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Align.h
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Align.h
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#ifndef __ALIGH_H
#define __ALIGH_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"
using namespace std;
struct align_matrices
{
//modified on 20190315 to allow aligning ultra long reads
int score[252][252];
int16_t path[252][252];
};
struct align_maps
{
map<int, map<int, int> > score, path;
};
struct align_info
{
bool SparseAlign;
int max_len;
bool Debug;
bool flip,success,force_flip;
vector<int> ref_aligned, qry_aligned;
vector<int> right_ext,right_dist,right_mismatch;
int ref_len,qry_len, match_len,mismatch_len[2],frontal_mismatch_len[4],rear_mismatch_len[4],max_score,ref_len_compressed,qry_len_compressed;
//FR_mismatch_len :0 ref mismatch score, 1: qry mismatch score, 2: ref mismatch region len, 3: qry mismatch region len
int ref_aligned_center,qry_aligned_center;
int aligned_nodes;
int min_overlap, max_mismatch_FR_score, min_extension_FR, min_match_qry, max_match_qry, min_match_ref, max_match_ref;
int offset;
int AbsOffsetSum, OffsetSum, MaxOffset, MaxOffsetRQ, MaxMismatchFR;
double mm_ratio,mm_penalty;
int band_width;
char adj;int ahg;int bhg;//AMOS,Celera format
int ref_idx;
int top_reads;
bool fix_orientation;
int min_match, max_match;
int aligned_range_ref, aligned_range_qry;
bool FAST;
bool CalculateOffset;
bool Inward, Outward;
int matching_method;
int scoring_method;
};
int classify_alignment(align_info *align_info)
{
/*
classify into 5 cases:
case 1: ref->qry overlap
f_mm1>>f_mm2, r_mm2>>r_mm1, m>>mm
case 2: qry->ref overlap
case 3: qry in ref
case 4: ref in qry
case 5: no relation
*/
if (align_info->matching_method == 3)
{
if (align_info->scoring_method == 1)
{
align_info->max_score = max(align_info->aligned_range_ref, align_info->aligned_range_qry);
}
if (align_info->scoring_method == 2)
{
align_info->max_score = min(align_info->aligned_range_ref, align_info->aligned_range_qry);
}
if (align_info->scoring_method == 3)
{
align_info->max_score = (align_info->aligned_range_ref + align_info->aligned_range_qry) / 2;
}
}
int result = 0;
if ((align_info->match_len < align_info->min_overlap) || (((double)align_info->match_len*align_info->mm_ratio) < max(align_info->mismatch_len[0], align_info->mismatch_len[1])))
{
result = 5;
return result;
}
if ((align_info->MaxMismatchFR)<min(align_info->frontal_mismatch_len[2], align_info->frontal_mismatch_len[3]) || (align_info->MaxMismatchFR)<min(align_info->rear_mismatch_len[2], align_info->rear_mismatch_len[3]))
{
//result = 5;
//return result;
}
int AbsOffsetSum = align_info->AbsOffsetSum;
int OffsetSum = align_info->OffsetSum;
int MaxOffsetRQ = align_info->MaxOffsetRQ;
if (AbsOffsetSum>1)
{
cout << "";
}
if (OffsetSum >align_info->MaxOffset)// align_info->mm_ratio*min(align_info->aligned_range_ref, align_info->aligned_range_qry)
{
//cout << AbsOffsetSum << endl;
//cout << "R: " << align_info->aligned_range_ref<<" ";// << endl;
//cout <<"Q: "<< align_info->aligned_range_qry << endl;
//cout << align_info->MaxOffset << endl;
result = 5;
//cout << "MM:" << align_info->aligned_range_ref << " " << align_info->aligned_range_qry << endl;
return result;
}
if (((double)align_info->match_len*align_info->mm_ratio)<min(align_info->frontal_mismatch_len[0], align_info->frontal_mismatch_len[1]) || ((double)align_info->match_len*align_info->mm_ratio)<min(align_info->rear_mismatch_len[0], align_info->rear_mismatch_len[1]))
{
result = 5;
return result;
}
if ((align_info->max_mismatch_FR_score)<min(align_info->frontal_mismatch_len[0], align_info->frontal_mismatch_len[1]) || (align_info->max_mismatch_FR_score)<min(align_info->rear_mismatch_len[0], align_info->rear_mismatch_len[1]))
{
result = 5;
return result;
}
if (align_info->success == 0)
{
result = 5;
return result;
}
if (max(align_info->frontal_mismatch_len[0], align_info->frontal_mismatch_len[1])<align_info->min_extension_FR)
{
align_info->frontal_mismatch_len[0] = 0;
align_info->frontal_mismatch_len[1] = 0;
}
if (max(align_info->rear_mismatch_len[0], align_info->rear_mismatch_len[1])<align_info->min_extension_FR)
{
align_info->rear_mismatch_len[0] = 0;
align_info->rear_mismatch_len[1] = 0;
}
//case 1 check:
if ((align_info->frontal_mismatch_len[0] > align_info->frontal_mismatch_len[1]) && (align_info->frontal_mismatch_len[1]<align_info->max_mismatch_FR_score) && (align_info->frontal_mismatch_len[0]>align_info->min_extension_FR))
{
if ((align_info->rear_mismatch_len[0] < align_info->rear_mismatch_len[1]) && (align_info->rear_mismatch_len[0]<align_info->max_mismatch_FR_score) && (align_info->rear_mismatch_len[1]>align_info->min_extension_FR))
{
result = 1;
return result;
}
}
//case 2 check:
if ((align_info->frontal_mismatch_len[0] < align_info->frontal_mismatch_len[1]) && (align_info->frontal_mismatch_len[0]<align_info->max_mismatch_FR_score) && (align_info->frontal_mismatch_len[1]>align_info->min_extension_FR))
{
if ((align_info->rear_mismatch_len[1] < align_info->rear_mismatch_len[0]) && (align_info->rear_mismatch_len[1]<align_info->max_mismatch_FR_score) && (align_info->rear_mismatch_len[0]>align_info->min_extension_FR))
{
result = 2;
return result;
}
}
//case 3 check:
//may modify condition to enforce strict contain
if ((align_info->frontal_mismatch_len[0] >= align_info->frontal_mismatch_len[1]) && (align_info->rear_mismatch_len[0] >= align_info->rear_mismatch_len[1]))// this is almost strict contain
{
if ((max(align_info->rear_mismatch_len[1], align_info->frontal_mismatch_len[1])<align_info->max_mismatch_FR_score))
{
result = 3;
return result;
}
}
//case 4 check:
if ((align_info->frontal_mismatch_len[1] >= align_info->frontal_mismatch_len[0]) && (align_info->rear_mismatch_len[1] >= align_info->rear_mismatch_len[0]))
{
if ((max(align_info->rear_mismatch_len[0], align_info->frontal_mismatch_len[0])<align_info->max_mismatch_FR_score))
{
//may add condition to enforce strict contain
result = 4;
return result;
}
}
return 0;
}
bool sparse_semi_global_align(contigs_info *contigs_info, vector<Coord_CTG_Cov> ref, vector<Coord_CTG_Cov> qry, align_matrices *align_matrices, align_info *align_info)
{
memset(align_matrices->score, 0, sizeof(align_matrices->score));
memset(align_matrices->path, 0, sizeof(align_matrices->path));
align_info->flip = 0;
align_info->success = 0;
align_info->ref_aligned.clear();
align_info->qry_aligned.clear();
align_info->right_ext.clear();
align_info->right_mismatch.clear();
int max_len = align_info->max_len;
align_info->CalculateOffset = 1;
if (align_info->force_flip)
{
align_info->flip = 1;
}
/*
semi global alignment,
if two contigs match, the score is the contig length,
mismatch: not defined.
gap: penalty score is the contig size
*/
map<int, int> shared_index, ref_index, qry_index;
int ref_sz = ref.size(), qry_sz = qry.size();
for (int i = 0; i < ref_sz; ++i)
{
shared_index[ref[i].contig_no] = 1;
}
if (align_info->fix_orientation == 0)
{
int flip = 0, non_flip = 0;
for (int i = 0; i < qry_sz; ++i)
{
if (shared_index.count(qry[i].contig_no))
{
non_flip++;
}
if (shared_index.count(-qry[i].contig_no))
{
flip++;
}
}
if (flip == non_flip)
{
return 0;
}
if (flip > non_flip)
{
align_info->flip = 1;
}
}
if (align_info->flip)
{
reverse(qry.begin(), qry.end());
for (int i = 0; i < qry_sz; ++i)
{
qry[i].contig_no = -qry[i].contig_no;
//also change coords
}
for (int i = 0; i < qry_sz; ++i)
{
qry[i].coord2 = align_info->qry_len - qry[i].coord2;
}
}
for (int i = 0; i < qry_sz; ++i)
{
if (shared_index.count(qry[i].contig_no))
{
shared_index[qry[i].contig_no] = 2;
}
}
//put matches idx into new structure, calculate match/gap score;
vector<Coord_CTG_Cov> ref_compressed, qry_compressed,ref_gap_compressed,qry_gap_compressed;
ref_compressed.reserve(max_len);
qry_compressed.reserve(max_len);
ref_gap_compressed.reserve(max_len);
qry_gap_compressed.reserve(max_len);
Coord_CTG_Cov Coord_CTG_Cov_null;
Coord_CTG_Cov_null.contig_no = 0;
Coord_CTG_Cov_null.cov = 0;
Coord_CTG_Cov_null.coord = 0;
Coord_CTG_Cov_null.coord2 = 0;
ref_gap_compressed.push_back(Coord_CTG_Cov_null);
qry_gap_compressed.push_back(Coord_CTG_Cov_null);
int n_ref_match = 0;
ref_index.clear();
for (int i = 0; i < ref_sz; ++i)
{
if (shared_index[ref[i].contig_no]==2)
{
ref_compressed.push_back(ref[i]);
ref_gap_compressed.push_back(Coord_CTG_Cov_null);
ref_index[n_ref_match] = i;
n_ref_match++;
}
else
{
if (align_info->matching_method == 1)
{
ref_gap_compressed[n_ref_match].cov += contigs_info->contig_sz_vt[abs(ref[i].contig_no)];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
ref_gap_compressed[n_ref_match].cov += ref[i].cov;
}
}
}
ref_compressed.push_back(Coord_CTG_Cov_null);// last one, stands for gaps;
//ref_compressed[ref_compressed.size() - 1].cov = -ref_compressed[ref_compressed.size() - 1].cov;
ref_index[n_ref_match] = ref_sz-1;
ref_index[-1] = - 1;
int n_qry_match = 0;
qry_index.clear();
for (int i = 0; i < qry_sz; ++i)
{
if (shared_index[qry[i].contig_no]==2)
{
qry_compressed.push_back(qry[i]);
qry_gap_compressed.push_back(Coord_CTG_Cov_null);
qry_index[n_qry_match] = i;
n_qry_match++;
}
else
{
if (align_info->matching_method == 1)
{
qry_gap_compressed[n_qry_match].cov += contigs_info->contig_sz_vt[abs(qry[i].contig_no)];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
qry_gap_compressed[n_qry_match].cov += qry[i].cov;
}
}
}
qry_compressed.push_back(Coord_CTG_Cov_null);// last one, stands for gaps;
//qry_compressed[qry_compressed.size() - 1].cov = -qry_compressed[qry_compressed.size() - 1].cov;
qry_index[n_qry_match] = qry_sz - 1;
qry_index[-1] = - 1;
if (ref_compressed.size() > max_len || qry_compressed.size() > max_len)
{
cout << "Error! Maximal alignment length reached. max_len: " << max_len << endl;
return 0;// no result
}
//calculate the sparse alignment using compressed reads;
ref_sz = ref_compressed.size();
qry_sz = qry_compressed.size();
align_info->ref_len_compressed = ref_sz;
align_info->qry_len_compressed = qry_sz;
if (ref_sz > 2 && qry_sz > 2)
{
cout << "";
}
for (int r = 0; r < ref_sz; ++r)
{
align_matrices->path[r][0] = 2;
for (int c = 0; c < qry_sz; ++c)
{
//
int max_score=0;
if (r>0)
{
max_score = align_matrices->score[r - 1][c] - align_info->mm_penalty*(double)(ref_compressed[r].cov + ref_gap_compressed[r].cov);
}
align_matrices->path[r][c] = 1;
int tmp_score;
if (c > 0)
{
tmp_score = align_matrices->score[r][c - 1] - align_info->mm_penalty*(double)(qry_compressed[c].cov + qry_gap_compressed[c].cov);
}
else
{
tmp_score = 0;
}
if (tmp_score > max_score)
{
align_matrices->path[r][c] = 2;
max_score = tmp_score;
}
if (qry_sz-1!=c&&ref_sz-1!=r)
if (ref_compressed[r ].contig_no == qry_compressed[c].contig_no)
{
// here use min, max_len use max
//use average resolves more ties
if (r > 0 && c > 0)
{
tmp_score = align_matrices->score[r - 1][c - 1];
}
else
{
tmp_score = 0;
}
if (align_info->scoring_method == 1)
{
tmp_score = tmp_score+ max(ref_compressed[r].cov, qry_compressed[c].cov);
}
if (align_info->scoring_method == 2)
{
tmp_score = tmp_score + min(ref_compressed[r].cov, qry_compressed[c].cov);
}
if (align_info->scoring_method == 3)
{
tmp_score = tmp_score + (ref_compressed[r].cov + qry_compressed[c].cov) / 2;
}
if (r > 0 && c > 0)
{
tmp_score -= align_info->mm_penalty*(double)(ref_gap_compressed[r].cov + qry_gap_compressed[c].cov);
}
}
if (tmp_score > max_score)
{
align_matrices->path[r][c] = 3;
max_score = tmp_score;
}
align_matrices->score[r][c] = max_score;
}
}
//return alignement result
int max_score = -1000000;
int opt_r = 0, opt_c = 0;
for (int r = 0; r < ref_sz; ++r)
{
if (align_matrices->score[r][qry_sz-1] > max_score)
{
max_score = align_matrices->score[r][qry_sz-1];
opt_r = r;
opt_c = qry_sz-1;
}
}
for (int c = 0; c < qry_sz; ++c)
{
if (align_matrices->score[ref_sz-1][c] > max_score)
{
max_score = align_matrices->score[ref_sz-1][c];
opt_r = ref_sz-1;
opt_c = c;
}
}
if(ref_sz-1 > opt_r)
{
for (int pp = ref_index[ref_sz-1]; pp > ref_index[opt_r]; --pp)
{
align_info->qry_aligned.push_back(0);
int contig_no = ref[pp].contig_no;
align_info->ref_aligned.push_back(contig_no);
}
}
if(qry_sz-1 > opt_c)
{
for (int pp = qry_index[qry_sz-1]; pp > qry_index[opt_c]; --pp)
{
align_info->ref_aligned.push_back(0);
int contig_no = qry[pp].contig_no;
align_info->qry_aligned.push_back(contig_no);
}
}
while (1)
{
if (opt_r == -1 || opt_c == -1)
{
if (opt_r>=0)
for (int pp = ref_index[opt_r] ; pp >= 0; --pp)
{
align_info->qry_aligned.push_back(0);
int contig_no = ref[pp].contig_no;
align_info->ref_aligned.push_back(contig_no);
}
if (opt_c >= 0)
for (int pp = qry_index[opt_c] ; pp >= 0; --pp)
{
align_info->ref_aligned.push_back(0);
int contig_no = qry[pp].contig_no;
align_info->qry_aligned.push_back(contig_no);
}
break;
}
if (align_matrices->path[opt_r][opt_c] == 1)
{
for (int pp = ref_index[opt_r]; pp > ref_index[opt_r - 1]; --pp)
{
align_info->qry_aligned.push_back(0);
int contig_no = ref[pp].contig_no;
align_info->ref_aligned.push_back(contig_no);
}
opt_r--;
}
if (align_matrices->path[opt_r][opt_c] == 2)
{
for (int pp = qry_index[opt_c]; pp > qry_index[opt_c-1]; --pp)
{
align_info->ref_aligned.push_back(0);
int contig_no = qry[pp].contig_no;
align_info->qry_aligned.push_back(contig_no);
}
opt_c--;
}
if (align_matrices->path[opt_r][opt_c] == 3)
{
int contig_no = ref[ref_index[opt_r]].contig_no;
align_info->ref_aligned.push_back(contig_no);
align_info->qry_aligned.push_back(contig_no);
for (int pp = ref_index[opt_r]-1; pp > ref_index[opt_r - 1]; --pp)
{
align_info->qry_aligned.push_back(0);
int contig_no = ref[pp].contig_no;
align_info->ref_aligned.push_back(contig_no);
}
for (int pp = qry_index[opt_c]-1; pp > qry_index[opt_c - 1]; --pp)
{
align_info->ref_aligned.push_back(0);
int contig_no = qry[pp].contig_no;
align_info->qry_aligned.push_back(contig_no);
}
opt_r--; opt_c--;
}
}
reverse(align_info->ref_aligned.begin(), align_info->ref_aligned.end());
reverse(align_info->qry_aligned.begin(), align_info->qry_aligned.end());
/*
report statistics
ref length
qry length
matching length
matching vs non matching
mismatch in the beginning and end
*/
ref_index.clear();
qry_index.clear();
int n_match = 0;
for (int i = 0; i < align_info->ref_aligned.size(); ++i)
{
if (align_info->ref_aligned[i] != 0)
{
ref_index[i] = n_match;
n_match++;
}
}
n_match = 0;
for (int i = 0; i < align_info->qry_aligned.size(); ++i)
{
if (align_info->qry_aligned[i] != 0)
{
qry_index[i] = n_match;
n_match++;
}
}
align_info->max_score = max_score;
int min_match = -1, max_match = -1;
for (int i = 0; i < align_info->ref_aligned.size(); ++i)
{
if (align_info->ref_aligned[i] == align_info->qry_aligned[i])
{
if (min_match < 0)
{
min_match = i;
}
if (max_match < i)
{
max_match = i;
}
}
}
if (min_match < 0 || max_match < 0)
{
align_info->success = 0;
return 0;
}
align_info->success = 1;
align_info->match_len = 0;
align_info->mismatch_len[0] = 0;
align_info->mismatch_len[1] = 0;
align_info->rear_mismatch_len[0] = 0;
align_info->rear_mismatch_len[1] = 0;
align_info->rear_mismatch_len[2] = 0;
align_info->rear_mismatch_len[3] = 0;
align_info->frontal_mismatch_len[0] = 0;
align_info->frontal_mismatch_len[1] = 0;
align_info->frontal_mismatch_len[2] = 0;
align_info->frontal_mismatch_len[3] = 0;
align_info->min_match = min_match;
align_info->max_match = max_match;
int temp_range = contigs_info->contig_sz_vt[abs(ref[ref_index[min_match]].contig_no)] + contigs_info->contig_sz_vt[abs(ref[ref_index[max_match]].contig_no)];
temp_range /= 2;
align_info->aligned_range_ref = abs(ref[ref_index[max_match]].coord2 - ref[ref_index[min_match]].coord2) + temp_range;
align_info->aligned_range_qry = abs(qry[qry_index[max_match]].coord2 - qry[qry_index[min_match]].coord2) + temp_range;
if (abs(align_info->aligned_range_ref - align_info->aligned_range_qry) > align_info->mm_ratio*min(align_info->aligned_range_ref, align_info->aligned_range_qry))
{
//cout << "MM:" << align_info->aligned_range_ref << " " << align_info->aligned_range_qry << endl;
}
vector<int> offset_vec0, offset_vec;
vector<int> ref_matched_positions0, qry_matched_positions0, ref_matched_positions, qry_matched_positions;
align_info->ref_aligned_center = 0;
align_info->qry_aligned_center = 0;
align_info->aligned_nodes = 0;
int max_cov = 0;
int last_match = -1;
align_info->MaxOffsetRQ = -1;
align_info->AbsOffsetSum = 0;
align_info->OffsetSum = abs(align_info->aligned_range_ref - align_info->aligned_range_qry);
for (int i = min_match; i <= max_match; ++i)
{
if (align_info->ref_aligned[i] == align_info->qry_aligned[i])
{
if (last_match >= 0)
{
int abs_offset = abs((int)abs(ref[ref_index[i]].coord2 - ref[ref_index[last_match]].coord2) - (int)abs(qry[qry_index[i]].coord2 - qry[qry_index[last_match]].coord2));
if (abs_offset > align_info->MaxOffsetRQ)
{
align_info->MaxOffsetRQ = abs_offset;
if (abs_offset > 500)
{
// cout << abs(ref[ref_index[i]].coord2 - ref[ref_index[last_match]].coord2) << endl;
// cout << abs(qry[qry_index[i]].coord2 - qry[qry_index[last_match]].coord2) << endl;
}
}
align_info->AbsOffsetSum += abs_offset;
}
last_match = i;
if (align_info->matching_method == 1)
{
align_info->match_len += contigs_info->contig_sz_vt[abs(align_info->ref_aligned[i])];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
if (ref_index.count(i) && qry_index.count(i))
{
//use average resolves more ties
if (align_info->scoring_method == 1)
{
//cout << "1";
align_info->match_len += max(ref[ref_index[i]].cov, qry[qry_index[i]].cov);
}
if (align_info->scoring_method == 2)
{
//cout << "2";
align_info->match_len += min(ref[ref_index[i]].cov, qry[qry_index[i]].cov);
}
if (align_info->scoring_method == 3)
{
//cout << "3";
align_info->match_len += (ref[ref_index[i]].cov + qry[qry_index[i]].cov) / 2;
}
}
else
{
cout << "Warning. Unexpected mismatch." << endl;
}
}
if (align_info->CalculateOffset)
{
//int ctg_matched = align_info->qry_aligned[i];
if (ref[ref_index[i]].cov > 1 && qry[qry_index[i]].cov > 1)
{
if (max_cov == 0 || max_cov< min(ref[ref_index[i]].cov, qry[qry_index[i]].cov))//very important. use > to minimize risk, use < to have best robustness
{
if (max(ref[ref_index[i]].cov, qry[qry_index[i]].cov) <= contigs_info->contig_sz_vt[abs(ref[ref_index[i]].contig_no)])
{
//cout << "o: " << max_cov << "n: " << min(ref[ref_index2[ctg_matched]].cov, qry[qry_index2[ctg_matched]].cov) << endl;
offset_vec0.push_back(ref[ref_index[i]].coord2 - qry[qry_index[i]].coord2);
max_cov = min(ref[ref_index[i]].cov, qry[qry_index[i]].cov);
ref_matched_positions0.push_back(ref[ref_index[i]].coord2);
qry_matched_positions0.push_back(qry[qry_index[i]].coord2);
}
}
align_info->aligned_nodes++;
}
offset_vec.push_back(ref[ref_index[i]].coord2 - qry[qry_index[i]].coord2);
ref_matched_positions.push_back(ref[ref_index[i]].coord2);
qry_matched_positions.push_back(qry[qry_index[i]].coord2);
}
}
else
{
if (align_info->matching_method == 1)
{
align_info->mismatch_len[0] += contigs_info->contig_sz_vt[abs(align_info->ref_aligned[i])];
align_info->mismatch_len[1] += contigs_info->contig_sz_vt[abs(align_info->qry_aligned[i])];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
if (ref_index.count(i))
{
align_info->mismatch_len[0] += ref[ref_index[i]].cov;
}
if (qry_index.count(i))
{
align_info->mismatch_len[1] += qry[qry_index[i]].cov;
}
}
}
}
int ref_beg = ref[0].coord2 + contigs_info->contig_sz_vt[abs(ref[0].contig_no)] / 2;
int qry_beg = qry[0].coord2 + contigs_info->contig_sz_vt[abs(qry[0].contig_no)] / 2;
align_info->frontal_mismatch_len[2] = ref[ref_index[min_match]].coord2 - contigs_info->contig_sz_vt[abs(align_info->ref_aligned[min_match])] / 2 - ref_beg;
align_info->frontal_mismatch_len[3] = qry[qry_index[min_match]].coord2 - contigs_info->contig_sz_vt[abs(align_info->qry_aligned[min_match])] / 2 - qry_beg;
int ref_len = ref[ref.size() - 1].coord2 - contigs_info->contig_sz_vt[abs(ref[ref.size() - 1].contig_no)] / 2;
int qry_len = qry[qry.size() - 1].coord2 - contigs_info->contig_sz_vt[abs(qry[qry.size() - 1].contig_no)] / 2;
align_info->rear_mismatch_len[2] = ref_len - ref[ref_index[max_match]].coord2 - contigs_info->contig_sz_vt[abs(align_info->ref_aligned[max_match])] / 2;
align_info->rear_mismatch_len[3] = qry_len - qry[qry_index[max_match]].coord2 - contigs_info->contig_sz_vt[abs(align_info->qry_aligned[max_match])] / 2;
/*
if (ref_index[min_match] == 0)
{
align_info->frontal_mismatch_len[2] = 0;
}
if (qry_index[min_match] == 0)
{
align_info->frontal_mismatch_len[3] = 0;
}
if (ref_index[max_match]+1 == ref.size())
{
align_info->rear_mismatch_len[2] = 0;
}
if (qry_index[max_match] + 1 == qry.size())
{
align_info->rear_mismatch_len[3] = 0;
}
*/
for (int i = 0; i < min_match; ++i)
{
if (align_info->matching_method == 1)
{
align_info->frontal_mismatch_len[0] += contigs_info->contig_sz_vt[abs(align_info->ref_aligned[i])];
align_info->frontal_mismatch_len[1] += contigs_info->contig_sz_vt[abs(align_info->qry_aligned[i])];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
if (ref_index.count(i))
{
align_info->frontal_mismatch_len[0] += ref[ref_index[i]].cov;
}
if (qry_index.count(i))
{
align_info->frontal_mismatch_len[1] += qry[qry_index[i]].cov;
}
}
}
for (int i = max_match + 1; i < align_info->ref_aligned.size(); ++i)
{
if (align_info->matching_method == 1)
{
align_info->rear_mismatch_len[0] += contigs_info->contig_sz_vt[abs(align_info->ref_aligned[i])];
align_info->rear_mismatch_len[1] += contigs_info->contig_sz_vt[abs(align_info->qry_aligned[i])];
}
if (align_info->matching_method == 2 || align_info->matching_method == 3)
{
if (ref_index.count(i))
{
align_info->rear_mismatch_len[0] += ref[ref_index[i]].cov;
}
if (qry_index.count(i))
{
align_info->rear_mismatch_len[1] += qry[qry_index[i]].cov;
}
}
}
for (int i = max_match + 1; i < align_info->ref_aligned.size(); ++i)
{
if (align_info->qry_aligned[i] != 0)
{
align_info->right_ext.push_back(align_info->qry_aligned[i]);
}
if (align_info->ref_aligned[i] != 0)
{
align_info->right_mismatch.push_back(align_info->ref_aligned[i]);
}
}
int ext_len = align_info->right_ext.size();
align_info->right_dist.resize(ext_len);
qry_sz = qry.size();//newly added 20190315
if (ext_len<qry_sz)
{
for (int i = 0; i < ext_len; ++i)
{
int dist = (qry[qry_sz - ext_len + i].coord2 - qry[qry_sz - ext_len - 1 + i].coord2);
align_info->right_dist[i] = abs(dist);
}
}
if (align_info->CalculateOffset)
{
if (offset_vec0.size()>0)
{
//cout << "catch." << endl;
//cout << offset_vec0.size() << endl;
//cout << ref_matched_positions0.size() << endl;
offset_vec = offset_vec0;
ref_matched_positions = ref_matched_positions0;
qry_matched_positions = qry_matched_positions0;
}
align_info->aligned_nodes = ref_matched_positions.size();
sort(offset_vec.begin(), offset_vec.end());
if (align_info->aligned_nodes>0)
{
align_info->ref_aligned_center = ref_matched_positions[ref_matched_positions.size() - 1];
align_info->qry_aligned_center = qry_matched_positions[qry_matched_positions.size() - 1];
if (align_info->aligned_nodes > 1)
{
for (int jj = 0; jj < align_info->aligned_nodes; ++jj)
{
//cout << jj<<" ref: " << ref_matched_positions[jj] << " qry: " << qry_matched_positions [jj ]<< endl;
}
}
align_info->aligned_nodes = 1;
}
align_info->offset = offset_vec[offset_vec.size() / 2];
align_info->ahg = align_info->offset;
align_info->bhg = align_info->qry_len - align_info->ref_len + align_info->offset;
if (align_info->flip)
{
align_info->adj = 'I';
}
else
{
align_info->adj = 'N';
}
//if (align_info->ref_len == 10322 || align_info->qry_len == 10322 || align_info->ref_len == 10625 || align_info->qry_len == 10625)
//cout << "offset: " << align_info->offset<<endl;
}
//align_info->max_score = align_info->max_score - align_info->mm_penalty*((double)min(align_info->frontal_mismatch_len[0], align_info->frontal_mismatch_len[1]));
//align_info->max_score = align_info->max_score - align_info->mm_penalty*((double)min(align_info->rear_mismatch_len[0], align_info->rear_mismatch_len[1]));
return 1;
}
bool approximate_semi_global_align(contigs_info *contigs_info, vector<Coord_CTG_Cov> ref, vector<Coord_CTG_Cov> qry, align_matrices *align_matrices, align_info *align_info)
{
memset(align_matrices->score, 0, sizeof(align_matrices->score));
memset(align_matrices->path, 0, sizeof(align_matrices->path));
align_info->flip = 0;
align_info->success = 0;
align_info->ref_aligned.clear();
align_info->qry_aligned.clear();
align_info->right_ext.clear();
align_info->right_mismatch.clear();
int max_len = align_info->max_len;
align_info->CalculateOffset = 1;
if (align_info->force_flip)
{
align_info->flip = 1;
}
/*
TBD: preprocess if input fragments are too long, keep the best ones.
*/
if (ref.size() > max_len || qry.size() > max_len)
{
return 0;// no result
}
/*
semi global alignment,
if two contigs match, the score is the contig length,
mismatch: not defined.
gap: penalty score is the contig size
*/
map<int, int> local_index, ref_index, qry_index;
int ref_sz = ref.size(), qry_sz = qry.size();
for (int i = 0; i < ref_sz; ++i)
{
local_index[ref[i].contig_no] = ref[i].coord;
}
if (align_info->fix_orientation == 0)
{
int flip = 0, non_flip = 0;
for (int i = 0; i < qry_sz; ++i)
{
if (local_index.count(qry[i].contig_no))
{
non_flip++;
}
if (local_index.count(-qry[i].contig_no))
{
flip++;
}
}
if (flip == non_flip)
{
return 0;
}
if (flip > non_flip)
{
align_info->flip = 1;
}
}
if (align_info->flip)
{
reverse(qry.begin(), qry.end());
for (int i = 0; i < qry_sz; ++i)
{
qry[i].contig_no = -qry[i].contig_no;
//also change coords
}
for (int i = 0; i < qry_sz; ++i)
{