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DBG2OLC.cpp
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DBG2OLC.cpp
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#include "iostream"
#include "stdio.h"
#include "string"
#include "vector"
#include "cstdlib"
#include "bitset"
#include <map>
#include <math.h>
#include "memory"
#include <algorithm>
#include "fstream"
#include "sstream"
#include "list"
#include "stdlib.h"
#include "time.h"
#include "stdint.h"
#include "BasicDataStructure.h"
#include "GraphConstruction.h"
#include "GraphSimplification.h"
#include "GraphSearch.h"
#include "BuildContigs.h"
using namespace std;
/*
The goal here is to take a set of illumina contigs and re-index them using small k-mers.
done
For each long read, we find the contigs that are covered and then we build another contig-long_read index
partially done
Based on this new index we analyze the overlap relation and glue together the long reads.
idea: sort the a-stats of the ctgs and start from the best ctg to glue the best pacbio reads
*/
/*
bug to fix:
tips removal,bubble merging to be improved
alignment to be improved
graph structure to be improved
*/
int main(int argc, char* argv[])
{
/*
test
string str0 = "";
stringstream ss(str0);
int coord = -1;
ss >> coord;
*/
int K_size = 17, KmerCovTh = 0, ContigCovTh = 1, ChimeraTh = 1;
double Redundancy = 1.1;
bool CloseGaps = 0;
double AdaptiveTh = -0.005;
bool SparseAlign = 1;
double mm_ratio = 0.5, mm_penalty = 0.3, mm_FR = 3.0, min_ext=1.0;
int max_readlen = 1000000000;
int max_dist = 5;
int max_depth = 5;
int ConsensusBestN = 10;
int MinOverlap = 50;
int MaxOffset = 10000;
int MaxMismatchFR = 5000;
int MatchMethod = 2;
int ScoreMethod = 3;
string ctg_filename = "Contigs.txt", ref_filename = "RefContigIndex_info.txt", qry_filename, qry_filename2, contig_graph_filename = "RefinedContigGraph.txt";
string Prefix = "LongRead";
vector<string> qry_filename_vec;
vector<string> qry_filename_vec2;
bool LOAD_CONTIG_KMER_INDEX = 0, LOAD_LONGREAD_CONTIG_INDEX = 0, LOAD_OVERLAP_GRAPH = 0;
bool ConstructBackbonesOnly=0;
bool ASSEMBLY = 1, ALIGN = 0;
bool CORRECT_WITH_CONTIG_GRAPH = 1;
bool RemoveChimera = 0, RecoverFalseNegatives = 0;
bool OUTPUT_NON_CONTAINED_READS = 0;
bool OutputGraph = 1;
bool FixOrientation = 0;
bool Debug = 0;
bool MSA = 0;
int CleanRound = 1;
int TopOverlaps = 50;
int PathCovTh = 0;
int64_t TotalReads = -1;
bool InwardPairs = 0, OutwardPairs = 0;
string ctg_kmer_idx_name = "ContigKmerIndex_";
vector<string> LongReadFilenameVec,LongReadsInfoFiles,NonContainedReadsFiles;
bool HELP = 1;
bool Consensus = 1;
int MinLen = 1;
int MaxLen = 150;// max compressed read length
for (int i = 1; i < argc; ++i)
{
if (strcmp(argv[i], "-h") == 0 || strcmp(argv[i], "h") == 0)
{
i++;
HELP = 1;
break;
}
if (strcmp(argv[i], "Contigs") == 0)
{
i++;
ctg_filename = (argv[i]);
continue;
}
if (strcmp(argv[i], "ContigGraph") == 0)
{
i++;
contig_graph_filename = (argv[i]);
continue;
}
if (strcmp(argv[i], "SparseAlign") == 0)
{
i++;
SparseAlign = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "r") == 0)
{
i++;
ref_filename = (argv[i]);
continue;
}
if (strcmp(argv[i], "R") == 0)
{
i++;
TotalReads = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "CloseGaps") == 0)
{
i++;
CloseGaps = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "BB") == 0)
{
i++;
ConstructBackbonesOnly = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "FixOrientation") == 0)
{
i++;
FixOrientation = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "ConsensusBestN") == 0)
{
i++;
ConsensusBestN = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "q") == 0)
{
i++;
qry_filename = (argv[i]);
qry_filename_vec.push_back(qry_filename);
continue;
}
if (strcmp(argv[i], "qr") == 0)
{
i++;
qry_filename2 = (argv[i]);
qry_filename_vec2.push_back(qry_filename2);
continue;
}
if (strcmp(argv[i], "f") == 0)
{
i++;
LongReadFilenameVec.push_back(argv[i]);
string name1= argv[i];
int n = 0;
for (n = name1.size() - 1; n >= 0; --n)
{
if (name1[n] == '\\'||name1[n]=='/')
{
break;
}
}
name1 = name1.substr(n + 1, name1.size());
name1="ReadsInfoFrom_" + name1;
LongReadsInfoFiles.push_back(name1);
name1 = argv[i];
n = 0;
for (n = name1.size() - 1; n >= 0; --n)
{
if (name1[n] == '\\' || name1[n] == '/')
{
break;
}
}
name1 = name1.substr(n + 1, name1.size());
name1 = "NonContainedReadsFrom_" + name1;
NonContainedReadsFiles.push_back(name1);
continue;
}
if (strcmp(argv[i], "k") == 0)
{
i++;
K_size = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Match") == 0)
{
i++;
MatchMethod = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Score") == 0)
{
i++;
ScoreMethod = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "ip") == 0)
{
i++;
InwardPairs = 1;
qry_filename_vec.push_back(argv[i]);
continue;
}
if (strcmp(argv[i], "ipr") == 0)
{
i++;
qry_filename_vec2.push_back(argv[i]);
continue;
}
if (strcmp(argv[i], "NC") == 0)
{
i++;
OUTPUT_NON_CONTAINED_READS = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Consensus") == 0)
{
i++;
Consensus = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "TopOverlaps") == 0)
{
i++;
TopOverlaps = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "PathCovTh") == 0)
{
i++;
PathCovTh = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "AdaptiveTh") == 0)
{
i++;
AdaptiveTh = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "mm_penalty") == 0)
{
i++;
mm_penalty = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "mm_FR") == 0)
{
i++;
mm_FR = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "min_ext") == 0)
{
i++;
min_ext = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "mm_ratio") == 0)
{
i++;
mm_ratio = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "max_depth") == 0)
{
i++;
max_depth = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "max_dist") == 0)
{
i++;
max_dist = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MSA") == 0)
{
i++;
MSA = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "CleanRound") == 0)
{
i++;
CleanRound = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Debug") == 0 || strcmp(argv[i], "DEBUG") == 0)
{
i++;
Debug = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MinLen") == 0)
{
i++;
MinLen = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MaxLen") == 0)
{
i++;
MaxLen = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MinOverlap") == 0)
{
i++;
MinOverlap = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MaxOffset") == 0)
{
i++;
MaxOffset = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "MaxMismatchFR") == 0)
{
i++;
MaxMismatchFR = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "LD0") == 0)
{
i++;
LOAD_CONTIG_KMER_INDEX = (bool)atoi(argv[i]);
//LOAD_LONGREAD_CONTIG_INDEX = LOAD_CONTIG_KMER_INDEX;
continue;
}
if (strcmp(argv[i], "LD1") == 0 || strcmp(argv[i], "LD") == 0)
{
i++;
LOAD_LONGREAD_CONTIG_INDEX = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "LD2") == 0)
{
i++;
LOAD_OVERLAP_GRAPH = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "RemoveChimera") == 0)
{
i++;
RemoveChimera = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "RecoverFalseNegatives") == 0)
{
i++;
RecoverFalseNegatives = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Assembly") == 0)
{
i++;
ASSEMBLY = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Prefix") == 0)
{
i++;
Prefix = (argv[i]);
continue;
}
if (strcmp(argv[i], "Align") == 0)
{
i++;
ALIGN = (bool)atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "KmerCovTh") == 0)
{
i++;
KmerCovTh = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "Redundancy") == 0)
{
i++;
Redundancy = atof(argv[i]);
continue;
}
if (strcmp(argv[i], "ContigCovTh") == 0)
{
i++;
ContigCovTh = atoi(argv[i]);
continue;
}
if (strcmp(argv[i], "ChimeraTh") == 0)
{
i++;
ChimeraTh = atoi(argv[i]);
continue;
}
}
if (HELP)
{
cout << " Example command: " << endl;
cout << "For third-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 17 KmerCovTh 2 MinOverlap 20 AdaptiveTh 0.005 f reads_file1.fq/fa f reads_file2.fq/fa" << endl;
cout << "For sec-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 31 KmerCovTh 0 MinOverlap 50 PathCovTh 1 f reads_file1.fq/fa f reads_file2.fq/fa" << endl;
cout << "Parameters:" << endl;
cout << "MinLen: min read length for a read to be used." << endl;
cout << "Contigs: contig file to be used." << endl;
cout << "k: k-mer size." << endl;
cout << "LD: load compressed reads information. You can set to 1 if you have run the algorithm for one round and just want to fine tune the following parameters." << endl;
cout << "PARAMETERS THAT ARE CRITICAL FOR THE PERFORMANCE:" << endl;
cout << "If you have high coverage, set large values to these parameters." << endl;
cout << "KmerCovTh: k-mer matching threshold for each solid contig. (suggest 2-10)" << endl;
cout << "MinOverlap: min matching k-mers for each two reads. (suggest 10-150)" << endl;
cout << "AdaptiveTh: [Specific for third-gen sequencing] adaptive k-mer threshold for each solid contig. (suggest 0.001-0.02)" << endl;
cout << "PathCovTh: [Specific for Illumina sequencing] occurence threshold for a compressed read. (suggest 1-3)" << endl;
cout << "Author: Chengxi Ye cxy@umd.edu." << endl;
cout << "last update: Jun 11, 2015." << endl;
}
//
if (RemoveChimera)
{
MSA = 1;
}
contigs_info contigs_info;
contigs_info.KmerCovTh = KmerCovTh;
contigs_info.ContigsFileName = ctg_filename;
if (AdaptiveTh > 0.0)
{
contigs_info.CallConsensus = Consensus;
}
else
{
contigs_info.CallConsensus = Consensus;
}
contigs_info.ContigCovTh = ContigCovTh;
contigs_info.ContigGraphName = contig_graph_filename;
ifstream ctgs_in(ctg_filename.c_str());
contigs_info.contig_tag.clear();
contigs_info.contig_tag.push_back("");
string str, contig_str;
size_t hashTableSZ = 0;
struct hashtable ht;
ht.ht_sz = 0;
// string LongReadContigIndex_name = Prefix + "ContigIndex_info.txt";
if (ASSEMBLY)
if (LOAD_LONGREAD_CONTIG_INDEX == 0)
if (LOAD_CONTIG_KMER_INDEX)
{
cout << "Loading kmer index..." << endl;
LoadContigKmerIndex(&ht, ctg_kmer_idx_name);
cout << "Done." << endl;
}
else
{
cout << "Loading contigs." << endl;
int max_ctg_len = -1;
int tot_ctgs = 0;
string tag, n_tag;
while (get_a_fasta_read(ctgs_in, tag, contig_str, n_tag))
{
contigs_info.contig_tag.push_back(tag);
int sz = contig_str.size();
hashTableSZ += sz - K_size + 1;
if (max_ctg_len < sz)
{
max_ctg_len = sz;
}
tot_ctgs++;
}
ctgs_in.close();
contigs_info.contig_sz_vt.clear();
contigs_info.contig_sz_vt.resize(tot_ctgs + 1);
ref_read_t ref;
ref.read_bits = (uint64_t *)myMalloc((size_t)(max_ctg_len / 4) + 100);
ref.alloc_sz = (size_t)(max_ctg_len / 4 + 100);
Init_HT(&ht, hashTableSZ);
for (int round = 1; round <= 2; ++round)
{
ht.round = round;
int bucket_count = 0;
ctgs_in.open(ctg_filename.c_str());
tot_ctgs = 0;
while (get_a_fasta_read(ctgs_in, tag, contig_str, n_tag))
{
int sz = contig_str.size();
tot_ctgs++;
ref.contig_no = tot_ctgs;
contigs_info.contig_sz_vt[tot_ctgs] = sz;
Init_Ref_Read(contig_str, ref);
//if (contig_str.size() > 100)
if (1)
{
Contig_Kmer_Index(&ref, &ht, K_size, &bucket_count);
}
}
ctgs_in.close();
if (ht.round == 1)
{
SwitchBuckets(&ht);
}
contigs_info.total_contigs = tot_ctgs;
cout << bucket_count << " k-mers in round " << round << "." << endl;
}
SaveContigKmerIndex(&ht, ctg_kmer_idx_name);
}
contigs_info.contig_sz_vt.clear();
contigs_info.contig_sz_vt.push_back(0);
int tot_ctgs = 0, ContigLen = 0;
string tag, n_tag;
ctgs_in.close();
ctgs_in.open(ctg_filename.c_str());
contigs_info.contig_tag.clear();
contigs_info.contig_tag.push_back("");
while (get_a_fasta_read(ctgs_in, tag, contig_str, n_tag))
{
int ContigLen = contig_str.size();
tot_ctgs++;
contigs_info.contig_tag.push_back(tag);
contigs_info.contig_sz_vt.push_back(ContigLen);
}
contigs_info.total_contigs = tot_ctgs;
ctgs_in.close();
/*
LoadRefinedContigGraph(&contigs_info,contig_graph_filename);
str.clear();
ctgs_in.open(ctg_filename.c_str());
contigs_info.contigs_str.push_back(str);
while (getline(ctgs_in, str) && str.size() > 0)
{
getline(ctgs_in, contig_str);
while (contig_str[contig_str.size() - 1] == '\n' || contig_str[contig_str.size() - 1] == '\r')
{
int sz = contig_str.size();
contig_str[sz - 1] = '\0';
contig_str.resize(sz - 1);
}
int sz = contig_str.size();
contigs_info.contigs_str.push_back(contig_str);
tot_ctgs++;
}
ctgs_in.close();
int cov = contigs_info.contig_adjacency_right[abs(17303)][-26604].cov;
OutputFastaContigs(&contigs_info, "ContigsByLongReadsNodes_info.txt");
*/
if (!LOAD_LONGREAD_CONTIG_INDEX&&LongReadFilenameVec.size())
{
ref_read_t long_read;
if (LongReadFilenameVec.size() == 0)
{
cout << "No input files." << endl;
return 0;
}
string Histogram_name = Prefix + "ContigIndex_Histogram.txt";
ofstream LongReadContigIndex_hist(Histogram_name.c_str());
ofstream LongReadContigIndex_log("LongReadContigIndex_log.txt");
ofstream out_refined_graph;
//ofstream out_positions_debug("CenterEstimates.txt");
ofstream NonContainedReads_o;
if (AdaptiveTh < 0.0)
{
OUTPUT_NON_CONTAINED_READS = 1;
out_refined_graph.open("RefinedContigGraph.txt");
}
long_read.read_bits = (uint64_t *)myMalloc((size_t)(max_readlen / 4) + 100);
long_read.alloc_sz = (size_t)(max_readlen / 4 + 100);
cout << "Analyzing reads..." << endl;
time_t beg_time, end_time;
time(&beg_time);
map<int, int> contigs_match_hist;
uint64_t total_kmers = 0, MatchingUniqueKmers = 0;
int read_idx = 0;
for (int i = 0; i < LongReadFilenameVec.size(); ++i)
{
cout << "File" << i + 1 << ": " << LongReadFilenameVec[i] << endl;
ofstream LongReadContigIndex_info(LongReadsInfoFiles[i].c_str());
if (OUTPUT_NON_CONTAINED_READS)
{
NonContainedReads_o.close();
NonContainedReads_o.open(NonContainedReadsFiles[i].c_str());
}
bool fq_flag = 0;
string tag, n_tag, read_str, quality_score;
ifstream LongReads_in(LongReadFilenameVec[i].c_str());
getline(LongReads_in, tag);
if (tag[0] == '@')
{
fq_flag = 1;
}
LongReads_in.close();
LongReads_in.open(LongReadFilenameVec[i].c_str());
bool read_success = 1;
while (read_success)
{
if (fq_flag == 0)
{
read_success = get_a_fasta_read(LongReads_in, tag, read_str, n_tag);
}
else
{
read_success = get_a_fastq_read(LongReads_in, tag, read_str, quality_score);
}
if (read_success == 0)
{
break;
}
//deal with 'N's in a stupid way
string temp_str, raw_read = read_str;
temp_str.resize(read_str.size());
size_t nn = 0;
for (int n = 0; n < read_str.size(); ++n)
{
if (read_str[n] != 'N')
{
temp_str[nn]=read_str[n];
nn++;
}
}
temp_str.resize(nn);
read_str = temp_str;
if (read_str.size() > max_readlen)
{
read_str.resize(max_readlen - 1);
}
if (read_str.size() < MinLen)
{
continue;
}
read_idx++;
//cout << tag << endl;
Init_Ref_Read(read_str, long_read);
long_read.read_idx = read_idx;
struct LongReadContigIndex LongReadContigIndex;
LongReadContigIndex.KmerCovTh = KmerCovTh;
LongReadContigIndex.nMatches = 0;
LongReadContigIndex.BlockSize = 1000;
LongReadContigIndex.FastMap = 1;
ReadCompression(&long_read, &ht, &contigs_info, K_size, &LongReadContigIndex);
MatchingUniqueKmers += LongReadContigIndex.nMatches;
total_kmers += long_read.readLen - K_size + 1;
map<int, ContigInRead>::iterator tmp_it;
int contig_matches = 0;
for (tmp_it = LongReadContigIndex.layout.begin(); tmp_it != LongReadContigIndex.layout.end(); ++tmp_it)
{
if (tmp_it->second.cov > KmerCovTh)
{
contig_matches++;
}
}
if (contig_matches > 1||AdaptiveTh>0.0)
{
LongReadContigIndex_info << tag << endl;
LongReadContigIndex_info << read_str.size() << endl;
for (tmp_it = LongReadContigIndex.layout.begin(); tmp_it != LongReadContigIndex.layout.end(); ++tmp_it)
{
if (tmp_it->second.cov > KmerCovTh)
{
LongReadContigIndex_info << tmp_it->first << ", " << tmp_it->second.ctg_no << ", " << tmp_it->second.cov << ", " << tmp_it->second.coord2 << endl;
}
}
contigs_match_hist[contig_matches]++;
if (OUTPUT_NON_CONTAINED_READS)
{
NonContainedReads_o << tag << endl;
NonContainedReads_o << raw_read << endl;
}
}
//newly added...
if (OUTPUT_NON_CONTAINED_READS)
{
map<int, KmerInContig>::iterator it1, it2;
for (it1 = LongReadContigIndex.LR2CTG.begin(); it1 != LongReadContigIndex.LR2CTG.end(); ++it1)
{
it2 = it1;
it2++;
if (it2 == LongReadContigIndex.LR2CTG.end())
{
break;
}
if (it2->second.contig_no != it1->second.contig_no)
{
bool flip1, flip2;
flip1 = it1->second.flip;
flip2 = it2->second.flip;
int pos1 = it1->second.pos;
int pos2 = it2->second.pos;
int extra_bases1, extra_bases2;
int contig1 = it1->second.contig_no;
int contig2 = it2->second.contig_no;
if (flip1)
{
contig1 = -contig1;
}
if (flip2)
{
contig2 = -contig2;
}
int dist = it2->first - it1->first;
if (flip1 == 0)
{
extra_bases1 = contigs_info.contig_sz_vt[abs(contig1)] - pos1;
}
else
{
extra_bases1 = pos1;
}
if (flip2 == 0)
{
extra_bases2 = pos2;
}
else
{
extra_bases2 = contigs_info.contig_sz_vt[abs(contig2)] - pos2;
}
int extra_bases = extra_bases1 + extra_bases2;
dist = dist - extra_bases;
if (contig1 != 0 && contig2 != 0)
{
if (contig1 > 0)
{
out_refined_graph << contig1 << " " << contig2 << " " << dist << endl;
}
else
{
out_refined_graph << contig1 << " " << -contig2 << " " << dist << endl;
}
}
}
}
//newly added...
}
}
}
cout << "Long reads indexed. " << endl;
for (map<int, int>::iterator hist_it = contigs_match_hist.begin(); hist_it != contigs_match_hist.end(); ++hist_it)
{
LongReadContigIndex_hist << hist_it->first << ", " << hist_it->second << endl;
}
cout << "Total Kmers: " << total_kmers << endl;
cout << "Matching Unique Kmers: " << MatchingUniqueKmers << endl;
LongReadContigIndex_log << "Total Kmers: " << total_kmers << endl;
LongReadContigIndex_log << "Matching Unique Kmers: " << MatchingUniqueKmers << endl;
time(&end_time);
cout <<"Compression time: "<< difftime(end_time, beg_time) << " secs." << endl;
}
if (ht.ht_sz > 0)
{
FreeSparseKmerGraph(&ht);
}
reads_info reads_info;
align_info align_info;
align_info.SparseAlign = SparseAlign;
align_info.Debug = Debug;
align_info.flip = 0;
align_info.force_flip = 0;
align_info.fix_orientation = 1;
align_info.max_mismatch_FR_score = MinOverlap * mm_FR;
if (align_info.max_mismatch_FR_score > 300)
{
//align_info.max_mismatch_FR = 300;
}
align_info.min_overlap = MinOverlap;
align_info.min_extension_FR = MinOverlap * min_ext;
align_info.mm_ratio = mm_ratio;// 0.4;//0.4
align_info.mm_penalty = mm_penalty;// 0.
align_info.max_len = 250;//modified on 20190315 to allow aligning ultra long reads
align_info.band_width = 20;
reads_info.K_size = K_size;
reads_info.CloseGaps = CloseGaps;
reads_info.ConsensusBestN = ConsensusBestN;
align_info.MaxOffset = MaxOffset;
align_info.MaxMismatchFR = MaxMismatchFR;
reads_info.Clean = 1;
if (AdaptiveTh < 0.0)
{
MatchMethod = 1;//not ready for sec gen yet
}
align_info.matching_method = MatchMethod;
cout << "Scoring method: " << ScoreMethod << endl;
cout << "Match method: " << MatchMethod << endl;
align_info.scoring_method = ScoreMethod;
reads_info.AdaptiveTh = AdaptiveTh;
reads_info.input_files = LongReadFilenameVec;
reads_info.TopOverlaps = TopOverlaps;
reads_info.PathCovTh = PathCovTh;
reads_info.ChimeraTh = ChimeraTh;
reads_info.RemoveChimera = RemoveChimera;
//cout << "Recover false negatives: " << RecoverFalseNegatives << endl;
reads_info.RecoverFalseNegatives = RecoverFalseNegatives;
reads_info.MSA = MSA;
reads_info.Debug = Debug;
reads_info.MinLen = MinLen;
reads_info.max_reads = 500;
reads_info.TotalReads = TotalReads;
reads_info.KmerCovTh = KmerCovTh;
reads_info.Redundancy = Redundancy;
if (ALIGN)
{
ofstream o_align("align2ref.txt");
ofstream o_align_rc("align2rc.txt");
ofstream o_align_rc_tags("align2rc_tags.txt");
ofstream o_align_chimera("chimera.txt");
ofstream o_align_chimera_tags("chimera_tags.txt");
ofstream o_corr_len("ContigLenEstCorr.txt");
align_info.fix_orientation = 1;
//align_info.InnerProduct = 0;
cout << "Loading reference." << endl;
//string RefContigIndex_name = "RefContigIndex_info.txt";
LoadingRefIndex(ref_filename, &reads_info, &contigs_info);
cout << "Reference loaded. Size: " << reads_info.RefIndexVec.size() - 1 << endl;
LoadLongReadIndex(qry_filename_vec, &reads_info, &contigs_info);
cout << "Queries loaded. Size: " << reads_info.LongReadIndexVec.size() - 1 << endl;
for (int i = 1; i != reads_info.LongReadIndexVec.size(); ++i)
{
vector<Coord_CTG_Cov> qry = reads_info.LongReadIndexVec[i];
align_maps align_maps;
vector<struct align_info> align_info_vec;
align_info_vec.push_back(align_info);
align2ref(&contigs_info, &reads_info, qry, &align_maps, align_info_vec);
//cout << align_info_vec.size() << endl;
for (int v = 0; v < align_info_vec.size(); ++v)//
{
struct align_info align_info_tmp = align_info_vec[v];
o_align << ">Read_" << i << "_ref_" << v + 1 << "(" << align_info_tmp.ref_idx << ")_score:" << align_info_tmp.max_score << endl;
for (int j = 0; j != align_info_tmp.ref_aligned.size(); ++j)
{
o_align << align_info_tmp.ref_aligned[j] << ", ";
}
o_align << endl;
for (int j = 0; j != align_info_tmp.qry_aligned.size(); ++j)
{
o_align << align_info_tmp.qry_aligned[j] << ", ";
}
o_align << endl;
o_corr_len << align_info_tmp.max_score << endl;
}
if (align_info_vec.size() > 1)
{
bool rc_match = 0;
if (align_info_vec[0].ref_idx == -align_info_vec[1].ref_idx)
{
//if ((align_info_vec[0].max_match_qry < align_info_vec[1].min_match_qry))// || (align_info_vec[1].max_match_qry < align_info_vec[0].min_match_qry))//non overlap match
if ((align_info_vec[0].max_match_ref < align_info_vec[1].min_match_ref))// || (align_info_vec[1].max_match_qry < align_info_vec[0].min_match_qry))//non overlap match
{
map<int, int> local_index_qry;