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GraphConstruction.h
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#ifndef __GRAPH_CONSTRUCTION_H
#define __GRAPH_CONSTRUCTION_H
#include <iostream>
#include <string>
#include <string.h>
#include <stdint.h>
#include <vector>
#include <map>
#include <list>
#include <algorithm>
#include <fstream>
#include <sstream>
#include "time.h"
#include "Align.h"
#include "BasicDataStructure.h"
using namespace std;
void Consensus_Kmer_Graph_Construction(struct ref_read_t *read, struct backbone_info *backbone_info, int K_size)
{
int readLen = read->readLen;
int OverlappingKmers = readLen - K_size + 1;
int Read_arr_sz = readLen / 32 + 1;
int rem = readLen % 32;
if (rem == 0)
{
Read_arr_sz--;
}
int Kmer_arr_sz = K_size / 32 + 1;
int rem1 = K_size % 32;
if (rem1 == 0)
{
Kmer_arr_sz--;
}
int tot_bits = Read_arr_sz * 64;
uint64_t seq;
//check the read to see if there is a saved kmer in the hashtable or bloom filter
consensus_node *previous_node = NULL, *current_node = NULL;
backbone_info->node_vec.resize(OverlappingKmers);
for (int j = 0; j < OverlappingKmers; j++)
{
previous_node = current_node;
get_sub_arr(read->read_bits, read->readLen, j, K_size, &seq);
current_node = (consensus_node*)malloc(sizeof(consensus_node));
backbone_info->node_vec[j] = current_node;
memset(current_node, 0, sizeof(consensus_node));
memcpy(&(current_node->kmer), &seq, sizeof(uint64_t));
current_node->in_backbone = 1;
current_node->cov++;
backbone_info->n_nodes++;
if (j >= 1)
{
//left edge,right edge
previous_node->right = (consensus_edge_node*)malloc(sizeof(consensus_edge_node));
memset(previous_node->right, 0, sizeof(consensus_edge_node));
previous_node->right->node_ptr = current_node;
//previous_node->right->edge_cov++;
previous_node->coord = j-1;
backbone_info->n_edges++;
current_node->left = (consensus_edge_node*)malloc(sizeof(consensus_edge_node));
memset(current_node->left, 0, sizeof(consensus_edge_node));
current_node->left->node_ptr = previous_node;
//current_node->left->edge_cov++;
backbone_info->n_edges++;
}
}
}
void Consensus_Sparse_Kmer_Graph_Construction(struct ref_read_t *read, struct backbone_info *backbone_info, int K_size)
{
int readLen = read->readLen;
int OverlappingKmers = readLen - K_size + 1;
int gap = backbone_info->gap;
int Read_arr_sz = readLen / 32 + 1;
int rem = readLen % 32;
if (rem == 0)
{
Read_arr_sz--;
}
int Kmer_arr_sz = K_size / 32 + 1;
int rem1 = K_size % 32;
if (rem1 == 0)
{
Kmer_arr_sz--;
}
int tot_bits = Read_arr_sz * 64;
uint64_t seq;
sparse_consensus_node *previous_node = NULL, *current_node = NULL;
backbone_info->sparse_node_vec.resize(OverlappingKmers);
for (int j = 0; j < OverlappingKmers; j++)
{
backbone_info->sparse_node_vec[j] = NULL;
}
int last_position = -1;
for (int j = 0; j < OverlappingKmers; j++)
{
if (j%gap == 0)
{
previous_node = current_node;
get_sub_arr(read->read_bits, read->readLen, j, K_size, &seq);
//char test[100];
//bitsarr2str(&seq, K_size, test, 1);
current_node = (sparse_consensus_node*)malloc(sizeof(sparse_consensus_node));
backbone_info->sparse_node_vec[j] = current_node;
memset(current_node, 0, sizeof(sparse_consensus_node));
current_node->kmer = (uint32_t)seq;
current_node->in_backbone = 1;
current_node->cov++;
current_node->coord = j;
backbone_info->n_nodes++;
//left edge,right edge
uint64_t edge_bits;
if (j >= 1)
{
get_sub_arr(read->read_bits, read->readLen, last_position + K_size, gap, &edge_bits);
previous_node->right = (sparse_consensus_edge_node*)malloc(sizeof(sparse_consensus_edge_node));
memset(previous_node->right, 0, sizeof(sparse_consensus_edge_node));
previous_node->right->node_ptr = current_node;
previous_node->right->edge = edge_bits;
previous_node->right->len = gap;
//previous_node->right->edge_cov++;//decide whether assign weight to the backbone edge
backbone_info->n_edges++;
get_sub_arr(read->read_bits, read->readLen, last_position, gap, &edge_bits);
current_node->left = (sparse_consensus_edge_node*)malloc(sizeof(sparse_consensus_edge_node));
memset(current_node->left, 0, sizeof(sparse_consensus_edge_node));
current_node->coord = j;
current_node->left->node_ptr = previous_node;
//current_node->left->edge_cov++;//decide whether assign weight to the backbone edge
current_node->left->len = gap;
current_node->left->edge = edge_bits;
backbone_info->n_edges++;
}
last_position = j;
}
}
}
void NormalizeAlignment(query_info *query_info)
{
string qAlignedSeq_new, tAlignedSeq_new;
size_t seq_sz = query_info->qAlignedSeq.size();
qAlignedSeq_new.resize(2 * seq_sz);
tAlignedSeq_new.resize(2 * seq_sz);
int target_position = query_info->tStart;
string target_crop, query_crop;
int n_char = 0;
for (int i = 0; i < seq_sz; ++i)
{
if (query_info->tAlignedSeq[i] != '-')
{
target_position++;
}
if (query_info->qAlignedSeq[i] == query_info->tAlignedSeq[i])
{
//qAlignedSeq_new.push_back(query_info->qAlignedSeq[i]);
//tAlignedSeq_new.push_back(query_info->tAlignedSeq[i]);
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
}
else
{
if (query_info->qAlignedSeq[i] != '-'&&query_info->tAlignedSeq[i] != '-')
{
//tAlignedSeq_new.push_back(query_info->tAlignedSeq[i]);
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
bool replace = 0;
for (int j = i + 1; j < query_info->tAlignedSeq.size(); ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
if (query_info->tAlignedSeq[j] == query_info->qAlignedSeq[i])
{
replace = 1;
query_info->tAlignedSeq[j] = '-';
//tAlignedSeq_new.push_back(query_info->qAlignedSeq[i]);
tAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
}
break;
}
}
if (replace == 0)
{
//tAlignedSeq_new.push_back('-');
tAlignedSeq_new[n_char] = '-';
}
n_char--;
//qAlignedSeq_new.push_back('-');
//qAlignedSeq_new.push_back(query_info->qAlignedSeq[i]);
qAlignedSeq_new[n_char] = '-';
n_char++;
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
n_char++;
}
else
{
if (query_info->qAlignedSeq[i] == '-')
{
for (int j = i + 1; j < query_info->qAlignedSeq.size(); ++j)
{
if (query_info->qAlignedSeq[j] != '-')
{
if (query_info->qAlignedSeq[j] == query_info->tAlignedSeq[i])
{
query_info->qAlignedSeq[i] = query_info->qAlignedSeq[j];
query_info->qAlignedSeq[j] = '-';
}
break;
}
}
}
else
{
for (int j = i + 1; j < query_info->qAlignedSeq.size(); ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
if (query_info->tAlignedSeq[j] == query_info->qAlignedSeq[i])
{
query_info->tAlignedSeq[i] = query_info->tAlignedSeq[j];
query_info->tAlignedSeq[j] = '-';
}
break;
}
}
}
//qAlignedSeq_new.push_back(query_info->qAlignedSeq[i]);
//tAlignedSeq_new.push_back(query_info->tAlignedSeq[i]);
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
}
}
}
qAlignedSeq_new.resize(n_char);
tAlignedSeq_new.resize(n_char);
query_info->qAlignedSeq = qAlignedSeq_new;
query_info->tAlignedSeq = tAlignedSeq_new;
}
void PatchGaps(query_info *query_info)
{
bool Align = 1;
string qAlignedSeq_new, tAlignedSeq_new;
size_t seq_sz = query_info->qAlignedSeq.size();
qAlignedSeq_new.resize(2* seq_sz);
tAlignedSeq_new.resize(2* seq_sz);
int target_position = query_info->tStart;
string target_crop, query_crop;
int MinGapSize = 2, K_size = query_info->Patch_K, SearchDepth = query_info->Patch_D;
int n_char = 0;
for (int i = 0; i < seq_sz; ++i)
{
if (query_info->tAlignedSeq[i] != '-')
{
target_position++;
}
bool Patch = 0;
if (query_info->qAlignedSeq[i] == '-')
{
int gap_bases = 1;
for (int j = i + 1; j <i+ MinGapSize; ++j)
{
if ((query_info->qAlignedSeq[j] != '-') || (j+1==seq_sz))
{
gap_bases = 0;
break;
}
gap_bases++;
}
if (gap_bases > 1)
{
Patch = 1;
}
}
if (!Patch&&Align)
{
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
}
if (Patch)
{
int shift = -1;
map<string, int> target_position, query_position;
vector<int> target_index, query_index;
target_index.resize(300);
query_index.resize(300);
string target_crop, query_crop;
int target_bases = 0, query_bases = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
target_crop.push_back(query_info->tAlignedSeq[j]);
target_index[target_bases] = j;
target_bases++;
}
if (target_bases >= SearchDepth + K_size)
{
break;
}
}
for (int j = i; j < seq_sz; ++j)
{
if (query_info->qAlignedSeq[j] != '-')
{
query_crop.push_back(query_info->qAlignedSeq[j]);
query_index[query_bases] = j;
query_bases++;
}
if (query_bases >= SearchDepth + K_size)
{
break;
}
}
if (!Align)
{
shift = MinGapSize;
for (int j = 0; j + K_size < target_crop.size(); ++j)
{
string kmer = target_crop.substr(j, K_size);
if (target_position.count(kmer) == 0)
{
target_position[kmer] = j;
}
}
int target_matched = -1, query_matched = -1;
for (int j = 0; j + K_size < query_crop.size(); ++j)
{
string kmer = query_crop.substr(j, K_size);
if (target_position.count(kmer))
{
target_matched = target_position[kmer];
query_matched = j;
break;
}
}
if (target_matched >= 0)
{
bool Debug = 0;
if (Debug)
{
cout << "before: " << endl;
cout << query_info->tAlignedSeq.substr(i, 100) << endl;
cout << query_info->qAlignedSeq.substr(i, 100) << endl;
}
//clear the query bases
for (int j = 0; j < query_matched + K_size; ++j)
{
query_info->qAlignedSeq[query_index[j]] = '-';
}
for (int j = 0; j < K_size; ++j)
{
query_info->qAlignedSeq[target_index[target_matched + j]] = query_info->tAlignedSeq[target_index[target_matched + j]];
}
if (Debug)
{
cout << "after: " << endl;
cout << query_info->tAlignedSeq.substr(i, 100) << endl;
cout << query_info->qAlignedSeq.substr(i, 100) << endl;
}
}
}
else
{
int match = 100, mismatch = -100, gap_cost = -10, band_width = 50;
string A_aln, B_aln;
struct aln_t aln_t;
int score = 0;
char qry_char[300];
char ref_char[300];
strcpy(ref_char, target_crop.c_str());
strcpy(qry_char, query_crop.c_str());
score = GlobalAlign(&aln_t, qry_char, ref_char, match, mismatch, gap_cost, band_width);
printAlign(&aln_t, qry_char, ref_char, A_aln, B_aln);
bool Debug = 0;
if (Debug)
{
cout << i << endl;
if (i == 27)
{
cout << "";
}
cout << "before: " << endl;
cout << query_info->tAlignedSeq.substr(i, 70) << endl;
cout << query_info->qAlignedSeq.substr(i, 70) << endl;
}
if (Debug)
{
cout << "after: " << endl;
cout << B_aln << endl;
cout << A_aln << endl;
}
int A_cnt = 0, B_cnt = 0;
for (int jj = 0; jj != A_aln.size(); ++jj)
{
if (A_aln[jj] != '-')
{
A_cnt++;
}
}
for (int jj = 0; jj != B_aln.size(); ++jj)
{
if (B_aln[jj] != '-')
{
B_cnt++;
}
}
int cnt = 0;
int match_position = -1;
for (int jj = (int)A_aln.size() - 1; jj >= 0; --jj)
{
if (A_aln[jj] == B_aln[jj])
{
cnt++;
}
else
{
cnt = 0;
}
if (cnt == K_size)
{
match_position = jj + K_size - 1;
break;
}
}
//append align
if (match_position == -1)
{
shift = MinGapSize - 1;
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
i=i + shift - 1;
continue;
}
for (int jj = 0; jj <= match_position; ++jj)
{
qAlignedSeq_new[n_char] = A_aln[jj];
tAlignedSeq_new[n_char] = B_aln[jj];
n_char++;
}
int target_shift = 0, query_shift = 0;
for (int jj = 0; jj <= match_position; ++jj)
{
if (B_aln[jj] != '-')
{
target_shift++;
}
if (A_aln[jj] != '-')
{
query_shift++;
}
}
//clear the query bases
int q_base = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->qAlignedSeq[j]!='-')
{
q_base++;
query_info->qAlignedSeq[j] = '-';
}
if (q_base >= query_shift)
{
break;
}
}
int t_base = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
t_base++;
query_info->tAlignedSeq[j] = '-';
}
if (t_base >= target_shift)
{
shift = j-i;
break;
}
}
}
i = i + shift - 1;
}
}
if (!Align)
{
for (int i = 0; i < seq_sz; ++i)
{
if (query_info->tAlignedSeq[i] != '-' || query_info->qAlignedSeq[i] != '-')
{
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
}
}
}
qAlignedSeq_new.resize(n_char);
tAlignedSeq_new.resize(n_char);
query_info->qAlignedSeq = qAlignedSeq_new;
query_info->tAlignedSeq = tAlignedSeq_new;
}
void FillGaps(query_info *query_info)
{
bool Align = 1;
string qAlignedSeq_new, tAlignedSeq_new;
size_t seq_sz = query_info->qAlignedSeq.size();
qAlignedSeq_new.resize(2 * seq_sz);
tAlignedSeq_new.resize(2 * seq_sz);
int target_position = query_info->tStart;
string target_crop, query_crop;
int MinGapSize = query_info->Patch_G, K_size = query_info->Patch_K, SearchDepth = query_info->Patch_D;
int n_char = 0;
for (int i = 0; i < seq_sz; ++i)
{
if (query_info->tAlignedSeq[i] != '-')
{
target_position++;
}
bool Patch = 0;
//detect gaps in query
if (query_info->qAlignedSeq[i] == '-')
{
int gap_bases = 1;
for (int j = i + 1; j <i + MinGapSize; ++j)
{
if ((query_info->qAlignedSeq[j] != '-') || (j + 1 == seq_sz))
{
gap_bases = 0;
break;
}
gap_bases++;
}
if (gap_bases > 1)
{
Patch = 1;
}
}
//detect gaps in target
if (query_info->tAlignedSeq[i] == '-')
{
int gap_bases = 1;
for (int j = i + 1; j <i + MinGapSize; ++j)
{
if ((query_info->tAlignedSeq[j] != '-') || (j + 1 == seq_sz))
{
gap_bases = 0;
break;
}
gap_bases++;
}
if (gap_bases > 1)
{
Patch = 1;
}
}
if (!Patch)
{
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[i];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[i];
n_char++;
continue;
}
int shift = -1;
vector<int> target_index, query_index;
target_index.resize(300);
query_index.resize(300);
string target_crop, query_crop;
target_crop.resize(300);
query_crop.resize(300);
int target_bases = 0, query_bases = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
target_crop[target_bases]=query_info->tAlignedSeq[j];
target_index[target_bases] = j;
target_bases++;
}
if (target_bases >= SearchDepth + K_size)
{
break;
}
}
for (int j = i; j < seq_sz; ++j)
{
if (query_info->qAlignedSeq[j] != '-')
{
query_crop[query_bases]=query_info->qAlignedSeq[j];
query_index[query_bases] = j;
query_bases++;
}
if (query_bases >= SearchDepth + K_size)
{
break;
}
}
target_crop.resize(target_bases);
query_crop.resize(query_bases);
int match = 100, mismatch = -100, gap_cost = -10, band_width = 50;
string Query_aln, Target_aln;
struct aln_t aln_t;
int score = 0;
char qry_char[300];
char ref_char[300];
strcpy(ref_char, target_crop.c_str());
strcpy(qry_char, query_crop.c_str());
score = GlobalAlign(&aln_t, qry_char, ref_char, match, mismatch, gap_cost, band_width);
printAlign(&aln_t, qry_char, ref_char, Query_aln, Target_aln);
bool Debug = 0;
if (Debug)
{
cout << i << endl;
cout << "before: " << endl;
cout << query_info->tAlignedSeq.substr(i, 70) << endl;
cout << query_info->qAlignedSeq.substr(i, 70) << endl;
}
if (Debug)
{
cout << "after: " << endl;
cout << Target_aln << endl;
cout << Query_aln << endl;
}
int cnt = 0;
int match_position = -1;
for (int jj = (int)Query_aln.size() - 1; jj >= 0; --jj)
{
if (Query_aln[jj] == Target_aln[jj])
{
cnt++;
}
else
{
cnt = 0;
}
if (cnt == K_size)
{
match_position = jj + K_size - 1;
break;
}
}
//append align
int shift_end;
shift_end = i + 1;
if (query_crop.size() == target_crop.size() && target_crop.size() == SearchDepth + K_size)
{
shift_end = i + SearchDepth;// min(target_index[SearchDepth + K_size - 1], query_index[SearchDepth + K_size - 1]);
}
if (match_position == -1)
{
int j;
for (j = i; j < shift_end ; ++j)
{
qAlignedSeq_new[n_char] = query_info->qAlignedSeq[j];
tAlignedSeq_new[n_char] = query_info->tAlignedSeq[j];
n_char++;
}
i=j-1;
continue;
}
for (int jj = 0; jj <= match_position; ++jj)
{
qAlignedSeq_new[n_char] = Query_aln[jj];
tAlignedSeq_new[n_char] = Target_aln[jj];
n_char++;
}
int target_shift = 0, query_shift = 0;
for (int jj = 0; jj <= match_position; ++jj)
{
if (Target_aln[jj] != '-')
{
target_shift++;
}
if (Query_aln[jj] != '-')
{
query_shift++;
}
}
//clear the aligned bases
int q_base = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->qAlignedSeq[j] != '-')
{
q_base++;
query_info->qAlignedSeq[j] = '-';
}
if (q_base >= query_shift)
{
shift = query_index[q_base - 1];
break;
}
}
int t_base = 0;
for (int j = i; j < seq_sz; ++j)
{
if (query_info->tAlignedSeq[j] != '-')
{
t_base++;
query_info->tAlignedSeq[j] = '-';
}
if (t_base >= target_shift)
{
shift = min(shift,target_index[t_base - 1]);
break;
}
}
i = shift ;
}
qAlignedSeq_new.resize(n_char);
tAlignedSeq_new.resize(n_char);
query_info->qAlignedSeq = qAlignedSeq_new;
query_info->tAlignedSeq = tAlignedSeq_new;
}
void Add_Path_To_Backbone(struct backbone_info *backbone_info, struct query_info *query_info, int K_size)
{
ofstream o_report_align;
bool boost_edges = 0;
string ContigPrefix = backbone_info->ContigPrefix;
if (ContigPrefix.size() > 0)
{
if (query_info->qName.substr(0, ContigPrefix.size()) == ContigPrefix)
{
boost_edges = 1;
}
}
bool DEBUG = 0;
if (query_info->tStrand == '-')
{
reverse_complement_str(query_info->qAlignedSeq);
reverse_complement_str(query_info->tAlignedSeq);
reverse(query_info->matchPattern.begin(), query_info->matchPattern.end());
}
NormalizeAlignment(query_info);
if (query_info->Patch)
{
PatchGaps(query_info);
}
else
{
if (query_info->Fill)
{
FillGaps(query_info);
}
}
// FillGaps(query_info);
for (int i = 0; i < query_info->tAlignedSeq.size(); ++i)
{
if (query_info->tAlignedSeq[i] != '-')
{
if (query_info->qAlignedSeq[i] != '-')
{
backbone_info->ref_matched++;
}
else
{
backbone_info->ref_mismatch++;
}
}
}
if ((query_info->report_e > query_info->report_b) && (query_info->tStart<query_info->report_b) && (query_info->tEnd>query_info->report_e))
{
o_report_align.open("subalign.txt", ios_base::app);
int target_position = query_info->tStart;
string target_crop, query_crop;
for (int k = 0; k < query_info->tAlignedSeq.size(); ++k)
{
if (query_info->tAlignedSeq[k] != '-')
{
target_position++;
}
if (target_position>query_info->report_b)
{
target_crop.push_back(query_info->tAlignedSeq[k]);
query_crop.push_back(query_info->qAlignedSeq[k]);
//
}
if (target_position>query_info->report_e)
{
o_report_align << ">target_" << query_info->read_idx << endl << target_crop << endl;//
o_report_align << ">query_" << query_info->read_idx << endl << query_crop << endl;//
break;
}
}
}
string backbone_seg = backbone_info->backbone.substr(query_info->tStart, query_info->tEnd - query_info->tStart);
//cout << backbone_seg << endl;
//cout << target_seg << endl;
int target_position = query_info->tStart;
consensus_node *previous_node = NULL, *current_node = NULL;
int MatchPosition = -100, PreviousMatchPosition = -100;
for (int i = 0; i + K_size <= query_info->qAlignedSeq.size(); ++i)
{
if (query_info->qAlignedSeq[i] == '-')
{
MatchPosition = -1;
PreviousMatchPosition = -1;
if (query_info->tAlignedSeq[i] != '-')
{
target_position++;
}
continue;
}
PreviousMatchPosition = MatchPosition;
MatchPosition = target_position;
for (int j = 0; j < K_size; ++j)
{
if (query_info->qAlignedSeq[i + j] != query_info->tAlignedSeq[i + j])
{
MatchPosition = -1;
break;
}
}
string KmerStr;
KmerStr.resize(K_size);
int KmerSize = 0;
for (int j = i; j < query_info->qAlignedSeq.size(); ++j)
{
if (query_info->qAlignedSeq[j] != '-')
{
KmerStr[KmerSize]=query_info->qAlignedSeq[j];
KmerSize++;
}
if (KmerSize == K_size)
{
break;
}
}
if (KmerSize != K_size)
{
break;
}
uint64_t seq = 0;
str2bitsarr(KmerStr.c_str(), K_size, &seq, 1);
if (MatchPosition >= 0)
{
query_info->n_exist++;
current_node = backbone_info->node_vec[MatchPosition];