fprintf(stderr, "\tfailed to generate read.\n");
num_tries++;
continue;
}
// generate sequencing errors
for (j = 0; j < 2; ++j) {
int n_n = 0;
for (i = 0; i < s[j]; ++i) {
int c = tmp_seq[j][i];
if (c >= 4) { // actually c should be never larger than 4 if everything is correct
c = 4;
++n_n;
} else if (drand48() < ERR_RATE) {
// c = (c + (int)(drand48() * 3.0 + 1)) & 3; // random sequencing errors
c = (c + 1) & 3; // recurrent sequencing errors
++n_err[j];
}
tmp_seq[j][i] = c;
}
if ((double)n_n / s[j] > MAX_N_RATIO) break;
}
if (j < 2) { // too many ambiguous bases on one of the reads
--ii;
if (DEBUG)
fprintf(stderr, "too many ambiguous bases on one of the reads\n");
num_tries++;
continue;
}
// print
for (j = 0; j < 2; ++j) {
for (i = 0; i < s[j]; ++i) qstr[i] = Q;
qstr[i] = 0;
fprintf(fpo[j], "@%s_%u_%u_%d:%d:%d_%d:%d:%d_%llx/%d\n", ks->name.s, ext_coor[0]+1, ext_coor[1]+1,
n_err[0], n_sub[0], n_indel[0], n_err[1], n_sub[1], n_indel[1],
(long long)ii, j==0? is_flip+1 : 2-is_flip);
for (i = 0; i < s[j]; ++i)
fputc("ACGTN"[(int)tmp_seq[j][i]], fpo[j]);
fprintf(fpo[j], "\n+\n%s\n", qstr);
}
}
free(rseq[0].s); free(rseq[1].s);
}
kseq_destroy(ks);
gzclose(fp_fa);
free(qstr);
free(tmp_seq[0]); free(tmp_seq[1]);
}
static int simu_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: wgsim (short read simulator)\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <[email protected]>, trans mods by [email protected]\n\n");
fprintf(stderr, "Usage: wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>\n\n");
fprintf(stderr, "Options: -e FLOAT base error rate [%.3f]\n", ERR_RATE);
fprintf(stderr, " -d INT outer distance between the two ends [500]\n");
fprintf(stderr, " -s INT standard deviation [50]\n");
fprintf(stderr, " -N INT number of read pairs [1000000]\n");
fprintf(stderr, " -1 INT length of the first read [70]\n");
fprintf(stderr, " -2 INT length of the second read [70]\n");
fprintf(stderr, " -r FLOAT rate of mutations [%.4f]\n", MUT_RATE);
fprintf(stderr, " -R FLOAT fraction of indels [%.2f]\n", INDEL_FRAC);
fprintf(stderr, " -X FLOAT probability an indel is extended [%.2f]\n", INDEL_EXTEND);
fprintf(stderr, " -S INT seed for random generator [-1]\n");
fprintf(stderr, " -A FLOAT disgard if the fraction of ambiguous bases higher than FLOAT [%.2f]\n", MAX_N_RATIO);
fprintf(stderr, " -h haplotype mode\n");
fprintf(stderr, " -Z INT strand specific mode: 1=FR, 2=RF\n");
fprintf(stderr, " -D debug mode... highly verbose\n");
fprintf(stderr, "\n");
return 1;
}
int main(int argc, char *argv[])
{
int64_t N;
int dist, std_dev, c, size_l, size_r, is_hap = 0;
FILE *fpout1, *fpout2;
int seed = -1;
int strand_specific_mode = 0;
N = 1000000; dist = 500; std_dev = 50;
size_l = size_r = 70;
while ((c = getopt(argc, argv, "e:d:s:N:1:2:r:R:hX:S:A:Z:D")) >= 0) {
switch (c) {
case 'd': dist = atoi(optarg); break;
case 's': std_dev = atoi(optarg); break;
case 'N': N = atoi(optarg); break;
case '1': size_l = atoi(optarg); break;
case '2': size_r = atoi(optarg); break;
case 'e': ERR_RATE = atof(optarg); break;
case 'r': MUT_RATE = atof(optarg); break;
case 'R': INDEL_FRAC = atof(optarg); break;
case 'X': INDEL_EXTEND = atof(optarg); break;
case 'A': MAX_N_RATIO = atof(optarg); break;
case 'S': seed = atoi(optarg); break;
case 'h': is_hap = 1; break;
case 'Z': strand_specific_mode = atoi(optarg); break;
case 'D': DEBUG = 1; break;
}
}
if (argc - optind < 3) return simu_usage();
fpout1 = fopen(argv[optind+1], "w");
fpout2 = fopen(argv[optind+2], "w");
if (!fpout1 || !fpout2) {
fprintf(stderr, "[wgsim] file open error\n");
return 1;
}
if (seed <= 0) seed = time(0)&0x7fffffff;
fprintf(stderr, "[wgsim] seed = %d\n", seed);
srand48(seed);
wgsim_core(fpout1, fpout2, argv[optind], is_hap, N, dist, std_dev, size_l, size_r, strand_specific_mode);
fclose(fpout1); fclose(fpout2);
return 0;
}