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BuildContigs.h
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#ifndef __BUILD_CONTIGS_H
#define __BUILD_CONTIGS_H
#include <iostream>
#include <string>
#include <string.h>
#include <stdint.h>
#include <vector>
#include <map>
#include <list>
#include <algorithm>
#include <fstream>
#include "time.h"
#include "BasicDataStructure.h"
#include "GraphConstruction.h"
using namespace std;
struct consensus_info
{
vector<int> ReadList;
string consensus;
int compare_len;
int consensus_idx;
double mm_penalty;
};
void extend_alignment(consensus_info *consensus_info, string &append_str)
{
int consensus_sz = consensus_info->consensus.size();
int beg = consensus_sz - consensus_info->compare_len;
if (beg < 0)
{
beg = 0;
}
string seq1 = consensus_info->consensus.substr(beg, consensus_info->compare_len);
string seq2 = append_str.substr(0, consensus_info->compare_len);
int seq1_sz = seq1.size(), seq2_sz = seq2.size();
//cout << "1";
//cout << seq1 << endl;
int max_score = 0, offset = 0;
for (int j = 0; j < consensus_info->compare_len; ++j)
{
int len = min(seq1_sz - j, seq2_sz);
int match_cnt = 0;
int mm_cnt = 0;
for (int k = 0; k < len; ++k)
{
if (seq1[j + k] == seq2[k])
{
match_cnt++;
}
else
{
mm_cnt++;
}
}
int score = (match_cnt - consensus_info->mm_penalty*(double)mm_cnt);
if (score>max_score)
{
//cout << seq1.substr(j,seq1.size()) << endl;
//cout << seq2 << endl;
max_score = score;
offset = len;
}
}
int append_sz = append_str.size();
int append_beg = offset;
if (append_beg < 0)
{
return;
}
/*
cout << "2";
for (int k = 0; k < seq1.size() - append_beg; ++k)
{
cout << " ";
}
cout << append_str << endl;
*/
for (int k = append_beg; k < append_sz; ++k)
{
consensus_info->consensus.push_back(append_str[k]);
}
}
void extend_alignment_fast(consensus_info *consensus_info, string &append_str)
{
int consensus_sz = consensus_info->consensus.size();
int beg = consensus_sz - consensus_info->compare_len;
if (beg < 0)
{
beg = 0;
}
string seq1 = consensus_info->consensus.substr(beg, consensus_info->compare_len);
string seq2 = append_str.substr(0, consensus_info->compare_len);
int seq1_sz = seq1.size(), seq2_sz = seq2.size();
//cout << "1";
//cout << seq1 << endl;
int max_score = 0, offset1 = 0,offset2=0;
map<string, int> key_pos;
map<int, int> offset_count;
int key_len = 17;
//method1:exact match
if (seq1_sz > 0)
{
//cout << "q" ;
for (int i = 0; i < seq1_sz - key_len; ++i)
{
string key = seq1.substr(i, key_len);
if (key_pos.count(key) == 0)
{
key_pos[key] = i;
}
else
{
key_pos[key] = -1;//repeat
}
}
for (int i = 0; i < seq2_sz - key_len; ++i)
{
string key = seq2.substr(i, key_len);
if (key_pos.count(key) > 0 )
{
offset1 = key_pos[key] - i;
if (offset1 > 0)
{
offset_count[offset1]++;
}
}
}
offset1 = -1;
if (offset_count.size() == 1)
{
offset1 = offset_count.begin()->first;
if (offset1 > 0)
{
offset1 = min(seq1_sz - offset1, seq2_sz);
}
//cout << "q";
}
else
{
/*
cout << endl;
for (map<int, int>::iterator it = offset_count.begin(); it != offset_count.end(); ++it)
{
cout << it->first << " " << it->second << endl;
}
*/
}
//cout << offset1 << ", ";
}
else
{
offset1 = 0;
}
//method2
if (offset1 < 0)//slow
{
//cout << "s";
for (int j = 0; j < consensus_info->compare_len; ++j)
{
int len = min(seq1_sz - j, seq2_sz);
int match_cnt = 0;
int mm_cnt = 0;
for (int k = 0; k < len; ++k)
{
if (seq1[j + k] == seq2[k])
{
match_cnt++;
}
else
{
mm_cnt++;
}
}
int score = (match_cnt - consensus_info->mm_penalty*(double)mm_cnt);
if (score>max_score)
{
//cout << seq1.substr(j,seq1.size()) << endl;
//cout << seq2 << endl;
max_score = score;
offset1= len;
}
}
}
int append_sz = append_str.size();
int append_beg = offset1;
/*
if (offset1 != offset2)
{
cout << offset1 << endl << offset2 << endl;
cout <<"r"<< seq1<< endl;
append_beg = offset1;
cout << "q";
for (int k = 0; k < seq1.size() - append_beg; ++k)
{
cout << " ";
}
cout << append_str.substr(0,150) << endl;
append_beg = offset2;
cout << "q";
for (int k = 0; k < seq1.size() - append_beg; ++k)
{
cout << " ";
}
cout << append_str.substr(0, 150) << endl;
}
*/
if (append_beg < 0)
{
return;
}
/*
cout << "2";
for (int k = 0; k < seq1.size() - append_beg; ++k)
{
cout << " ";
}
cout << append_str << endl;
*/
for (int k = append_beg; k < append_sz; ++k)
{
consensus_info->consensus.push_back(append_str[k]);
}
}
void SimpleConsensus(contigs_info *contigs_info, reads_info *reads_info, consensus_info *consensus_info)
{
// consensus with no indel
consensus_info->consensus.clear();
ofstream o_debug;
if (reads_info->Debug)
{
o_debug.open("consensus_debug.txt");
}
bool append_ctg = 1;
int current_len = 0;
int last_ctg = 0, first_ctg = 0;
for (int r = 0; r < consensus_info->ReadList.size(); ++r)
{
string append_str;
vector<Coord_CTG_Cov> current_read_layout = reads_info->LongReadIndexVec[abs(consensus_info->ReadList[r])];
vector<int> read_vec;
for (int cc = 0; cc < current_read_layout.size(); ++cc)
{
read_vec.push_back(current_read_layout[cc].contig_no);
}
//o_contigs << ReadsList[0] << endl;
if (consensus_info->ReadList[r] < 0)
{
reverse(current_read_layout.begin(), current_read_layout.end());
for (int cc = 0; cc < current_read_layout.size(); ++cc)
{
current_read_layout[cc].contig_no = -current_read_layout[cc].contig_no;
}
}
first_ctg = current_read_layout[0].contig_no;
if ((last_ctg == first_ctg) || (r == 0))
{
append_ctg = 1;
}
else
{
append_ctg = 0;
}
last_ctg = current_read_layout[current_read_layout.size() - 1].contig_no;
if (append_ctg)
{
int ctg_no = current_read_layout[0].contig_no;
append_str = contigs_info->contigs_str[abs(ctg_no)];
if (ctg_no < 0)
{
reverse_complement_str(append_str);
}
if (reads_info->Debug)
{
cout << ">ctg_" << ctg_no << endl;
o_debug << ">ctg_" << ctg_no << endl;
o_debug << append_str << endl;
}
extend_alignment_fast(consensus_info, append_str);
}
if (reads_info->Selected_Overlaps[read_vec].size() > 0)
{
append_str = reads_info->Selected_Overlaps[read_vec][0].raw_seq;
if (consensus_info->ReadList[r] < 0)
{
reverse_complement_str(append_str);
}
if (reads_info->Debug)
{
cout << ">read_" << consensus_info->ReadList[r] << endl;
o_debug << ">read_" << consensus_info->ReadList[r] << endl;
o_debug << append_str << endl;
}
extend_alignment(consensus_info, append_str);
}
else
{
cout << "Missing read: " << consensus_info->ReadList[r] << endl;
}
if (r + 1 == consensus_info->ReadList.size())
{
append_str = contigs_info->contigs_str[abs(last_ctg)];
if (last_ctg < 0)
{
reverse(append_str.begin(), append_str.end());
complement_str(append_str);
}
if (reads_info->Debug)
{
cout << ">ctg_" << last_ctg << endl;
o_debug << ">ctg_" << last_ctg << endl;
o_debug << append_str << endl << endl;
}
extend_alignment(consensus_info, append_str);
}
}
}
void LoadRefinedContigGraph(contigs_info *contigs_info, string filename)
{
ifstream cg_in;
cg_in.open(filename.c_str());
//cg_in >> contigs_info->total_contigs;
int contig_idx;
contigs_info->contig_adjacency_left.clear();
contigs_info->contig_adjacency_left.resize(contigs_info->total_contigs + 1);
contigs_info->contig_adjacency_right.clear();
contigs_info->contig_adjacency_right.resize(contigs_info->total_contigs + 1);
string str;
while (getline(cg_in, str))
{
stringstream ss(str);
int contig1, contig2, dist, cov;
string bridge;
ss >> contig1 >> contig2 >> dist >> cov >> bridge;
if (cov > 100)
{
cov = 100;
}
if (contig1 > 0)
{
if (contigs_info->contig_adjacency_right[contig1][contig2].cov<cov)
{
contigs_info->contig_adjacency_right[contig1][contig2].dist_sum = dist*cov;
contigs_info->contig_adjacency_right[contig1][contig2].cov = cov;
contigs_info->contig_adjacency_right[contig1][contig2].bridge = bridge;
}
if (contig2>0)
{
if (contigs_info->contig_adjacency_left[contig2][contig1].cov < cov)
{
contigs_info->contig_adjacency_left[contig2][contig1].dist_sum = dist*cov;
contigs_info->contig_adjacency_left[contig2][contig1].cov = cov;
contigs_info->contig_adjacency_left[contig2][contig1].bridge = bridge;
}
}
else
{
if (contigs_info->contig_adjacency_right[-contig2][-contig1].cov < cov)
{
contigs_info->contig_adjacency_right[-contig2][-contig1].dist_sum = dist*cov;
contigs_info->contig_adjacency_right[-contig2][-contig1].cov = cov;
if (bridge.size()>0)
{
reverse(bridge.begin(), bridge.end());
complement_str(bridge);
}
contigs_info->contig_adjacency_right[-contig2][-contig1].bridge = bridge;
}
}
}
else
{
if (contigs_info->contig_adjacency_left[-contig1][contig2].cov<cov)
{
contigs_info->contig_adjacency_left[-contig1][contig2].dist_sum = dist*cov;
contigs_info->contig_adjacency_left[-contig1][contig2].cov = cov;
contigs_info->contig_adjacency_left[-contig1][contig2].bridge = bridge;
}
if (contig2>0)
{
if (contigs_info->contig_adjacency_right[contig2][-contig1].cov < cov)
{
contigs_info->contig_adjacency_right[contig2][-contig1].dist_sum = dist*cov;
contigs_info->contig_adjacency_right[contig2][-contig1].cov = cov;
contigs_info->contig_adjacency_right[contig2][-contig1].bridge = bridge;
}
}
else
{
if (contigs_info->contig_adjacency_left[-contig2][contig1].cov < cov)
{
contigs_info->contig_adjacency_left[-contig2][contig1].dist_sum = dist*cov;
contigs_info->contig_adjacency_left[-contig2][contig1].cov = cov;
if (bridge.size()>0)
{
reverse(bridge.begin(), bridge.end());
complement_str(bridge);
}
contigs_info->contig_adjacency_left[-contig2][contig1].bridge = bridge;
}
}
}
}
}
void OutputFastaContigs(contigs_info *contigs_info, string filename)
{
ifstream in_contig_paths(filename.c_str());
bool read_success = 1;
string tag, n_tag;
int Len = 0;
int n_gaps = 0;
vector<Coord_CTG_Cov> TempIndex;
ofstream out_fasta_contigs("ContigsByDBG2OLC.txt");
int n_contigs = 0;
while (read_success)
{
read_success = get_a_contig_path(in_contig_paths, tag, TempIndex, Len, 0, n_tag);
n_contigs++;
string joint_contig_str;
for (int i = 0; i < TempIndex.size(); ++i)
{
int current_contig = TempIndex[i].contig_no;
string contig_str = contigs_info->contigs_str[abs(current_contig)];
if (current_contig<0)
{
reverse(contig_str.begin(), contig_str.end());
complement_str(contig_str);
}
if (i < TempIndex.size() - 1)
{
int next_contig = TempIndex[i + 1].contig_no;
int dist = 0;
string bridge;
if (current_contig < 0)
{
if (contigs_info->contig_adjacency_left[abs(current_contig)].count(-next_contig))
{
dist = contigs_info->contig_adjacency_left[abs(current_contig)][-next_contig].dist_sum / contigs_info->contig_adjacency_left[abs(current_contig)][-next_contig].cov;
bridge = contigs_info->contig_adjacency_left[abs(current_contig)][-next_contig].bridge;
reverse_complement_str(bridge);
}
else
{
n_gaps++;
}
}
else
{
if (contigs_info->contig_adjacency_right[abs(current_contig)].count(next_contig))
{
int cov = contigs_info->contig_adjacency_right[abs(current_contig)][next_contig].cov;
int dist_sum = contigs_info->contig_adjacency_right[abs(current_contig)][next_contig].dist_sum;
dist = contigs_info->contig_adjacency_right[abs(current_contig)][next_contig].dist_sum / contigs_info->contig_adjacency_right[abs(current_contig)][next_contig].cov;
bridge = contigs_info->contig_adjacency_right[abs(current_contig)][next_contig].bridge;
}
else
{
n_gaps++;
}
}
if (dist < 0)
{
int contig_sz = contig_str.size();
contig_sz += dist;
if (contig_sz < 0)
{
contig_sz = 0;
}
contig_str = contig_str.substr(0, contig_sz);
}
else
{
contig_str += bridge;
}
}
joint_contig_str += contig_str;
}
out_fasta_contigs << ">DBG2OLC_" << n_contigs << endl;
out_fasta_contigs << joint_contig_str << endl;
}
cout << n_gaps << " unexpected gaps." << endl;
}
void ConstructCompressedOverlapGraph(contigs_info *contigs_info, reads_info *reads_info, align_info *align_info, string filename)
{
string ContigName = filename + "Nodes.txt";
ofstream o_contigs(ContigName.c_str());
string ContigPathsName = filename + "ContigPaths.txt";
ofstream o_ContigPaths(ContigPathsName.c_str());
string SuperContigsName = filename + "Nodes_info.txt";
ofstream o_supercontig(SuperContigsName.c_str());
string ContigLenName = filename + "NodeSizeEst.txt";
ofstream o_contigs_len(ContigLenName.c_str());
string Consensus_info = filename + "Consensus_info.txt";
ofstream o_consensus_info;
if (reads_info->AdaptiveTh > 0.0)
{
o_consensus_info.open(Consensus_info.c_str());
}
string GraphName = filename + "CompressedOverlapGraph.dot";
ofstream o_graph(GraphName.c_str());
GraphName = filename + "CompressedOverlapGraph.txt";
ofstream o_graph2(GraphName.c_str());
ofstream o_consensus;
ofstream o_layout;
ofstream o_layout2;
ofstream debug_warnings;
ofstream ext_log;
if (reads_info->AdaptiveTh > 0.0)
{
o_layout.open("layout_reads.txt");
o_layout2.open("layout_compressed_reads.txt");
}
if (reads_info->Debug)
{
debug_warnings.open("layout_warnings.txt");
}
if (contigs_info->CallConsensus&&reads_info->AdaptiveTh<0.0)
{
string consensus_name = filename + "Consensus.fasta";
o_consensus.open(consensus_name.c_str());
}
//vector<int> LeftOverlapsBest, RightOverlapsBest;
vector< map<int, int> > LeftBestOverlapsTemp, RightBestOverlapsTemp;
map<int, int> read2node;
vector<vector<int> > NodeInReads;
vector<bool> used, contigs_used_vt;
int total_ctgs = 0;
align_matrices align_matrices;
int frag_sum = 0;
int offset_sum = 0;
int ctg_cnt = 0;
LeftBestOverlapsTemp = reads_info->LeftOverlaps;
RightBestOverlapsTemp = reads_info->RightOverlaps;
//either is ok
//LeftBestOverlapsTemp = reads_info->LeftBestOverlapsTemp;
//RightBestOverlapsTemp = reads_info->RightBestOverlapsTemp;
contigs_used_vt.resize(contigs_info->total_contigs + 1);
int numReads = reads_info->LenVec.size();
used.resize(numReads);
consensus_info consensus_info;
consensus_info.consensus.reserve(1000000);
int n_layout = 0;
for (int i = 1; i < numReads; ++i)
{
if (used[i] == 0 && (LeftBestOverlapsTemp[i].size() != 0 || RightBestOverlapsTemp[i].size() != 0))
{
vector<int> ReadsOnTheRight, ReadsOnTheLeft, ReadsList;
used[i] = 1;
bool Right = 0;
total_ctgs++;
ReadsList.clear();
for (int round = 1; round <= 2; ++round)
{
int current_read = i;
int next_read = 0;
if (round == 1)
{
Right = 0;
}
else
{
Right = 1;
}
while (1)
{
if (Right)
{
if (RightBestOverlapsTemp[current_read].size() != 1)
{
break;
}
else
{
next_read = RightBestOverlapsTemp[current_read].begin()->first;
if (used[abs(next_read)] == 1)
{
break;
}
if (next_read< 0)
{
Right = 0;
if (RightBestOverlapsTemp[abs(next_read)].size() > 1)
{
break;
}
}
else
{
Right = 1;
if (LeftBestOverlapsTemp[abs(next_read)].size() > 1)
{
break;
}
}
ReadsList.push_back(next_read);
current_read = abs(next_read);
}
}
else
{
if (!Right)
{
if (LeftBestOverlapsTemp[current_read].size() != 1)
{
break;
}
else
{
next_read = -LeftBestOverlapsTemp[current_read].begin()->first;
if (used[abs(next_read)] == 1)
{
break;
}
if (next_read< 0)
{
Right = 0;
if (RightBestOverlapsTemp[abs(next_read)].size() > 1)
{
break;
}
}
else
{
Right = 1;
if (LeftBestOverlapsTemp[abs(next_read)].size() > 1)
{
break;
}
}
ReadsList.push_back(next_read);
current_read = abs(next_read);
}
}
}
used[current_read] = 1;
}
if (round == 1)
{
reverse(ReadsList.begin(), ReadsList.end());
for (int r = 0; r < ReadsList.size(); ++r)
{
ReadsList[r] = -ReadsList[r];
}
ReadsList.push_back(i);
}
}
bool skip_contig = 1;
for (int r = 0; r < ReadsList.size(); ++r)
{
if (reads_info->chimeric[abs(ReadsList[r])] == 0)
{
skip_contig = 0;
break;
}
}
if (ReadsList.size()>=3)
{
skip_contig = 0;
}
if (skip_contig)
{
//cout << "skip" << endl;
ReadsList.clear();
total_ctgs--;
continue;
}
int len_est = 0;
o_contigs << ">" << total_ctgs << endl;
o_supercontig << ">" << total_ctgs << endl;
o_ContigPaths << ">" << total_ctgs << endl;
consensus_info.consensus_idx = total_ctgs;
string consensus;
NodeInReads.push_back(ReadsList);
for (int c = 0; c < ReadsList.size(); ++c)
{
o_contigs << ReadsList[c] << ", ";
o_ContigPaths << ReadsList[c] << ", ";
if (ReadsList[c]>0)
{
read2node[ReadsList[c]] = total_ctgs;
}
else
{
read2node[-ReadsList[c]] = -total_ctgs;
}
}
o_contigs << endl;
o_ContigPaths << endl;
vector<Coord_CTG_Cov> current_read_layout = reads_info->LongReadIndexVec[abs(ReadsList[0])];
if (ReadsList[0] < 0)
{
reverse(current_read_layout.begin(), current_read_layout.end());
for (int cc = 0; cc < current_read_layout.size(); ++cc)
{
current_read_layout[cc].contig_no = -current_read_layout[cc].contig_no;
}
}
int coord = 0;
list<int> coord_lst, contig_lst, cov_lst;
for (int cc = 0; cc < current_read_layout.size(); ++cc)
{
len_est += contigs_info->contig_sz_vt[abs(current_read_layout[cc].contig_no)];
if (cc>0)
{
coord += abs(current_read_layout[cc].coord2 - current_read_layout[cc - 1].coord2);
}
coord_lst.push_back(coord);
contig_lst.push_back(current_read_layout[cc].contig_no);
cov_lst.push_back(contigs_info->contig_sz_vt[abs(current_read_layout[cc].contig_no)]);
contigs_used_vt[abs(current_read_layout[cc].contig_no)] = 1;
}
if (contigs_info->CallConsensus&&reads_info->AdaptiveTh<0.0)
{
consensus_info.compare_len = reads_info->MaxReadLen;
consensus_info.mm_penalty = align_info->mm_penalty;
consensus_info.ReadList = ReadsList;
if (reads_info->AdaptiveTh < 0.0)
{
o_consensus << ">" << total_ctgs << endl;
SimpleConsensus(contigs_info, reads_info, &consensus_info);
o_consensus << consensus_info.consensus << endl;
}
}
vector<int> offset_vt;
vector<string> raw_reads;
offset_vt.push_back(0);
for (int c = 0; c < ReadsList.size() - 1; ++c)
{
int current_read = ReadsList[c], next_read = ReadsList[c + 1];
vector<Coord_CTG_Cov> current_read_layout = reads_info->LongReadIndexVec[abs(current_read)];
vector<Coord_CTG_Cov> next_read_layout = reads_info->LongReadIndexVec[abs(next_read)];
if (current_read < 0)
{
int RLen = reads_info->LenVec[abs(current_read)];
if (RLen == 0)
{
RLen = current_read_layout[current_read_layout.size() - 1].coord2;
}
reverse(current_read_layout.begin(), current_read_layout.end());
for (int cc = 0; cc < current_read_layout.size(); ++cc)
{
current_read_layout[cc].contig_no = -current_read_layout[cc].contig_no;
current_read_layout[cc].coord2 = RLen - current_read_layout[cc].coord2;
}
}
if (next_read < 0)
{
int RLen = reads_info->LenVec[abs(next_read)];
if (RLen == 0)
{
RLen = next_read_layout[next_read_layout.size() - 1].coord2;
}
reverse(next_read_layout.begin(), next_read_layout.end());
for (int cc = 0; cc < next_read_layout.size(); ++cc)
{
next_read_layout[cc].contig_no = -next_read_layout[cc].contig_no;
next_read_layout[cc].coord2 = RLen - next_read_layout[cc].coord2;
}
}
if (reads_info->AdaptiveTh>0.0)
{
align_info->CalculateOffset = 1;
align_info->ref_len = reads_info->LenVec[abs(current_read)];
align_info->qry_len = reads_info->LenVec[abs(next_read)];
}
align_info->fix_orientation = 1;
align_info->force_flip = 0;
if (align_info->SparseAlign)
{
sparse_semi_global_align(contigs_info, current_read_layout, next_read_layout, &align_matrices, align_info);
}
else
{
approximate_semi_global_align(contigs_info, current_read_layout, next_read_layout, &align_matrices, align_info);
}
int result = classify_alignment(align_info);
bool debug_flag = 0;
if (result != 1)
{
debug_flag = 1;
offset_vt.push_back(1);
debug_warnings << "Warning. Alignment error: " << result << endl;
debug_warnings << "ref: " << endl;
for (int l = 0; l < current_read_layout.size(); ++l)
{
debug_warnings << current_read_layout[l].coord << ", ";
debug_warnings << current_read_layout[l].contig_no << ", ";
debug_warnings << current_read_layout[l].cov << ", ";
debug_warnings << current_read_layout[l].coord2 << ", ";
debug_warnings << endl;
}
debug_warnings << "qry: " << endl;
for (int l = 0; l < next_read_layout.size(); ++l)
{
debug_warnings << next_read_layout[l].coord << ", ";
debug_warnings << next_read_layout[l].contig_no << ", ";
debug_warnings << next_read_layout[l].cov << ", ";
debug_warnings << next_read_layout[l].coord2 << ", ";
debug_warnings << endl;
}
debug_warnings << "Result:" << result << endl;
debug_warnings << endl;
}
result = 1;
if (1)
{
offset_vt.push_back(align_info->ahg);
if (coord_lst.size() >= align_info->right_mismatch.size())
{
for (int cc = 0; cc < align_info->right_mismatch.size(); ++cc)
{
coord_lst.pop_back();
contig_lst.pop_back();
cov_lst.pop_back();
}
}
else
{
debug_warnings << "Pop error." << endl;
debug_warnings << "Pop " << align_info->right_mismatch.size() << " nodes from size " << coord_lst.size()<<" list." <<endl;
//cout << "Pop error." << endl;
//cout<< "Pop " << align_info->right_mismatch.size() << " nodes from size " << coord_lst.size() << " list." << endl;
debug_warnings << "Mismatch list: ";
for (int cc = 0; cc < align_info->right_mismatch.size(); ++cc)
{
debug_warnings << align_info->right_mismatch[cc] << " ";
}
list<int>::iterator lit = contig_lst.begin();
debug_warnings << "contig list: ";
for (int cc = 0; cc < contig_lst.size(); ++cc)
{
debug_warnings << *lit << " ";
lit++;
}
debug_warnings << endl;
}
for (int cc = 0; cc < align_info->right_ext.size(); ++cc)
{
len_est += contigs_info->contig_sz_vt[abs(align_info->right_ext[cc])];
coord += align_info->right_dist[cc];
coord_lst.push_back(coord);
contig_lst.push_back(align_info->right_ext[cc]);
cov_lst.push_back(contigs_info->contig_sz_vt[abs(align_info->right_ext[cc])]);
contigs_used_vt[abs(align_info->right_ext[cc])] = 1;
}
}
o_ContigPaths <<"id: "<< current_read << endl;
for (int cc = 0; cc < align_info->ref_aligned.size(); ++cc)
{
o_ContigPaths << align_info->ref_aligned[cc] << ", ";