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Fix VCF position int overflow (long long) & fix args.ploidy typo (arggs -> args) #47

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Fix VCF position int overflow (long long) & fix args.ploidy typo (arggs -> args) #47

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26 changes: 13 additions & 13 deletions SINGER/SINGER/Sampler.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ void Sampler::naive_read_vcf_haploid(string prefix, double start_pos, double end
ifstream file(vcf_file);
string line;
int num_individuals = 0;
int prev_pos = -1;
long long prev_pos = -1;
vector<Node_ptr> nodes = {};
int valid_mutation = 0;
int removed_mutation = 0;
Expand All @@ -84,23 +84,23 @@ void Sampler::naive_read_vcf_haploid(string prefix, double start_pos, double end
}
istringstream iss(line);
string chrom, id, ref, alt, qual, filter, info, format, genotype;
int pos;
long long pos;
iss >> chrom >> pos >> id >> ref >> alt >> qual >> filter >> info >> format;

if (pos < start_pos) {continue;}
if (pos > end_pos) {break;}
if (pos == prev_pos) {continue;} // skip multi-allelic sites
if (ref.size() > 1 or alt.size() > 1) {
removed_mutation += 1;
continue;
} // skip multi-allelic sites or structural variant

streampos old_pos = file.tellg();
string next_line;
if (getline(file, next_line)) {
istringstream next_iss(next_line);
string next_chrom;
int next_pos;
long long next_pos;
next_iss >> next_chrom >> next_pos;
if (next_pos == pos) {
removed_mutation += 1;
Expand Down Expand Up @@ -137,7 +137,7 @@ void Sampler::naive_read_vcf(string prefix, double start_pos, double end_pos) {
ifstream file(vcf_file);
string line;
int num_individuals = 0;
int prev_pos = -1;
long long prev_pos = -1;
vector<Node_ptr> nodes = {};
int valid_mutation = 0;
int removed_mutation = 0;
Expand All @@ -164,23 +164,23 @@ void Sampler::naive_read_vcf(string prefix, double start_pos, double end_pos) {
}
istringstream iss(line);
string chrom, id, ref, alt, qual, filter, info, format, genotype;
int pos;
long long pos;
iss >> chrom >> pos >> id >> ref >> alt >> qual >> filter >> info >> format;

if (pos < start_pos) {continue;}
if (pos > end_pos) {break;}
if (pos == prev_pos) {continue;} // skip multi-allelic sites
if (ref.size() > 1 or alt.size() > 1) {
removed_mutation += 1;
continue;
} // skip multi-allelic sites or structural variant

streampos old_pos = file.tellg();
string next_line;
if (getline(file, next_line)) {
istringstream next_iss(next_line);
string next_chrom;
int next_pos;
long long next_pos;
next_iss >> next_chrom >> next_pos;
if (next_pos == pos) {
removed_mutation += 1;
Expand Down Expand Up @@ -251,15 +251,15 @@ void Sampler::guide_read_vcf(string prefix, double start, double end) {
cerr << "VCF file not found: " + vcf_file << endl;
}
vcf_stream.seekg(byte_offset, ios::beg);
int prev_pos = -1;
long long prev_pos = -1;
vector<Node_ptr> nodes = {};
int valid_mutation = 0;
int removed_mutation = 0;
vector<double> genotypes = {};
while (getline(vcf_stream, line)) {
istringstream iss(line);
string chrom, id, ref, alt, qual, filter, info, format, genotype;
int pos;
long long pos;
iss >> chrom >> pos >> id >> ref >> alt >> qual >> filter >> info >> format;
if (pos == prev_pos) {continue;} // skip multi-allelic sites
if (pos >= end) {break;} // variant out of scope
Expand All @@ -272,7 +272,7 @@ void Sampler::guide_read_vcf(string prefix, double start, double end) {
if (getline(vcf_stream, next_line)) {
istringstream next_iss(next_line);
string next_chrom;
int next_pos;
long long next_pos;
next_iss >> next_chrom >> next_pos;
if (next_pos == pos) {
removed_mutation += 1;
Expand Down
2 changes: 1 addition & 1 deletion SINGER/SINGER/singer_master
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Original file line number Diff line number Diff line change
Expand Up @@ -299,7 +299,7 @@ def main():
if (args.resume):
resume_rate_singer(args.Ne, args.m, args.m*args.ratio, args.start, args.end, args.vcf, args.output, args.n, args.thin, args.polar, args.seed)
else:
run_rate_singer(args.Ne, args.m, args.m*args.ratio, args.start, args.end, args.vcf, args.output, args.n, args.thin, args.polar, arggs.ploidy, args.seed)
run_rate_singer(args.Ne, args.m, args.m*args.ratio, args.start, args.end, args.vcf, args.output, args.n, args.thin, args.polar, args.ploidy, args.seed)
return

if args.mut_map and not args.m:
Expand Down