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errorgraph.h
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/*
* karect version 1.0
* Copyright (c) 2014 KAUST All Rights Reserved.
* Author: Amin Allam
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#include <cmath>
#include "stack.h"
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
struct PatNodeConn
{
int node; // save
double prob;
double wacc; // save
};
struct PatNode
{
char ch; // save
vector<PatNodeConn> adj; // save
union{int path_prev_node; int num_incoming_edges;
};
long double path_weight;
};
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
struct ErrorGraph
{
int max_str_len;
int min_overlap; // The minimum allowed overlap size (try compute it using ac randomization)
double min_overlap_percentage;
double max_overlap_error_rate; // The maximum allowed error rate in any overlap
double truncate_factor;
double min_straight_edge_val;
double min_straight_edge_percentage;
double min_read_weight;
int max_mul_len_matches;
int match_type;
int* T;
int num_nodes; // save (also in hamming)
int start_node; // save
int end_node; // save
bool load_mode;
bool save_mode;
vector<PatNode> pat_nodes; // save
unsigned short num_hamming_scores; // save hamming (actually this is pat_len)
double* hamming_weights; // save hamming
bool confirmed; // save both
bool excluded; // save both
};
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template<class Type>
int CompactGetErrorGraphSize(ErrorGraph* eg)
{
int i, total_size=0;
Type node_ind;
total_size+=sizeof(eg->confirmed);
if(eg->confirmed) return total_size;
total_size+=sizeof(eg->excluded)+sizeof(eg->num_nodes)+sizeof(node_ind)+sizeof(node_ind);
total_size+=eg->num_nodes*(sizeof(char)+sizeof(node_ind));
for(i=0;i<eg->num_nodes;i++)
{
int sz=eg->pat_nodes[i].adj.size();
total_size+=sz*(sizeof(node_ind)+sizeof(float));
}
return total_size;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int GetErrorGraphSize(ErrorGraph* eg)
{
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
int total_size=sizeof(eg->confirmed);
if(eg->confirmed) return total_size;
total_size+=sizeof(eg->excluded)+sizeof(eg->num_hamming_scores);
total_size+=sizeof(float)*NUM_VALID_CHARS*eg->num_hamming_scores;
return total_size;
}
if(eg->num_nodes<0xFF) return CompactGetErrorGraphSize<unsigned char>(eg);
else if(eg->num_nodes<0xFFFF) return CompactGetErrorGraphSize<unsigned short>(eg);
return CompactGetErrorGraphSize<unsigned int>(eg);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template<class Type>
void CompactSaveErrorGraph(ErrorGraph* eg, char* buf_eg)
{
int i;
int cur=0;
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
int i;
for(i=0;i<eg->num_hamming_scores*NUM_VALID_CHARS;i++)
{
Type val=(Type)eg->hamming_weights[i];
memcpy(buf_eg+cur, &val, sizeof(Type)); cur+=sizeof(Type);
}
return;
}
Type j;
Type node_ind;
node_ind=eg->start_node; memcpy(buf_eg+cur, &node_ind, sizeof(node_ind)); cur+=sizeof(node_ind);
node_ind=eg->end_node; memcpy(buf_eg+cur, &node_ind, sizeof(node_ind)); cur+=sizeof(node_ind);
for(i=0;i<eg->num_nodes;i++)
{
memcpy(buf_eg+cur, &eg->pat_nodes[i].ch, sizeof(eg->pat_nodes[i].ch)); cur+=sizeof(eg->pat_nodes[i].ch);
Type sz=eg->pat_nodes[i].adj.size(); memcpy(buf_eg+cur, &sz, sizeof(sz)); cur+=sizeof(sz);
for(j=0;j<sz;j++)
{
node_ind=eg->pat_nodes[i].adj[j].node; memcpy(buf_eg+cur, &node_ind, sizeof(node_ind)); cur+=sizeof(node_ind);
float wacc=eg->pat_nodes[i].adj[j].wacc; memcpy(buf_eg+cur, &wacc, sizeof(wacc)); cur+=sizeof(wacc);
}
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void SaveErrorGraph(ErrorGraph* eg, char* buf_eg)
{
int cur=0;
memcpy(buf_eg+cur, &eg->confirmed, sizeof(eg->confirmed)); cur+=sizeof(eg->confirmed);
if(eg->confirmed) return;
memcpy(buf_eg+cur, &eg->excluded, sizeof(eg->excluded)); cur+=sizeof(eg->excluded);
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
memcpy(buf_eg+cur, &eg->num_hamming_scores, sizeof(eg->num_hamming_scores)); cur+=sizeof(eg->num_hamming_scores);
return CompactSaveErrorGraph<float>(eg, buf_eg+cur);
}
memcpy(buf_eg+cur, &eg->num_nodes, sizeof(eg->num_nodes)); cur+=sizeof(eg->num_nodes);
if(eg->num_nodes<0xFF) CompactSaveErrorGraph<unsigned char>(eg, buf_eg+cur);
else if(eg->num_nodes<0xFFFF) CompactSaveErrorGraph<unsigned short>(eg, buf_eg+cur);
else CompactSaveErrorGraph<unsigned int>(eg, buf_eg+cur);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template<class Type>
void CompactLoadErrorGraph(ErrorGraph* eg, char* buf_eg)
{
int i;
int cur=0;
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
int i;
for(i=0;i<eg->num_hamming_scores*NUM_VALID_CHARS;i++)
{
Type val;
memcpy(&val, buf_eg+cur, sizeof(Type)); cur+=sizeof(Type);
eg->hamming_weights[i]=val;
}
return;
}
Type j;
Type node_ind;
memcpy(&node_ind, buf_eg+cur, sizeof(node_ind)); cur+=sizeof(node_ind); eg->start_node=node_ind;
memcpy(&node_ind, buf_eg+cur, sizeof(node_ind)); cur+=sizeof(node_ind); eg->end_node=node_ind;
for(i=0;i<eg->num_nodes;i++)
{
PatNode pn; eg->pat_nodes.push_back(pn);
memcpy(&eg->pat_nodes[i].ch, buf_eg+cur, sizeof(eg->pat_nodes[i].ch)); cur+=sizeof(eg->pat_nodes[i].ch);
Type sz=0; memcpy(&sz, buf_eg+cur, sizeof(sz)); cur+=sizeof(sz); //eg->pat_nodes[i].adj.size();
for(j=0;j<sz;j++)
{
PatNodeConn pnc; eg->pat_nodes[i].adj.push_back(pnc);
memcpy(&node_ind, buf_eg+cur, sizeof(node_ind)); cur+=sizeof(node_ind); eg->pat_nodes[i].adj[j].node=node_ind;
float wacc; memcpy(&wacc, buf_eg+cur, sizeof(wacc)); cur+=sizeof(wacc); eg->pat_nodes[i].adj[j].wacc=wacc;
}
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void LoadErrorGraph(ErrorGraph* eg, char* buf_eg)
{
int cur=0;
memcpy(&eg->confirmed, buf_eg+cur, sizeof(eg->confirmed)); cur+=sizeof(eg->confirmed);
if(eg->confirmed) return;
memcpy(&eg->excluded, buf_eg+cur, sizeof(eg->excluded)); cur+=sizeof(eg->excluded);
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
memcpy(&eg->num_hamming_scores, buf_eg+cur, sizeof(eg->num_hamming_scores)); cur+=sizeof(eg->num_hamming_scores);
return CompactLoadErrorGraph<float>(eg, buf_eg+cur);
}
eg->pat_nodes.clear();
memcpy(&eg->num_nodes, buf_eg+cur, sizeof(eg->num_nodes)); cur+=sizeof(eg->num_nodes);
if(eg->num_nodes<0xFF) CompactLoadErrorGraph<unsigned char>(eg, buf_eg+cur);
else if(eg->num_nodes<0xFFFF) CompactLoadErrorGraph<unsigned short>(eg, buf_eg+cur);
else CompactLoadErrorGraph<unsigned int>(eg, buf_eg+cur);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void InitErrorGraph(ErrorGraph* eg, bool load_mode, bool save_mode, int max_str_len, int min_overlap, double min_overlap_percentage, double max_overlap_error_rate, double truncate_factor, double min_straight_edge_val, double min_straight_edge_percentage, double min_read_weight, int max_mul_len_matches, int match_type)
{
eg->max_str_len=max_str_len;
eg->max_overlap_error_rate=max_overlap_error_rate;
eg->min_overlap=min_overlap;
eg->min_overlap_percentage=min_overlap_percentage;
eg->truncate_factor=truncate_factor;
eg->min_straight_edge_val=min_straight_edge_val;
eg->min_straight_edge_percentage=min_straight_edge_percentage;
eg->min_read_weight=min_read_weight;
eg->max_mul_len_matches=max_mul_len_matches;
eg->match_type=match_type;
eg->load_mode=load_mode;
eg->save_mode=save_mode;
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
eg->hamming_weights=(double*)AllocateHeap(sizeof(double)*eg->max_str_len*NUM_VALID_CHARS);
}
else
{
eg->T=(int*)AllocateHeap(3*(eg->max_str_len+1)*sizeof(int));
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void DestroyErrorGraph(ErrorGraph* eg)
{
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
FreeHeap(eg->hamming_weights, sizeof(double)*eg->max_str_len*NUM_VALID_CHARS);
}
else
{
FreeHeap(eg->T, 3*(eg->max_str_len+1)*sizeof(int));
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void TruncatePath(ErrorGraph* eg, vector<double>& path_w, int& st_path, int& en_path, int& num_truncated)
{
int i;
st_path=0;
en_path=path_w.size();
double EPS=1e-4;
if(eg->truncate_factor>EPS)
{
int f=1;
while(f)
{
f=0;
for(i=st_path;i<en_path && en_path>st_path+2;i++)
{
if(path_w[i]<=eg->truncate_factor)
{
f=1;
if(i+1-st_path<en_path-i)
{
num_truncated+=i+1-st_path;
st_path=i+1;
}
else
{
num_truncated+=en_path-i;
en_path=i;
}
break;
}
}
}
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void InitializeMatching(ErrorGraph* eg, char* pat, int pat_len, char* pat_quality)
{
int i;
eg->pat_nodes.clear();
// node 0 is start node (does not contain characters)
// node pat_len+1 is end node (does not contain characters)
for(i=0;i<pat_len+2;i++)
{
PatNode pn;
eg->pat_nodes.push_back(pn);
eg->pat_nodes[i].ch=0;
if(i>0 && i<pat_len+1) eg->pat_nodes[i].ch=pat[i-1];
if(i<pat_len+1)
{
PatNodeConn pnc;
pnc.node=i+1;
pnc.wacc=1.0;
if(pat_quality && i<pat_len) pnc.wacc=CharToProb[(unsigned char)pat_quality[i]];
eg->pat_nodes[i].adj.push_back(pnc);
}
}
eg->start_node=0;
eg->end_node=pat_len+1;
eg->num_nodes=pat_len+2;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void GetTopologicalOrder(ErrorGraph* eg, int* ordered_nodes)
{
int i,j;
for(i=0;i<eg->num_nodes;i++) eg->pat_nodes[i].num_incoming_edges=0;
for(i=0;i<eg->num_nodes;i++)
{
for(j=0;j<(int)eg->pat_nodes[i].adj.size();j++)
{
eg->pat_nodes[eg->pat_nodes[i].adj[j].node].num_incoming_edges++;
}
}
int num_ordered_nodes=0;
for(i=0;i<eg->num_nodes;i++)
{
if(eg->pat_nodes[i].num_incoming_edges==0) ordered_nodes[num_ordered_nodes++]=i;
}
int num_processed_nodes=0;
while(num_processed_nodes<num_ordered_nodes)
{
int cur_node=ordered_nodes[num_processed_nodes++];
for(j=0;j<(int)eg->pat_nodes[cur_node].adj.size();j++)
{
int next_node=eg->pat_nodes[cur_node].adj[j].node;
eg->pat_nodes[next_node].num_incoming_edges--;
if(eg->pat_nodes[next_node].num_incoming_edges==0) ordered_nodes[num_ordered_nodes++]=next_node;
}
}
for(i=0;i<eg->num_nodes;i++)
{
if(eg->pat_nodes[i].num_incoming_edges!=0)
{
printf("Cycle Detected %d %d\n", i, eg->pat_nodes[i].num_incoming_edges);
fflush(NULL);
}
}
if(num_ordered_nodes!=eg->num_nodes)
{
printf("Unexpected Error NumNode Topology %d %d\n", num_ordered_nodes, eg->num_nodes);
fflush(NULL);
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void FinalizeMatching(ErrorGraph* eg, int read_len, char* read_quality, char* result_str, int& result_len, char* result_quality, int& num_truncated)
{
int i,j;
int* ordered_nodes=new int[eg->num_nodes];
GetTopologicalOrder(eg, ordered_nodes);
double EPS=1e-4;
for(i=0;i<eg->num_nodes;i++)
{
eg->pat_nodes[i].path_weight=-1.0;
eg->pat_nodes[i].path_prev_node=-1;
}
eg->pat_nodes[eg->start_node].path_weight=1;
for(i=0;i<eg->num_nodes;i++)
{
int cur_node=ordered_nodes[i];
double weight_with_n=0;
double weight_without_n=0;
double best_score=-1.0;
double org_best_score=-1.0;
int num_adj=eg->pat_nodes[cur_node].adj.size();
for(j=0;j<num_adj;j++)
{
PatNodeConn& pnc=eg->pat_nodes[cur_node].adj[j];
if(cur_node>=eg->start_node && cur_node<eg->end_node && pnc.node==cur_node+1 && eg->pat_nodes[pnc.node].ch!='N') org_best_score=pnc.wacc;
weight_with_n+=pnc.wacc;
if(pnc.wacc>best_score) best_score=pnc.wacc;
if(eg->pat_nodes[pnc.node].ch!='N') weight_without_n+=pnc.wacc;
pnc.prob=0;
}
if(org_best_score>=eg->min_straight_edge_val || best_score<EPS || org_best_score/best_score>=eg->min_straight_edge_percentage)
{
if(num_adj) eg->pat_nodes[cur_node].adj[0].prob=1;
}
else if(weight_with_n>EPS)
{
for(j=0;j<num_adj;j++)
{
PatNodeConn& pnc=eg->pat_nodes[cur_node].adj[j];
if(weight_without_n>EPS){if(eg->pat_nodes[pnc.node].ch!='N') pnc.prob=pnc.wacc/weight_without_n;} else
pnc.prob=pnc.wacc/weight_with_n;
}
}
}
long double best_weight=-1.0;
for(i=0;i<eg->num_nodes;i++)
{
int cur_node=ordered_nodes[i];
for(j=0;j<(int)eg->pat_nodes[cur_node].adj.size();j++)
{
PatNodeConn& pnc=eg->pat_nodes[cur_node].adj[j];
long double new_path_weight=eg->pat_nodes[cur_node].path_weight*pnc.prob;
if(new_path_weight>eg->pat_nodes[pnc.node].path_weight)
{
eg->pat_nodes[pnc.node].path_weight=new_path_weight;
eg->pat_nodes[pnc.node].path_prev_node=cur_node;
if(pnc.node==eg->end_node && new_path_weight>best_weight)
{
best_weight=new_path_weight;
}
}
}
}
vector<char> path_ch; // the size of path_ch is less than the size of path_w by 1
vector<double> path_w;
vector<int> path_quality_ind;
vector<char> path_quality;
int cur_node=eg->end_node;
while(cur_node!=eg->start_node)
{
int prev_node=eg->pat_nodes[cur_node].path_prev_node;
for(i=0;prev_node>=0 && i<(int)eg->pat_nodes[prev_node].adj.size();i++)
{
if(eg->pat_nodes[prev_node].adj[i].node==cur_node)
{
char ch=eg->pat_nodes[cur_node].ch; if(ch) path_ch.push_back(ch);
path_w.push_back(eg->pat_nodes[prev_node].adj[i].wacc);
if(read_quality)
{
int q_ind=-1; if(cur_node>eg->start_node && cur_node<eg->end_node) q_ind=cur_node-1;
if(ch) path_quality_ind.push_back(q_ind); // if(ch) to make sure path_quality_ind.size()==path_ch.size()
}
break;
}
}
cur_node=prev_node;
}
if(read_quality)
{
int pqsz=(int)path_quality_ind.size();
for(i=0;i<pqsz;i++)
{
if(path_quality_ind[i]<0)
{
for(j=i;j>=0;j--) if(path_quality_ind[j]>=0) break;
int en=read_len-1; if(j>=0) en=path_quality_ind[j];
for(j=i;j<pqsz;j++) if(path_quality_ind[j]>=0) break;
int st=0; if(j<pqsz) st=path_quality_ind[j];
int sc=0; for(j=st;j<=en;j++) sc+=CharToQual[(unsigned char)read_quality[j]]; sc/=(en-st+1); path_quality.push_back(QualToChar(sc));
}
else
{
path_quality.push_back(read_quality[path_quality_ind[i]]);
}
}
}
int st_path, en_path;
TruncatePath(eg, path_w, st_path, en_path, num_truncated);
result_len=en_path-st_path-1;
if(result_len>eg->max_str_len*2){result_len=0;result_str[0]=0;read_quality[0]=0;return;}
for(i=result_len-1;i>=0;i--)
{
if(i+st_path>=(int)path_ch.size() || (read_quality && path_ch.size()!=path_quality.size())) {printf("Unexpected Error FinalizeMatching\n"); fflush(NULL);}
result_str[result_len-1-i]=path_ch[i+st_path];
if(read_quality) result_quality[result_len-1-i]=path_quality[i+st_path];
}
result_str[result_len]=0;
if(read_quality) result_quality[result_len]=0;
delete[] ordered_nodes;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
bool IsConfirmed(ErrorGraph* eg, char* pat, int pat_len)
{
int j;
for(j=0;j<=pat_len;j++) if(pat[j]=='N' || eg->pat_nodes[j].adj[0].wacc<eg->min_straight_edge_val) break;
return (j==pat_len+1);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int NewNode(ErrorGraph* eg)
{
eg->num_nodes++;
if((int)eg->pat_nodes.size()<eg->num_nodes) {PatNode pn; eg->pat_nodes.push_back(pn);}
return eg->num_nodes-1;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int LinkNodes(ErrorGraph* eg, int prev_node, char ch, int cur_node, double w) //, int org_start, double w) // ch = char of destination node
{
int i;
if(cur_node==0) {printf("NP Link to Start Node\n"); fflush(NULL);}
if(prev_node==cur_node) printf("CYCLE %d %d *------------*\n", prev_node, cur_node);
if(cur_node==-1)
{
for(i=0;i<(int)eg->pat_nodes[prev_node].adj.size();i++)
{
PatNodeConn& pnc=eg->pat_nodes[prev_node].adj[i];
if(pnc.node>eg->end_node && eg->pat_nodes[pnc.node].ch==ch)
{
pnc.wacc+=w;
cur_node=pnc.node;
break;
}
}
if(cur_node==-1)
{
cur_node=NewNode(eg);
PatNodeConn pnc;
pnc.node=cur_node;
pnc.wacc=w;
eg->pat_nodes[cur_node].ch=ch;
eg->pat_nodes[prev_node].adj.push_back(pnc);
}
}
else
{
for(i=0;i<(int)eg->pat_nodes[prev_node].adj.size();i++)
{
PatNodeConn& pnc=eg->pat_nodes[prev_node].adj[i];
if(pnc.node==cur_node)
{
if(eg->pat_nodes[pnc.node].ch!=ch) {printf("ERRRRRROR\n"); fflush(NULL);}
pnc.wacc+=w;
break;
}
}
if(i==(int)eg->pat_nodes[prev_node].adj.size())
{
PatNodeConn pnc;
pnc.node=cur_node;
pnc.wacc=w;
eg->pat_nodes[prev_node].adj.push_back(pnc);
}
}
return cur_node;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
struct LinkOperation
{
int a_st, a_en; // a_en=after end
int type;
vector<char> chs;
};
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int AddNormalizedMatchToGraph(ErrorGraph* eg, char* a, int na, int first_a, int last_a, vector<ShortNode>& normalized, double w, char* qual)
{
int i,j;
int cur_a=first_a;
int start_node=-1;
vector<LinkOperation> v;
for(i=0;i<(int)normalized.size();i++)
{
ShortNode node=normalized[i];
int ca=node.ia;
char ch=node.ch;
if(cur_a<ca)
{
LinkOperation op;
op.a_st=cur_a;
op.a_en=ca;
op.type=0;
v.push_back(op);
cur_a=ca;
i--;
}
else
{
LinkOperation op;
op.a_st=ca;
op.a_en=ca;
op.type=1;
if(node.type==ED_DELETE) {op.a_en++; cur_a++;}
else op.chs.push_back(ch);
i++;
for(;i<(int)normalized.size();i++)
{
if(normalized[i].ia>cur_a) break;
if(normalized[i].type==ED_DELETE) {op.a_en++; cur_a++;}
else op.chs.push_back(normalized[i].ch);
}
i--;
v.push_back(op);
}
}
if(cur_a<last_a)
{
LinkOperation op;
op.a_st=cur_a;
op.a_en=last_a;
op.type=0;
v.push_back(op);
}
int prev_node=first_a;
if(first_a==0)
{
prev_node=eg->start_node;
start_node=prev_node;
}
else
{
prev_node=-1;
}
int q=0;
for(i=0;i<(int)v.size();i++)
{
if(v[i].type==0)
{
for(j=v[i].a_st;j<v[i].a_en;j++)
{
if(prev_node==-1) {prev_node=j+1; start_node=prev_node;} //InsertStartNode(eg, prev_node);}
else
{
double cw=w; if(qual) cw*=CharToProb[(unsigned char)qual[q]];
prev_node=LinkNodes(eg, prev_node, a[j], j+1, cw);
}
q++;
}
}
else
{
for(j=0;j<(int)v[i].chs.size();j++)
{
if(prev_node==-1)
{
prev_node=NewNode(eg);
eg->pat_nodes[prev_node].ch=v[i].chs[j];
start_node=prev_node;
}
else
{
double cw=w; if(qual) cw*=CharToProb[(unsigned char)qual[q]];
prev_node=LinkNodes(eg, prev_node, v[i].chs[j], -1, w);
}
q++;
}
}
}
if(last_a==na)
{
LinkNodes(eg, prev_node, 0, eg->end_node, w);
}
return start_node;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
double GetWeight(double min_read_weight, int num_errors, int cur_allowed_overlap_errors)
{
double cur_whole_weight=1.0-(1-min_read_weight)*sqrt((double)num_errors/cur_allowed_overlap_errors);
return cur_whole_weight;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int ProcessLocation(ErrorGraph* eg, char* a, int na, char* b, int nb, int first_a, int first_b, int last_a, int last_b, int edit, vector<ShortNode>& v, char* qual)
{
int i;
int cur_overlap_size=last_a-first_a;
int cur_allowed_overlap_errors=eg->max_overlap_error_rate*cur_overlap_size;
int cur_min_overlap=eg->min_overlap_percentage*na;
if(cur_min_overlap<eg->min_overlap) cur_min_overlap=eg->min_overlap;
if(cur_overlap_size-edit<cur_min_overlap || edit>cur_allowed_overlap_errors)
{
return -1;
}
double cur_whole_weight=GetWeight(eg->min_read_weight, edit, cur_allowed_overlap_errors);
vector<ShortNode> normalized;
for(i=0;i<(int)v.size();i++)
{
ShortNode& node=v[i];
if(node.type==ED_SUBSTITUTE)
{
ShortNode sn;
sn.ia=node.ia; sn.ch=node.ch; sn.type=ED_INSERT; normalized.push_back(sn);
sn.ia=node.ia; sn.ch=a[node.ia]; sn.type=ED_DELETE; normalized.push_back(sn);
}
else
{
if(node.type==ED_DELETE) node.ch=a[node.ia];
normalized.push_back(node);
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int last_val=na;
for(i=(int)normalized.size()-1;i>=0;i--)
{
if(normalized[i].type==ED_DELETE)
{
int ia=normalized[i].ia;
int ch=normalized[i].ch;
ia++; while(ia<last_val && a[ia]==ch) ia++; ia--;
normalized[i].ia=ia;
last_val=ia;
int j=i;
for(j=i;j<(int)normalized.size()-1;j++)
{
if(normalized[j+1].type==ED_DELETE)
break;
if(normalized[j].ia>=normalized[j+1].ia)
{
ShortNode temp=normalized[j]; normalized[j]=normalized[j+1]; normalized[j+1]=temp;
normalized[j].ia--;
}
else break;
}
}
else if(normalized[i].type==ED_INSERT)
{
int ia=normalized[i].ia;
int ch=normalized[i].ch;
if(ia<na && a[ia]==ch)
{
ia++; while(ia<na && a[ia]==ch) ia++;
normalized[i].ia=ia;
}
int j=i;
for(j=i;j<(int)normalized.size()-1;j++)
{
if(normalized[j+1].type==ED_DELETE)
{
if(normalized[j].ia>=normalized[j+1].ia)
{
if(normalized[j].ch==normalized[j+1].ch)
{
normalized.erase(normalized.begin()+j+1);
normalized.erase(normalized.begin()+j);
break;
}
ShortNode temp=normalized[j]; normalized[j]=normalized[j+1]; normalized[j+1]=temp;
if(normalized[j+1].ia<na) normalized[j+1].ia++;
int ia=normalized[j+1].ia;
char ch=normalized[j+1].ch;
if(ia<na && a[ia]==ch)
{
ia++; while(ia<na && a[ia]==ch) ia++;
normalized[j+1].ia=ia;
}
}
else break;
}
else
{
if(normalized[j].ia>normalized[j+1].ia)
{
ShortNode temp=normalized[j]; normalized[j]=normalized[j+1]; normalized[j+1]=temp;
normalized[j].ia++;
}
else break;
}
}
}
}
int start_node=AddNormalizedMatchToGraph(eg, a, na, first_a, last_a, normalized, cur_whole_weight, qual);
return start_node;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void FixReadUsingGraph(ErrorGraph* eg, unsigned short* kmer_first, int kmer_size, char* pat, int pat_len, char* pat_quality, vector<PossibleMatch>& possible_matches, char* result_str, int& result_len, char* result_quality, int& num_truncated)
{
int i;
if(eg->match_type==MATCH_SUBSTITUTE_ONLY)
{
int j,k;
if(!eg->load_mode)
{
eg->confirmed=false;
eg->excluded=false;
eg->num_hamming_scores=pat_len;
for(j=0;j<pat_len;j++)
{
for(k=0;k<NUM_VALID_CHARS;k++) eg->hamming_weights[j*NUM_VALID_CHARS+k]=0;
int cti=CharToInt5Val[(int)pat[j]];
if(cti<NUM_VALID_CHARS)
{
eg->hamming_weights[j*NUM_VALID_CHARS+cti]=1.0;
if(pat_quality) eg->hamming_weights[j*NUM_VALID_CHARS+cti]=CharToProb[(unsigned char)pat_quality[j]];
}
}
}
int num=0;
int cur_min_overlap=eg->min_overlap_percentage*pat_len;
if(cur_min_overlap<eg->min_overlap) cur_min_overlap=eg->min_overlap;
for(i=0;i<(int)possible_matches.size() && !eg->confirmed;i++)
{
for(j=0;j<pat_len;j++)
{
int cti=CharToInt5Val[(int)pat[j]];
if(cti>=NUM_VALID_CHARS || eg->hamming_weights[j*NUM_VALID_CHARS+cti]<eg->min_straight_edge_val) break;
}
if(j==pat_len) {eg->confirmed=true; break;}
if(!eg->excluded && possible_matches[i].str_len==pat_len && memcmp(pat, possible_matches[i].str, pat_len)==0 &&
(!pat_quality || !possible_matches[i].qual || memcmp(pat_quality, possible_matches[i].qual, pat_len)==0))
{
eg->excluded=true;
continue;
}
int max_overlap_errors=possible_matches[i].max_overlap*eg->max_overlap_error_rate;
int min_hamming_dist=max_overlap_errors+1;
double cur_whole_weight=0;
vector<int> shifts;
// b starts at a[shift]
for(k=possible_matches[i].shift1;k<=possible_matches[i].shift2;k++)
{
int hd=0;
int cur_overlap_size=0;
for(j=0;j<pat_len && hd<min_hamming_dist;j++)
{
int ib=j-k;
if(ib>=0 && ib<possible_matches[i].str_len)
{
cur_overlap_size++;
hd+=(pat[j]!=possible_matches[i].str[ib]);
}
}
int cur_allowed_overlap_errors=eg->max_overlap_error_rate*cur_overlap_size;
if(cur_overlap_size-hd<cur_min_overlap || hd>cur_allowed_overlap_errors)
continue;
if(hd<min_hamming_dist)
{
min_hamming_dist=hd;
shifts.clear();
shifts.push_back(k);
double weight=GetWeight(eg->min_read_weight, hd, cur_allowed_overlap_errors);
cur_whole_weight=weight;
}
else if(hd==min_hamming_dist)