void align_reads(vector<pair<string, string> >& reference, string& read_file, string& sam_file, vector<reference_index>& refindex)
{
time_t tstrt, tbgn, tnd;
time(&tstrt);
/*//Can be used for analyzing the difference between LAST and NanoBLASTer
ifstream fp_nano;
string nano_input;
string nano_file = "last_but_not_nano.txt";
char *nano = new char[nano_file.length() + 1];
strcpy(nano, nano_file.c_str());
fp_nano.open(nano, ifstream::in);
unordered_map<string, int> nano_read;
while(getline(fp_nano, nano_input))
{
//cout << "" << nano_input << endl;
nano_read[nano_input] = 1;
//continue;
}
cout << "Total Size of Nano Read = " << nano_read.size() << endl << endl;
fp_nano.close();
delete [] nano;
*/
ifstream fp_read;
ofstream fp_sam;
char *read = new char[read_file.length() + 1];
strcpy(read, read_file.c_str());
char *sam = new char[sam_file.length() + 1];
strcpy(sam, sam_file.c_str());
fp_read.open(read, ifstream::in);
fp_sam.open(sam, ofstream::out | ofstream::app);
string input, read_name, ref_name;
string readseq, refgenome;
string slash = "/";
int map = 0;
int count = 0;
int cant_map = 0;
int invalid_count = 0;
fp_csv << "cnt, red_nam, red_len, red_dir, ref_nam, ref_len, ref_pos, score, span, " <<
"percent, aln_len, spn_rat, aln_tim, tot_tim" << endl;
getline(fp_read, input);
while(!fp_read.eof())
{
//int find = input.find(slash);
//if(find != string::npos)
// read_name = input.substr(1, find - 1);
//else
// read_name = input.substr(1);
read_name = input.substr(1);
readseq = "";
while(getline(fp_read, input))
{
if(input.length() == 0)
continue;
if(input.at(0) == '>')
break;
readseq += input;
}
//getline(fp_read, input);
//getline(fp_read, input);
//ratio problem with channel_46_read_98_1406145606_2D
//if(read_name.find("channel_407_read_0_1405093831_2D") == std::string::npos)//to optimize the output
//if(read_name.find("channel_17_read_24_1405524767_2D") == std::string::npos)//small read to optimize
//if(read_name.find("channel_201_read_10_1405541481_2D") == std::string::npos)//to compare version 1 and 2
//if(read_name.find("channel_64_read_7_1403826200_template") == std::string::npos)//max length reads analysis
//if(read_name.find("channel_424_read_1_1403566249_template") == std::string::npos)//found in last but not in nano
//if(read_name.find("2D") == std::string::npos)//03-09-2015
//if(read_name.find("channel_237_read_42_1406145606_2D") == std::string::npos)
//if(read_name.find("channel_322_read_11_1405524767_template") == std::string::npos)
//if(read_name.find("channel_171_read_2_1403855963_2D") == std::string::npos)//20 times higher than last
//if(read_name.find("channel_82_read_0_1403855963_2D") == std::string::npos)//20 times higher than last
//if(read_name.find("channel_221_read_19_1406145606_2D") == std::string::npos)//has maximul length of deletion
//if(read_name.find("channel_415_read_6_1406242409_template") == std::string::npos)//has 5 times less length than last
//if(read_name.find("channel_167_read_19_1403811400_2D") == std::string::npos)//analyze output validity
//if(read_name.find("channel_474_read_32_1405524767_template") == std::string::npos)//found in last and nano repeat
//if(read_name.find("channel_468_read_12_1403811400_complement") == std::string::npos)//cause exception in nano repeat
//if(read_name.find("channel_345_read_7_1403811400_2D") == std::string::npos)//max length increased
//if(read_name.find("channel_104_read_1_1403551548_template") == std::string::npos)//different in edit not lis
//if(read_name.find("channel_216_read_0_1403551548_template") == std::string::npos)//different in lis not edit
//if(read_name.find("channel_118_read_6_1403551548_template") == std::string::npos)//different in lis and edit
//if(read_name.find("channel_486_read_0_1403566249_template") == std::string::npos)//reverse problem
//if(nano_read.find(read_name) == nano_read.end())
//if(read_name.find("channel_352_read_34_1405541481_template") == std::string::npos)//Why there are multiple results
//if(read_name.find("channel_68_read_22_1405541481_template") == std::string::npos)//multiple results, boundary problem
//if(read_name.find("channel_261_read_39_1405541481_template") == std::string::npos)//multiple result indexing
//if(read_name.find("channel_302_read_2_1403855963_2D") == std::string::npos)//found in mms not in ssg = align length
//if(read_name.find("channel_243_read_0_1403595798_template") == std::string::npos)//found in 40655 not in lis+edit
//if(read_name.find("channel_452_read_46_1405541481_template") == std::string::npos)//same problem as above
//if(read_name.find("channel_431_read_2_1403915857_template") == std::string::npos)//require top 40 tuple list to solve
//readseq = readseq.substr(readseq.length() / 2, readseq.length() - readseq.length() / 2);
//if(read_name.find("channel_199_read_0_1403841073_template") == std::string::npos)//solved
//if(read_name.find("channel_480_read_91_1406242409_template") == std::string::npos)//in last and not in nano
//if(read_name.find("channel_389_read_57_1406242409_template") == std::string::npos)//solved
//if(read_name.find("channel_56_read_1_1403826200_template") == std::string::npos)
//if(read_name.find("channel_356_read_29_1406242409_template") == std::string::npos)// < 40 in nano very weird
//if(read_name.find("channel_131_read_5_1403826200_template") == string::npos)// < 100 in nano seems weird
//if(read_name.find("channel_75_read_80_1406145606_template") == std::string::npos)//80% last not found now solved
// continue;
if(count >= MAXREAD && MAXREAD != 0) break;
count += 1;
//if(count < 11762) continue;
cout << count << ") " << read_name << endl;
if(readseq.length() < MINREADLEN || readseq.length() > MAXREADLEN)//03-09-2015
{
cout << "Invalid String Found" << endl;
invalid_count += 1;
count -= 1;
fp_sam << read_name << "\t4\t*\t0\t0\t*\t*\t0\t0\t" << readseq << "\t*" << endl;
time(&tnd);
//fp_csv << count << ", " << readseq.length() << ", 0, 0, 0, " <<
// "0, 0, 0, 0, 0, 0, 0, " << difftime(tnd, tstrt) << endl;
continue;
}
if(count <= MINREAD) continue;
//if(count < 318) continue;
time(&tbgn);
if(DEBUG == 99)
fp_csv << count << ", " << read_name << ", " << readseq.length() << ", ";
upper_case(readseq);
//reverse_str(readseq);
//readseq = reverse_complement(readseq);
int match_info, global_match = -1, indpos;
int match, max_match = 0, match_index, dir;
vector<vector<string> > list_final_result;
//time_t start, end;
//clock_t t_start, t_end;
//for(int i = 0; i < reference.size(); i++)
{
//vector<pair<int, pair<int, int> > > kmer_ref;
vector<pair<int, vector<pair<int, int> > > > kmer_ref;
//cout << "Analysis for forward:" << endl;
//
//time(&start);
//t_start = clock();
read_vs_reference(readseq, read_name, FF, refindex, kmer_ref);
//t_end = clock();
//time(&end);
//cout << "Total time taken for calling forward read_vs_ref = " << difftime(end, start) << endl;
//t_lookup += t_end - t_start;
//align(readseq, read_name, FF, refindex, kmer_ref, final_result);
//cout << "Data for reverse:" << endl;
//time(&start);
//t_start = clock();
if(SINGLE == 1)
{
string reverse = reverse_complement(readseq);
read_vs_reference(reverse, read_name, FR, refindex, kmer_ref);
}
//t_end = clock();
//time(&end);
//cout << "Total time taken for calling reverse read_vs_ref = " << difftime(end, start) << endl;
//t_lookup += t_end - t_start;
//cout << endl <<endl;
//uncomment here for aligninng read
list_final_result.clear();
align(readseq, read_name, FR, refindex, kmer_ref, list_final_result);
if(list_final_result.size() == 0)
{
cant_map += 1;
kmer_ref.clear();
//time(&tnd);
//fp_csv << difftime(tnd, tbgn) << ", " << difftime(tnd, tstrt) << endl;
fp_sam << read_name << "\t4\t*\t0\t0\t*\t*\t0\t0\t" << readseq << "\t*" << endl;
continue;
}
kmer_ref.clear();
}
for(int i = 0; i < list_final_result.size(); i++)
{
vector<string>& final_result = list_final_result[i];
fp_sam << final_result[0];
for(int k = 1; k < final_result.size(); k++)
{
fp_sam << "\t" << final_result[k];
//cout << i << ": " << output[k] << endl;
}
fp_sam << endl;
map += 1;
final_result.clear();
}
/*
if(list_final_result.size() == 0 && SAM_FORMAT == 1)
{
fp_sam << read_name << "\t4\t*\t0\t0\t*\t*\t0\t0\t" << readseq << "\t*" << endl;
}
*/
//time(&tnd);
list_final_result.clear();
if(DEBUG == 99)
fp_csv << endl;//difftime(tnd, tbgn) << ", " << difftime(tnd, tstrt) << endl;
//cout << "\nTime taken to process " << count << "th read = " << difftime(tnd, tstrt) << "\n" << endl;
//break;
}
cout << endl;
cout << "Overall Statistics - " << endl;
cout << "total reference size = " << reference.size() << endl << endl;
cout << "Total read = " << count << endl << endl;
cout << "Total read mapped = " << map << endl << endl;
cout << "Total unmapped read = " << cant_map << endl << endl;
cout << "Out of range read (< 100 or > 15000) = " << invalid_count << endl << endl;
//cout << "Total MAX_MATCHED (= " << MAX_MATCHED << ") Reads = " << MAX_SCORED << endl << endl;
fp_read.close();
fp_sam.close();
delete [] read;
delete [] sam;
}
// kmer rank
REQUIRE( kmer_rank("AAAAA", 5) == 0 );
REQUIRE( kmer_rank("GATGA", 5) == 568 );
REQUIRE( kmer_rank("TTTTT", 5) == 1023 );
REQUIRE( kmer_rank("GATGA", 5) == rc_kmer_rank("TCATC", 5 ) );
// lexicographic increment
std::string str = "AAAAA";
lexicographic_next(str);
REQUIRE( str == "AAAAC" );
str = "AAAAT";
lexicographic_next(str);
REQUIRE( str == "AAACA" );
// complement, reverse complement
REQUIRE( complement('A') == 'T' );
REQUIRE( reverse_complement("GATGA") == "TCATC" );
}
TEST_CASE( "math", "[math]") {
GaussianParameters params;
params.mean = 4;
params.stdv = 2;
params.log_stdv = log(params.stdv);
REQUIRE( normal_pdf(2.25, params) == Approx(0.1360275) );
REQUIRE( log_normal_pdf(2.25, params) == Approx(log(normal_pdf(2.25, params))) );
}
