bool is_transition(SkView* view) {
SkEvent isTransition(gIsTransitionQuery);
return view->doQuery(&isTransition);
}
int main (int argc, char** argv) {
double snp_mutation_rate = 0.001;
double indel_mutation_rate = 0.0001;
double het_rate = 0.5;
double afs_alpha = 1;
double indel_alpha = 3;
double microsatellite_afs_alpha = 1;
double microsatellite_len_alpha = 1.7;
double microsatellite_mutation_rate = 0.0001;
double mnp_ratio = 0.01;
double tstv_ratio = 2.5;
double deamination_ratio = 1.8;
int microsatellite_min_length = 1;
int indel_max = 1000;
int ploidy = 1;
int population_size = 1;
int sample_id_max_digits = 1;
int seed = time(NULL);
string fastaFileName;
string file_prefix = "";
string sample_prefix = "";
bool dry_run = false;
int repeat_size_max = 20;
bool uniform_indel_distribution = false;
double p, lambda, shape, mu, sigma;
string command_line = argv[0];
for (int i = 1; i < argc; ++i) {
command_line += " ";
command_line += argv[i];
}
int c;
while (true) {
static struct option long_options[] =
{
/* These options set a flag. */
//{"verbose", no_argument, &verbose_flag, 1},
//{"brief", no_argument, &verbose_flag, 0},
{"help", no_argument, 0, 'h'},
{"snp-rate", required_argument, 0, 's'},
{"mnp-ratio", required_argument, 0, 'M'},
{"indel-rate", required_argument, 0, 'i'},
{"indel-alpha", required_argument, 0, 'z'},
{"indel-max", required_argument, 0, 'X'},
{"repeat-size-max", required_argument, 0, 'q'},
{"microsat-rate", required_argument, 0, 'm'},
{"microsat-afs-alpha", required_argument, 0, 't'},
{"microsat-len-alpha", required_argument, 0, 'j'},
{"microsat-min-len", required_argument, 0, 'l'},
{"afs-alpha", required_argument, 0, 'a'},
{"ploidy", required_argument, 0, 'p'},
{"population-size", required_argument, 0, 'n'},
{"file-prefix", required_argument, 0, 'P'},
{"sample-prefix", required_argument, 0, 'S'},
{"random-seed", required_argument, 0, 'g'},
{"dry-run", no_argument, 0, 'd'},
{"uniform-indels", no_argument, 0, 'U'},
{"ts-tv-ratio", required_argument, 0, 'T'},
{"deamination-ratio", required_argument, 0, 'D'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
c = getopt_long (argc, argv, "hdUa:z:s:i:q:p:n:M:X:t:m:P:S:g:l:j:T:", long_options, &option_index);
/* Detect the end of the options. */
if (c == -1)
break;
switch (c)
{
case 0:
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
printf ("option %s", long_options[option_index].name);
if (optarg)
printf (" with arg %s", optarg);
printf ("\n");
break;
case 'd':
dry_run = true;
break;
case 'U':
uniform_indel_distribution = true;
break;
case 'q':
if (!convert(optarg, repeat_size_max)) {
cerr << "could not read -q, --repeat-size-max" << endl;
exit(1);
}
break;
case 's':
if (!convert(optarg, snp_mutation_rate)) {
cerr << "could not read -s, --snp-rate" << endl;
exit(1);
}
break;
case 'i':
if (!convert(optarg, indel_mutation_rate)) {
cerr << "could not read -i, --indel-rate" << endl;
exit(1);
}
break;
case 'a':
if (!convert(optarg, afs_alpha)) {
cerr << "could not read -a, --afs-alpha" << endl;
exit(1);
}
break;
case 'z':
if (!convert(optarg, indel_alpha)) {
cerr << "could not read -z, --indel-alpha" << endl;
exit(1);
}
break;
case 'X':
if (!convert(optarg, indel_max)) {
cerr << "could not read -M, --indel-max" << endl;
exit(1);
}
break;
case 'M':
if (!convert(optarg, mnp_ratio)) {
cerr << "could not read -m, --mnp-ratio" << endl;
exit(1);
}
break;
case 'm':
if (!convert(optarg, microsatellite_mutation_rate)) {
cerr << "could not read -m, --microsat-rate" << endl;
exit(1);
}
break;
case 'T':
if (!convert(optarg, tstv_ratio)) {
cerr << "could not read -T, --ts-tv-ratio" << endl;
exit(1);
}
break;
case 't':
if (!convert(optarg, microsatellite_afs_alpha)) {
cerr << "could not read -m, --microsatellite-afs-alpha" << endl;
exit(1);
}
break;
case 'j':
if (!convert(optarg, microsatellite_len_alpha)) {
cerr << "could not read -m, --microsatellite-len-alpha" << endl;
exit(1);
}
break;
case 'l':
if (!convert(optarg, microsatellite_min_length)) {
cerr << "could not read -l, --microsat-min-len" << endl;
exit(1);
}
break;
case 'p':
if (!convert(optarg, ploidy)) {
cerr << "could not read -p, --ploidy" << endl;
exit(1);
}
break;
case 'P':
file_prefix = optarg;
break;
case 'S':
sample_prefix = optarg;
break;
case 'n':
if (!convert(optarg, population_size)) {
cerr << "could not read -n, --population-size" << endl;
exit(1);
}
sample_id_max_digits = strlen(optarg);
break;
case 'g':
if (!convert(optarg, seed)) {
cerr << "could not read -g, --random-seed" << endl;
exit(1);
}
break;
case 'h':
printSummary();
exit(0);
break;
case '?':
/* getopt_long already printed an error message. */
printSummary();
exit(1);
break;
default:
abort ();
}
}
/* Print any remaining command line arguments (not options). */
if (optind < argc) {
//cerr << "fasta file: " << argv[optind] << endl;
fastaFileName = argv[optind];
} else {
cerr << "please specify a fasta file" << endl;
printSummary();
exit(1);
}
init_genrand(seed); // seed mt with current time
//mt19937 eng(seed);
int bpPerHaplotypeMean = 1000;
double bpPerHaplotypeSigma = 200;
normal_distribution<double> normal(mu, sigma);
//lambda = 7.0;
//poisson_distribution<int> poisson(lambda);
//poisson(eng);
string seqname;
string sequence; // holds sequence so we can process it
FastaReference fr;
fr.open(fastaFileName);
string bases = "ATGC";
vcf::VariantCallFile vcfFile;
// write the VCF header
stringstream headerss;
headerss
<< "##fileformat=VCFv4.1" << endl
<< "##fileDate=" << dateStr() << endl
<< "##source=mutatrix population genome simulator" << endl
<< "##seed=" << seed << endl
<< "##reference=" << fastaFileName << endl
<< "##phasing=true" << endl
<< "##commandline=" << command_line << endl
<< "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Alternate allele count\">" << endl
<< "##INFO=<ID=TYPE,Number=A,Type=String,Description=\"Type of each allele (snp, ins, del, mnp, complex)\">" << endl
<< "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of samples at the site\">" << endl
<< "##INFO=<ID=NA,Number=1,Type=Integer,Description=\"Number of alternate alleles\">" << endl
<< "##INFO=<ID=LEN,Number=A,Type=Integer,Description=\"Length of each alternate allele\">" << endl
<< "##INFO=<ID=MICROSAT,Number=0,Type=Flag,Description=\"Generated at a sequence repeat loci\">" << endl
<< "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">" << endl
<< "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT";
vector<string> samples;
for (int i = 0; i < population_size; ++i) {
stringstream sampless;
sampless << sample_prefix << setfill('0') << setw(sample_id_max_digits) << i + 1; // one-based sample names
samples.push_back(sampless.str());
headerss << "\t" << sampless.str();
}
// and set up our VCF output file
string header = headerss.str();
vcfFile.openForOutput(header);
cout << vcfFile.header << endl;
int copies = ploidy * population_size;
map<string, vector<SampleFastaFile*> > sequencesByRefseq;
if (!dry_run) {
for (FastaIndex::iterator s = fr.index->begin(); s != fr.index->end(); ++s) {
FastaIndexEntry& indexEntry = s->second;
seqname = indexEntry.name;
vector<SampleFastaFile*>& sequences = sequencesByRefseq[seqname];
for (int i = 0; i < population_size; ++i) {
stringstream sname;
sname << sample_prefix << setfill('0') << setw(sample_id_max_digits) << i + 1;
string samplename = sname.str();
for (int j = 0; j < ploidy; ++j) {
stringstream cname;
cname << j;
string chromname = cname.str();
string fullname = samplename + ":" + seqname + ":" + chromname;
string filename = file_prefix + fullname + ".fa";
//sequences.push_back(SampleFastaFile(filename, seqname));
sequences.push_back(new SampleFastaFile(filename, seqname));
}
}
}
}
for (FastaIndex::iterator s = fr.index->begin(); s != fr.index->end(); ++s) {
FastaIndexEntry& indexEntry = s->second;
seqname = indexEntry.name;
sequence = fr.getSequence(s->first);
vector<SampleFastaFile*>& sequences = sequencesByRefseq[seqname];
//sequences.resize(copies);
long int pos = 0;
long int microsatellite_end_pos = 0;
while (pos < sequence.size()) {
//cout << pos + 1 << " microsat end pos " << microsatellite_end_pos << endl;
string ref = sequence.substr(pos, 1); // by default, ref is just the current base
// skip non-DNA sequence information
if (!(ref == "A" || ref == "T" || ref == "C" || ref == "G")) {
pos += ref.size();
for (vector<SampleFastaFile*>::iterator s = sequences.begin(); s != sequences.end(); ++s) {
(*s)->write(ref);
}
continue;
}
vector<Allele> alleles;
// establish if we are in a repeat
// and what motif is being repeated, how many times
int len = 1;
// get reference repeats
// if we have a repeat, adjust the mutation rate
// using length and direction-dependent
// formula from "Likelihood-Based Estimation of Microsatellite Mutation Rates"
// http://www.genetics.org/cgi/content/full/164/2/781#T1
if (pos > microsatellite_end_pos) {
map<string, int> repeats = repeatCounts(pos + 1, (const string&) sequence, repeat_size_max);
string seq;
int repeat_count = 0;
// get the "biggest" repeat, the most likely ms allele at this site
for (map<string, int>::iterator r = repeats.begin(); r != repeats.end(); ++r) {
if (repeat_count < r->second) {
repeat_count = r->second;
seq = r->first;
}
}
//cout << pos + 1 << " " << sequence.substr(pos + 1, seq.size() * repeat_count) << " ?= " << seq * repeat_count << endl;
// guard ensures that we are in a pure repeat situoation, tandem-tandem repeats are not handled presently
if (repeats.size() > 0 && sequence.substr(pos + 1, seq.size() * repeat_count) == seq * repeat_count) {
int microsatellite_length = repeat_count * seq.size();
// record end of microsatellite so we don't generate more mutations until we pass it
microsatellite_end_pos = pos + microsatellite_length - 1;
if (microsatellite_length > microsatellite_min_length
//&& genrand_real1() / copies
// < microsatellite_mutation_rate * repeat_count) {
&& genrand_real1() > pow(1 - (microsatellite_mutation_rate * repeat_count), log(copies) * 2)) {
// establish the relative rate of ins and del events
/*
long double repeatMutationDelProbability = microsatelliteDelProb(repeat_count);
long double repeatMutationInsProbability = microsatelliteInsProb(repeat_count);
long double indel_balance = 1;
if (repeatMutationInsProbability > repeatMutationDelProbability) {
indel_balance = repeatMutationInsProbability / repeatMutationDelProbability;
} else {
indel_balance = 1 - (repeatMutationInsProbability / repeatMutationDelProbability);
}
*/
double indel_balance = 0.5;
// how many alleles at the site?
//int numalleles = min((int) floor(zetarandom(microsatellite_afs_alpha)), (int) ((double) repeat_count * indel_balance));
int numalleles = random_allele_frequency(repeat_count, microsatellite_afs_alpha);
//cout << "repeat_count: " << repeat_count << " numalleles: " << numalleles << endl;
map<int, bool> allele_lengths;
// lengths of the alleles
while (allele_lengths.size() < numalleles) {
int allele_length;
// TODO adjust length so that shorter events are more likely...
if (genrand_real1() > indel_balance) {
allele_length = -1 * min((int) floor(zetarandom(microsatellite_len_alpha)), repeat_count);
} else {
allele_length = min((int) floor(zetarandom(microsatellite_len_alpha)), repeat_count);
}
//cout << allele_length << endl;
map<int, bool>::iterator f = allele_lengths.find(allele_length);
if (f == allele_lengths.end()) {
allele_lengths[allele_length] = true;
}
}
// generate alleles
for (map<int, bool>::iterator f = allele_lengths.begin();
f != allele_lengths.end(); ++f) {
int allele_length = f->first;
int c = abs(f->first);
string alt = seq;
for (int i = 1; i < c; ++i)
alt += seq;
if (allele_length > 0) {
alleles.push_back(Allele(ref, ref + alt, "MICROSAT"));
} else {
alleles.push_back(Allele(ref + alt, ref, "MICROSAT"));
}
//cout << pos + 1 << " " << microsatellite_length << " " << alleles.back() << endl;
}
//cout << "alleles.size() == " << alleles.size() << endl;
}
}
}
// snp case
if (genrand_real1() > pow(1 - snp_mutation_rate, log(max(copies, 2)) * 2)) {
// make an alternate allele
/*
string alt = ref;
while (alt == ref) {
alt = string(1, bases.at(genrand_int32() % 4));
}
*/
string alt = ref;
if (genrand_real1() > 1 / (1 + tstv_ratio)) {
if (ref == "A") {
alt = "G";
} else if (ref == "G") {
alt = "A";
} else if (ref == "C") {
alt = "T";
} else if (ref == "T") {
alt = "C";
}
} else {
while (alt == ref || isTransition(ref, alt)) {
alt = string(1, bases.at(genrand_int32() % 4));
}
}
if (genrand_real1() < mnp_ratio) {
int i = 1;
do {
ref += sequence.substr(pos + i, 1);
alt += sequence.substr(pos + i, 1);
++i;
while (alt.at(alt.size() - 1) == ref.at(ref.size() - 1)) {
alt.at(alt.size() - 1) = bases.at(genrand_int32() % 4);
}
} while (genrand_real1() < mnp_ratio);
len = alt.size();
}
alleles.push_back(Allele(ref, alt));
}
// indel case
if (genrand_real1() > pow(1 - indel_mutation_rate, log(max(copies, 2)) * 2)) {
// how many bp?
if (uniform_indel_distribution) {
len = (int) floor(genrand_real1() * indel_max);
} else {
len = (int) floor(zetarandom(indel_alpha));
}
// guard against out-of-sequence indels
if (pos + len < sequence.size() && len <= indel_max) {
if (genrand_int32() % 2 == 0) {
// deletion
alleles.push_back(Allele(sequence.substr(pos, 1 + len), sequence.substr(pos, 1)));
} else {
string alt = ref;
// insertion?
// insert some random de novo bases
while (alt.length() < len + 1) {
alt += string(1, bases.at(genrand_int32() % 4));
}
alleles.push_back(Allele(ref, alt));
}
} else {
// fall through
}
}
// no mutation generated
if (alleles.empty()) {
for (int i = 0; i < copies; ++i) {
if (!dry_run) {
sequences.at(i)->write(ref);
}
}
pos += ref.size();
} else {
// TODO randomly distribute all the alleles throughout the population
// generate allele frequencies for each
// fun times...
string genotype;
vector<bool> alts;
random_shuffle(alleles.begin(), alleles.end());
vector<Allele*> population_alleles;
list<Allele> present_alleles; // filtered for AFS > 0 in the sample
// AFS simulation
int remaining_copies = copies;
while (remaining_copies > 0 && !alleles.empty()) {
Allele allele = alleles.back();
alleles.pop_back();
int allele_freq = random_allele_frequency(remaining_copies, afs_alpha);
if (allele_freq > 0) {
present_alleles.push_back(allele);
Allele* allelePtr = &present_alleles.back();
for (int i = 0; i < allele_freq; ++i) {
population_alleles.push_back(allelePtr);
}
remaining_copies -= allele_freq;
}
}
if (present_alleles.empty()) {
for (int i = 0; i < copies; ++i) {
if (!dry_run) {
sequences.at(i)->write(ref);
}
}
pos += ref.size();
continue;
}
reverse(present_alleles.begin(), present_alleles.end());
// establish the correct reference sequence and alternate allele set
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
//cout << allele << endl;
if (allele.ref.size() > ref.size()) {
ref = allele.ref;
}
}
// reference alleles take up the rest
Allele reference_allele = Allele(ref, ref);
for (int i = 0; i < remaining_copies; ++i) {
population_alleles.push_back(&reference_allele);
}
vector<string> altstrs;
// now the reference allele is the largest possible, adjust the alt allele strings to reflect this
// if we have indels, add the base before, set the position back one
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
string alleleStr = ref;
if (allele.ref.size() == allele.alt.size()) {
alleleStr.replace(0, allele.alt.size(), allele.alt);
} else {
alleleStr.replace(0, allele.ref.size(), allele.alt);
}
allele.ref = ref;
allele.alt = alleleStr;
altstrs.push_back(alleleStr);
}
assert(population_alleles.size() == copies);
// shuffle the alleles around the population
random_shuffle(population_alleles.begin(), population_alleles.end());
vcf::Variant var(vcfFile);
var.sequenceName = seqname;
var.position = pos + 1;
var.quality = 99;
var.id = ".";
var.filter = ".";
var.info["NS"].push_back(convert(population_size));
var.info["NA"].push_back(convert(present_alleles.size()));
var.format.push_back("GT");
var.ref = ref;
var.alt = altstrs;
// debugging, uncomment to see sequence context
//cout << sequence.substr(pos - 10, 10) << "*" << ref << "*" << sequence.substr(pos + 1, 9) << endl;
map<string, int> alleleIndexes;
alleleIndexes[convert(reference_allele)] = 0; // XXX should we handle this differently, by adding the reference allele to present_alleles?
int i = 1;
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a, ++i) {
Allele& allele = *a;
//cout << allele << " " << i << endl;
alleleIndexes[convert(allele)] = i;
//cout << allele << " " << i << endl;
}
//for (map<string, int>::iterator a = alleleIndexes.begin(); a != alleleIndexes.end(); ++a) {
// cout << a->first << " = " << a->second << endl;
//}
int j = 0;
for (vector<string>::iterator s = samples.begin(); s != samples.end(); ++s, ++j) {
string& sample = *s;
vector<string> genotype;
// XXX hack, maybe this should get stored in another map for easier access?
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
//cout << l << " " << population_alleles.at(l) << " " << alleleIndexes[convert(population_alleles.at(l))] << endl;
genotype.push_back(convert(alleleIndexes[convert(*population_alleles.at(l))]));
}
var.samples[sample]["GT"].push_back(join(genotype, "|"));
//cout << var.samples[sample]["GT"].front() << endl;
}
// XXX THIS IS BROKEN BECAUSE YOUR REFERENCE ALLELE CHANGES
// LENGTH WITH DELETIONS.
//
// IT'S POSSIBLE TO GET COMPLEX ALLELES AT THE INTERSECTIONS
// BETWEEN ONE ALLELIC VARIANT AND ANOTHER. THIS IS BROKEN!
//
// TO FIX--- BUILD HAPLOTYPES, THEN DISTRIBUTE THEM WITHIN THE POPULATION
//
// now write out our sequence data (FASTA files)
for (int j = 0; j < population_size; ++j) {
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
Allele* allele = population_alleles.at(l);
if (!dry_run) {
sequences.at(l)->write(allele->alt);
}
}
}
// tabulate allele frequency, and write some details to the VCF
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
Allele* allelePtr = &*a;
vector<string> genotypes;
genotypes.resize(population_size);
int allele_freq = 0;
// obtain allele frequencies and output FASTA sequence data
// for each simulated sample
for (int j = 0; j < population_size; ++j) {
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
if (population_alleles.at(l) == allelePtr) {
++allele_freq;
}
}
}
// set up the allele-specific INFO fields in the VCF record
var.info["AC"].push_back(convert(allele_freq));
int delta = allele.alt.size() - allele.ref.size();
if (delta == 0) {
if (allele.ref.size() == 1) {
var.info["TYPE"].push_back("snp");
var.info["LEN"].push_back(convert(allele.ref.size()));
} else {
var.info["TYPE"].push_back("mnp");;
var.info["LEN"].push_back(convert(allele.ref.size()));
}
} else if (delta > 0) {
var.info["TYPE"].push_back("ins");;
var.info["LEN"].push_back(convert(abs(delta)));
} else {
var.info["TYPE"].push_back("del");;
var.info["LEN"].push_back(convert(abs(delta)));
}
if (!allele.type.empty()) {
var.infoFlags[allele.type] = true;
}
}
// write the VCF record to stdout
cout << var << endl;
int largest_ref = 1; // enforce one pos
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
if (a->ref.size() > largest_ref) {
largest_ref = a->ref.size();
}
}
pos += largest_ref; // step by the size of the last event
}
}
}
// close, clean up files
for (map<string, vector<SampleFastaFile*> >::iterator s = sequencesByRefseq.begin(); s != sequencesByRefseq.end(); ++s) {
vector<SampleFastaFile*>& files = s->second;
for (vector<SampleFastaFile*>::iterator f = files.begin(); f != files.end(); ++f) {
delete *f;
}
files.clear();
}
return 0;
}
