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#include <string>
#include <iostream>
#include <fstream>
#include <sstream>
#include <map>
#include <set>
#include <algorithm>
#include <vector>
#include <stdexcept>
#include "error_checker.h"
#ifndef WIN32
#define HTS
#endif
#ifdef HTS
#include "htslib/sam.h"
#endif
#ifdef _DEBUG
ofstream SAM_OFH("scaffolding_entries.sam");
#endif
using namespace std;
void examine_frags(const set<string>& iworm_left, const set<string>& iworm_right, map<pair<string, string>, int>& paired_iworm_contigs)
{
if (iworm_left.size() == 0 || iworm_right.size() == 0)
return; // no pairs
if (iworm_left.size() == 1 && iworm_right.size() == 1)
{
string k1 = *iworm_left.begin();
string k2 = *iworm_right.begin();
if (k1 != k2)
{
if (k2 < k1) swap(k1, k2);
pair<string, string> key(k1, k2);
if (paired_iworm_contigs.find(key) == paired_iworm_contigs.end())
paired_iworm_contigs[key] = 1;
else
paired_iworm_contigs[key]++;
#ifdef _DEBUG
SAM_OFH << k1 << k2 << endl;
#endif
}
}
}
struct map_key
{
template <typename T>
typename T::first_type operator()(T keyValuePair) const
{
return keyValuePair.first;
}
};
template <typename T>
struct sort_pred {
map<T, int> &_hash;
sort_pred(map<T, int>& h) : _hash(h) {}
bool operator()(const T &left, const T &right) {
return _hash[left] > _hash[right];
}
};
template <typename T>
void copy_to_out(map<T, int>& paired_iworm_contigs, map<string, int>& iworm_acc_to_fasta_index)
{
vector<T> outvec;
const char *my_endl = "\n";
outvec.reserve(paired_iworm_contigs.size());
transform(paired_iworm_contigs.begin(), paired_iworm_contigs.end(), back_inserter(outvec), map_key());
sort(outvec.begin(), outvec.end(), sort_pred<T >(paired_iworm_contigs));
for (typename vector<T>::const_iterator a = outvec.begin(); a != outvec.end(); ++a)
{
const int index_A = iworm_acc_to_fasta_index[a->first];
const int index_B = iworm_acc_to_fasta_index[a->second];
cout << a->first << '\t' << index_A << '\t';
cout << a->second << '\t' << index_B << '\t';
cout << paired_iworm_contigs[*a] << my_endl;
}
}
void index_iworm(string iworm_fasta, map<string, int>& aMap)
{
int counter = 0;
ifstream fh(iworm_fasta.c_str());
while (fh)
{
string line;
fh >> line;
if (line[0] == '>')
aMap[line.substr(1, string::npos)] = counter++;
}
}
void validate_iworm(string iworm_acc)
{
pair<int, int> a;
if (iworm_acc[0] == 'a') iworm_acc[0] = ' ';
replace(iworm_acc.begin(), iworm_acc.end(), ';', ' ');
istringstream iss2(iworm_acc);
iss2 >> a.first >> a.second;
if (iss2.fail())
throw bad_name_exception();
}
pair<string, int> parse_read_name(string read_acc)
{
pair<string, int> result;
size_t s = read_acc.rfind('/');
result.first = read_acc.substr(0, s);
result.second = read_acc[s + 1] - '1';
if (s == string::npos || (result.second != 0 && result.second != 1))
throw single_read_exception();
return result;
}
void process_line(string read_acc, string iworm_acc, set<string>& iworm_left,
set<string>& iworm_right, string& prev_core_acc,
map<pair<string, string>, int>& paired_iworm_contigs,
error_checker& checker)
{
try
{
validate_iworm(iworm_acc);
pair<string, int> read = parse_read_name(read_acc);
const string core_acc = read.first;
int frag_end = read.second;
if (core_acc != prev_core_acc)
{
examine_frags(iworm_left, iworm_right, paired_iworm_contigs);
iworm_left.clear();
iworm_right.clear();
}
if (frag_end == 0)
iworm_left.insert(iworm_acc);
if (frag_end == 1)
iworm_right.insert(iworm_acc);
prev_core_acc = core_acc;
}
catch (const bad_name_exception&)
{
checker.add_bad_name(iworm_acc, read_acc);
}
catch (const single_read_exception&)
{
checker.add_single_read(read_acc);
}
}
int main(int argc, char* argv[])
{
string usage = "\n\nusage: ScaffoldIwormContigs nameSorted.sam iworm_fasta_file\n\n";
if (argc != 3)
{
cerr << usage;
return -1;
}
string name_sorted_sam_file(argv[1]);
map<string, int> iworm_acc_to_fasta_index;
index_iworm(argv[2], iworm_acc_to_fasta_index);
string prev_core_acc;
map<pair<string,string>, int> paired_iworm_contigs;
set<string> iworm_left;
set<string> iworm_right;
error_checker errors;
samFile *in = sam_open(name_sorted_sam_file.c_str(), "r");
bam_hdr_t *h = sam_hdr_read(in);
bam1_t *b = bam_init1();
while (sam_read1(in, h, b) > 0)
{
string read_acc(bam_get_qname(b));
if (b->core.tid >= 0)
{
string iworm_acc(h->target_name[b->core.tid]);
process_line(read_acc, iworm_acc, iworm_left, iworm_right, prev_core_acc, paired_iworm_contigs, errors);
}
}
int r = sam_close(in);
if (r < 0) {
throw runtime_error("Error closing input");
}
// get last one
examine_frags(iworm_left, iworm_right, paired_iworm_contigs);
errors.report();
copy_to_out(paired_iworm_contigs, iworm_acc_to_fasta_index);
return 0;
}
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