// Usage information

// > ./a.out -snp_rate=<double>, -err_rate=<double>, -coverage=<int>, -max_read_len=<int>, -min_read_len=<int>, -ref_file=<string> -snp_file=<string> -indel_file=<string> -ncells=<int> -out_base=<string> -region=<int>

//

// All parameters are optional. Check is performed for duplicate parametes, but not for inconsistency of values.

#include<stdio.h>

#include<stdlib.h>

#include<string.h>

#define FULL

#define DEBUG

int reads_hap[111] = {1,1,1,2,2,2,1,2,1,2,1,1,2,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,2,1,2,1,1,1,1,2,2,2,1,2,1,2,1,1,2,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,2,1,2,1,1,1,1,2,2,2,1,2,1,2,1,1,2,2,1,2,1,2,2,1,2,1,1,2,1,2,1,2,1,2,2,1};

//long int nbp[23] = {0, 24724971, 24295114, 19950182, 19127306, 18085786, 17089999, 15882142, 14627482, 14027325, 13537473, 13445238, 13234953, 11414298, 10636858, 10033891, 8882725, 7877474, 7611715, 6381165, 6243596, 4694432, 4969143};

long int nbp[23] = {0, 247249719, 242951149, 199501827, 191273063, 180857866, 170899992, 158821424, 146274826, 140273252, 135374737, 134452384, 132349534, 114142980, 106368585, 100338915, 88827254, 78774742, 76117153, 63811651, 62435964, 46944323, 49691432};

struct snp_struct {

int position;

char all[2];

};

struct indel_struct {

};

struct read_struct {

};

// By default, it will run only for chr21 if FULL is defined, or a small portion of it if FULL is not defined.

#ifdef FULL

struct snp_struct snps[300000];

struct indel_struct indels[35000];

long int N_BP = 46944323; // chr21

int reads_max = 140000;

#else

struct snp_struct snps[100];

struct indel_struct indels[50];

long int N_BP = 20000;

int reads_max = 1000;

#endif

double def_snp_rate = 0.01;

double def_err_rate = 0.04;

double snp_rate;

double err_rate;

int CLT = 30;

char A[3] = "TCG";

char T[3] = "CGA";

char C[3] = "GAT";

char G[3] = "ATC";

int def_coverage = 10;

int coverage;

int max_read_len = 5000;

int min_read_len = 2000;

int max_ref_len = 250000000;

int ncells = 0;

int region = 21;

char *snp_file, *indel_file;

FILE *fq_file, *log_file;

const char *file_base = "simulated_reads";

const char *ref_file = "/ifs/scratch/c2b2/ys_lab/aps2157/Haplotype/reference/bcm_hg18.fasta";

int read_cmp(const void *r1, const void *r2)

{

return (((struct read_struct*)r1)->start < ((struct read_struct*)r2)->start ? -1 : (((struct read_struct*)r1)->start == ((struct read_struct*)r2)->start ? 0 : 1) );

}

void simulate(int chrnum);

int main(int argc, char **argv)

{

snp_rate = def_snp_rate;

err_rate = def_err_rate;

coverage = def_coverage;

snp_file = (char*)malloc(sizeof(char)*200);

indel_file = (char*)malloc(sizeof(char)*200);

// override parameters

if(argc>1) {

int param = 1;

int snp_ck = 0, err_ck = 0, max_ck = 0, min_ck = 0, cov_ck = 0, ref_ck = 0, snf_ck = 0, ind_ck = 0, cel_ck = 0, out_ck = 0, reg_ck = 0;

for(param=1;param<argc;param++) {

char *token[2];

token[0] = strtok(argv[param], "=");

if(token[0]==NULL) {

printf("Ignoring incorrect parameter #%d\n", param);

} else if((token[1] = strtok(NULL, "=")) == NULL) {

printf("Ignoring incorrect parameter #%d\n", param);

} else {

if(strcmp(token[0],"-snp_rate")==0) {

if(snp_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

snp_ck++;

snp_rate = atof((const char *)token[1]);

}

} else if(strcmp(token[0],"-err_rate")==0) {

if(err_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

err_ck++;

err_rate = atof((const char *)token[1]);

}

} else if(strcmp(token[0],"-min_read_len")==0) {

if(min_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

min_ck++;

min_read_len = atoi((const char *)token[1]);

}

} else if(strcmp(token[0],"-max_read_len")==0) {

if(max_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

max_ck++;

max_read_len = atoi((const char *)token[1]);

}

} else if(strcmp(token[0],"-coverage")==0) {

if(cov_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

cov_ck++;

coverage = atoi((const char *)token[1]);

if(coverage<2) {

printf ("Insufficient coverage %dX provided. Ignoring..\n",coverage);

coverage = def_coverage;

}

}

} else if(strcmp(token[0],"-ref_file")==0) {

if(ref_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

ref_ck++;

ref_file = token[1];

}

} else if(strcmp(token[0],"-snp_file")==0) {

if(snf_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

snf_ck++;

snp_file = token[1];

}

} else if(strcmp(token[0],"-indel_file")==0) {

if(ind_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

ind_ck++;

indel_file = token[1];

}

} else if(strcmp(token[0],"-ncells")==0) {

if(cel_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

cel_ck++;

ncells = atoi((const char *)token[1]);

}

} else if(strcmp(token[0],"-out_base")==0) {

if(out_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

out_ck++;

file_base = token[1];

}

} else if(strcmp(token[0],"-region")==0) {

if(reg_ck>0) {

printf("Duplicate parameter %s=%s, ignoring..\n", token[0],token[1]);

} else {

reg_ck++;

region = atoi((const char *)token[1]);

}

} else {

printf("Invalid parameter %s=%s. Ignoring..\n", token[0],token[1]);

}

}

}

if(snp_rate>err_rate) {

printf("SNP rate (default 0.01) should be lower than error rate (default 0.04). Using default values now...\n");

snp_rate = def_snp_rate;

err_rate = def_err_rate;

}

}

int chrnum;

char file_name[200];

char log_file_name[200];

char *ext = ".fq";

char *log = ".log";

sprintf(file_name, "%s%s", file_base, ext);

sprintf(log_file_name, "%s%s", file_base, log);

fq_file = fopen(file_name, "w");

//log_file = fopen(log_file_name, "w");

if (fq_file == NULL)

printf("Error opening output file [%s]\n", (const char *) file_name);

if (log_file == NULL)

printf("Error opening output file [%s]\n", (const char *) log_file_name);

simulate(region);

fclose(fq_file);

}

void simulate(int chrnum)

{

int c=0;

long int i=0;

N_BP = nbp[chrnum];

sprintf(snp_file, "/ifs/scratch/c2b2/ys_lab/aps2157/Haplotype/snps/snp_%d.list",chrnum);

sprintf(indel_file, "/ifs/scratch/c2b2/ys_lab/aps2157/Haplotype/snps/indel_%d.list",chrnum);

long int n_reads = 2 * (nbp[chrnum] * coverage)/(max_read_len + min_read_len);

struct read_struct *reads = (struct read_struct*)malloc(sizeof(struct read_struct)*n_reads);

for(c=0;c<n_reads;c++) {

reads[c].str = NULL;

}

int ctr=0;

char line[100];

char *ref_s = (char*) malloc(sizeof(char)*max_ref_len);

// Read ref fasta here

FILE *ref = fopen(ref_file,"rt");

if(ref == NULL) { printf("Can't open ref file \"%s\"\n", ref_file); exit(1); }

int read_flag = 0;

while(1) {

fgets(line,sizeof(line),ref);

if(feof(ref))

break;

int c_ptr = 0;

int line_len = strlen(line) - 1;

if(line[0]=='>') {

if(read_flag==1) {

break;

} else {

if((line_len==5&&line[4]-48==chrnum)||(line_len==6&&(line[4]-48)*10+line[5]-48==chrnum))

read_flag = 1;

continue;

}

}

if(read_flag==0)

continue;

for(c_ptr = 0;c_ptr<line_len;c_ptr++) {

ref_s[ctr+c_ptr] = line[c_ptr];

}

ctr += line_len;

}

ref_s[ctr] = '\0';

fclose(ref);

// Read snp file here

FILE *snp_f = fopen(snp_file,"rt");

if(snp_f == NULL) { printf("Can't open snp file \"%s\"\n", snp_f); exit(1); }

int sctr = 0;

while(1) {

int pos=0,hap=0;

char ref,alt;

fgets(line,sizeof(line),snp_f);

if(feof(snp_f))

break;

strtok(line," ");

snps[sctr].position = atoi(strtok(NULL," "));

strtok(NULL," ");

strtok(NULL," ");

strtok(NULL," ");

strtok(NULL," ");

snps[sctr].all[0] = strtok(NULL," ")[0];

snps[sctr].all[1] = strtok(NULL," ")[0];

sctr++;

}

fclose(snp_f);

// Read indel file here

FILE *indel_f = fopen(indel_file,"rt");

if(indel_f == NULL) { printf("Can't open snp file \"%s\"\n", indel_f); exit(1); }

int ictr = 0;

while(1) {

int pos=0,hap=0,sit=0;

char sptr[100];

fgets(line,sizeof(line),indel_f);

line[strlen(line)-1] = '\0';

if(feof(indel_f))

break;

strtok(line," ");

indels[ictr].position = atoi(strtok(NULL," "));

memset(sptr,'\0',100);

strcpy(sptr,strtok(NULL," "));

indels[ictr].reflen = strlen(sptr);

strtok(NULL," ");

strtok(NULL," ");

strtok(NULL," ");

memset(indels[ictr].all[0],'\0',100);

memset(indels[ictr].all[1],'\0',100);

strcpy(indels[ictr].all[0],strtok(NULL," ")); // ref and alt are misnomers here. they're actually the two alleles

strcpy(indels[ictr].all[1],strtok(NULL," "));

ictr++;

}

fclose(indel_f);

srand ( (unsigned)time ( NULL ) );

for(i=0;i<n_reads;i++) {

#ifdef FULL

int rnd = rand();

reads[i].start = (int)((rnd*(N_BP-max_read_len))/RAND_MAX) + 1;

#else

int read_position_start = 9880000;

int rnd = rand();

reads[i].start = (int)((rnd*N_BP)/RAND_MAX) + read_position_start;

#endif

}

for(i=0;i<n_reads;i++) {

int rnd = rand();

reads[i].len = (int)((rnd*(long int)(max_read_len-min_read_len))/RAND_MAX) + min_read_len;

reads[i].str = (char*)malloc(sizeof(char)*(reads[i].len+1));

}

for(i=0;i<n_reads;i++) {

int clt;

double sum=0, ssum=0;

for(clt=0;clt<CLT;clt++) {

sum += (((rand()*(err_rate*1000))/RAND_MAX) + (err_rate*1000/2));

ssum += (((rand()*(snp_rate*1000))/RAND_MAX) + (snp_rate*1000/2));

}

reads[i].del_errors = sum/(CLT*10);

reads[i].snp_errors = ssum/(CLT*10);

sum = 0; ssum = 0;

}

#ifdef DEBUG

printf("Before sorting\n");

for(i=0; i<n_reads; i++) {

// printf("Read %d starts at %d,%d,%f,%f\n", i, reads[i].start,reads[i].len,reads[i].del_errors,reads[i].snp_errors);

}

#endif

qsort(reads, n_reads, sizeof(struct read_struct), read_cmp);

#ifdef DEBUG

printf("After sorting\n");

for(i=0; i<n_reads; i++) {

// printf("Read %d starts at %d,%d,%d,%f,%f\n", i, reads[i].start,reads[i].len,reads[i].start+reads[i].len,reads[i].del_errors,reads[i].snp_errors);

}

#endif

int snp_ct_start = 0, indel_ct_start = 0;

char *qualstr = (char *)malloc(sizeof(char) * max_read_len);

for(i=0;i<n_reads;i++) {

int j, k = 0;

int j_st = 0, k_st = 0;

int snp_flag = 0, indel_flag = 0;

for(j=0;j<reads[i].len;j++) {

int homon_hash = 100;

int snp_ct = 0, common_snp = 0;

int ctj_start = snp_ct_start > j_st ? snp_ct_start : j_st;

for(snp_ct = ctj_start; snp_ct <= ctr; snp_ct++) {

common_snp = 0;

if(snps[snp_ct].position < reads[i].start) {

if(snp_flag==0) {

snp_ct_start = snp_ct+1;

snp_flag = 1;

}

} else if(snps[snp_ct].position == reads[i].start+j+1) {

j_st = snp_ct+1;

reads[i].str[k] = snps[snp_ct].all[reads_hap[i%100]-1];

common_snp = 1;

#ifdef DEBUG

//printf("Replacing common snp %c with %c on read %d at position %d,%d,%d\n",*(ref_s+reads[i].start+j),snps[snp_ct].all[reads_hap[i%100]-1],i,k+1,j+1,reads[i].start+j+1);

#endif

break;

} else {

break;

}

}

int indel_ct = 0, common_indel = 0;

int ctk_start = indel_ct_start > k_st ? indel_ct_start : k_st;

for(indel_ct = ctk_start; indel_ct <= ctr; indel_ct++) {

common_indel = 0;

if(indels[indel_ct].position < reads[i].start) {

if(indel_flag==0) {

indel_ct_start = indel_ct+1;

indel_flag = 1;

}

} else if(indels[indel_ct].position == reads[i].start+j+1) {

k_st = indel_ct+1;

int inct = 0;

while(reads[i].str[k++] = (indels[indel_ct].all[reads_hap[i%100]-1])[inct++]);

k--;

common_indel = 1;

//j += indels[indel_ct].reflen - strlen(indels[indel_ct].all[reads_hap[i%100]-1]);

j += (indels[indel_ct].reflen - 1);

#ifdef DEBUG

printf("Indeling site %c with %s on read %d up to position %d,%d,%d\n",*(ref_s+reads[i].start+j),indels[indel_ct].all[reads_hap[i%100]-1],i,k,j+1,reads[i].start+j+1);

#endif

break;

} else {

break;

}

}

if(common_indel==1) continue;

double check = (100*(double)rand())/RAND_MAX;

if(check > reads[i].del_errors+1.0) {

if(common_snp==0) {

reads[i].str[k] = *(ref_s+reads[i].start+j);

#ifdef DEBUG

//printf("inserting %c on read %d at position %d,%d,%d\n",*(ref_s+reads[i].start+j),i,k+1,j+1,reads[i].start+j+1);

#endif

}

k++;

} else if(check <= reads[i].snp_errors) {

if(*(ref_s+reads[i].start+j) == 'A'||*(ref_s+reads[i].start+j) == 'a') {

reads[i].str[k] = A[(int)((long int)3*rand()/RAND_MAX)];

} else if(*(ref_s+reads[i].start+j) == 'T'||*(ref_s+reads[i].start+j) == 't') {

reads[i].str[k] = T[(int)((long int)3*rand()/RAND_MAX)];

} else if(*(ref_s+reads[i].start+j) == 'C'||*(ref_s+reads[i].start+j) == 'c') {

reads[i].str[k] = C[(int)((long int)3*rand()/RAND_MAX)];

} else if(*(ref_s+reads[i].start+j) == 'G'||*(ref_s+reads[i].start+j) == 'g') {

reads[i].str[k] = G[(int)((long int)3*rand()/RAND_MAX)];

} else { reads[i].str[k] = *(ref_s+reads[i].start+j); }

k++;

#ifdef DEBUG

//printf("replacing %c with %c on read %d at position %d,%d,%d\n",*(ref_s+reads[i].start+j),reads[i].str[k-1],i,k,j+1,reads[i].start+j+1);

#endif

} else {

#ifdef DEBUG

//printf("Deleting %c on read %d\t%d at position %d,%d,%d\n",*(ref_s+reads[i].start+j),i,reads[i].start,k+1,j+1,reads[i].start+j+1);

#endif

}

}

reads[i].str[k] = '\0';

int l = 0;

for(l=0;l<strlen(reads[i].str);l++) {

qualstr[l] = '>';

}

qualstr[l] = '\0';

fprintf(fq_file, "@Start_POS:%d:%d\n", reads[i].start+1,reads_hap[i%100]);

fprintf(fq_file, "%s\n", reads[i].str);

fprintf(fq_file, "+\n");

fprintf(fq_file, "%s\n", qualstr);

// fprintf(log_file,"%d\t%d\n",startsi,reads_hap[i%100]);

} // end n_reads

for(i=0;i<n_reads;i++) {

free(reads[i].str);

}

free(qualstr);

free(ref_s);

}