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align.cpp
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align.cpp
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/*
* align.cpp for FR-HIT
* Copyright (c) 2010-2011 Beifang Niu All Rights Reserved.
*
* 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<algorithm>
#include<cmath>
#include<bitset>
#include<omp.h>
#include "align.h"
using namespace std;
extern bit8_t alphabet[];
extern bit8_t reg_alphabet[];
extern bit8_t rev_alphabet[];
// Reads Ns filtering
extern bit8_t nvfilter[];
extern char rev_char[];
extern char chain_flag[];
extern char nt_code[];
extern char revnt_code[];
// For alignment DP
int BLOSUM62[] =
{
4, // A
-1, 5, // R
-2, 0, 6, // N
-2,-2, 1, 6, // D
0,-3,-3,-3, 9, // C
-1, 1, 0, 0,-3, 5, // Q
-1, 0, 0, 2,-4, 2, 5, // E
0,-2, 0,-1,-3,-2,-2, 6, // G
-2, 0, 1,-1,-3, 0, 0,-2, 8, // H
-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, // I
-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4, // L
-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5, // K
-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, // M
-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6, // F
-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7, // P
1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, // S
0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5, // T
-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, // W
-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7, // Y
0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4, // V
-2,-1, 3, 4,-3, 0, 1,-1, 0,-3,-4, 0,-3,-3,-2, 0,-1,-4,-3,-3, 4, // B
-1, 0, 0, 1,-3, 3, 4,-2, 0,-3,-3, 1,-1,-3,-1, 0,-1,-3,-2,-2, 1, 4, // Z
0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-1,-1,-1 // X
//A R N D C Q E G H I L K M F P S T W Y V B Z X
//0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 2 6 20
};
int na2idx[] = {0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4};
// idx for A B C D E F G H I J K L M N O P
// Q R S T U V W X Y Z
// so aa2idx[ X - 'A'] => idx_of_X, eg aa2idx['A' - 'A'] => 0,
// and aa2idx['M'-'A'] => 4
int BLOSUM62_na[] =
{
1, // A
-2, 1, // C
-2,-2, 1, // G
-2,-2,-2, 1, // T
-2,-2,-2, 1, 1, // U
-2,-2,-2,-2,-2, 1 // N
//A C G T U N
//0 1 2 3 3 4
};
void AA_MATRIX::init()
{
gap = -11;
ext_gap = -1;
for (int i=0; i<MAX_GAP; i++)
{
gap_array[i] = gap + i * ext_gap;
}
int k = 0;
for (int i=0; i<MAX_AA; i++)
{
for ( int j=0; j<=i; j++)
{
matrix[j][i] = matrix[i][j] = BLOSUM62[k++];
}
}
} // END void AA_MATRIX::init()
void AA_MATRIX::set_gap(int gap1, int ext_gap1)
{
gap = gap1;
ext_gap = ext_gap1;
for (int i=0; i<MAX_GAP; i++)
{
gap_array[i] = gap + i * ext_gap;
}
} // END void AA_MATRIX::set_gap
void AA_MATRIX::set_matrix(int *mat1)
{
int k = 0;
for (int i=0; i<MAX_AA; i++)
{
for (int j=0; j<=i; j++)
{
matrix[j][i] = matrix[i][j] = mat1[k++];
}
}
} // END void AA_MATRIX::set_matrix
void AA_MATRIX::set_to_na()
{
gap = -6;
ext_gap = -1;
for (int i=0; i<MAX_GAP; i++)
{
gap_array[i] = gap + i * ext_gap;
}
int k = 0;
for (int i=0; i<MAX_NA; i++)
{
for (int j=0; j<=i; j++)
{
matrix[j][i] = matrix[i][j] = BLOSUM62_na[k++];
}
}
} // END void AA_MATRIX::set_to_na
// Assign memory for DP alignment variables
void WorkingPara::init()
{
for (int i=0; i<_MaxPartLen; i++)
{
score_mat[i] = new int [_MaxPartLen];
iden_mat[i] = new int [_MaxPartLen];
from1_mat[i] = new int [_MaxPartLen];
from2_mat[i] = new int [_MaxPartLen];
alnln_mat[i] = new int [_MaxPartLen];
}
align_len=param.align_len;
best_nas=param.best_nas;
best_kmers=param.best_kmers;
}
void WorkingPara::final()
{
// Release dp variables
for (int i=0; i<_MaxPartLen; i++)
{
delete [] score_mat[i];
delete [] iden_mat[i];
delete [] from1_mat[i];
delete [] from2_mat[i];
delete [] alnln_mat[i];
}
}
// Create seed profile
ReadAlign::ReadAlign()
{
// count aligned reads num
n_aligned = 0;
// cutoff parameters
band_width = param.band;
}
// Entry point for parallel
void ReadAlign::DoBatch(RefSeq &ref, ReadClass &readA, ifstream &finRead, ofstream &fout)
{
_str_align.clear();
bit32_t naligned(0);
vector<ReadInf>::iterator _pread;
WorkingPara wp;
int morereads(1);
int iam=0;
int np=1;
// Parallel entry point
#pragma omp parallel private(_pread, wp)
{
#if defined (_OPENMP)
iam = omp_get_thread_num();
#pragma omp single
if (param.ncpu == 0)
{
param.ncpu=omp_get_num_threads();
}
//cerr<<param.ncpu<<" cpu used"<<endl;
//np = omp_get_num_threads();
#endif
while (morereads)
{
#pragma omp barrier
#pragma omp single
{
morereads = readA.LoadBatchReads(finRead);
ImportBatchReads(readA.num, &readA.mreads);
}
if (morereads)
{
naligned=0;
#pragma omp for schedule(dynamic, 100) reduction(+:naligned)
for (long tt=0; tt<num_reads; tt++)
{
_pread = pmreads->begin() + tt;
// min read filtering
if (_pread->seq.size() >= param.min_read_size)
{
//-g=1 (global), using new filtering cutoff
if (param.global_signal == 1)
{
//wp.align_len = (_pread->length*param.global_part)/100;//nbps
wp.align_len = _pread->length;
wp.best_nas = (wp.align_len*param.identity)/100;
wp.best_kmers = wp.align_len - (wp.align_len-wp.best_nas)*4 - 3;//4-mers
}
//Ns filtering
if (ConvertBinaySeq(_pread, wp) == 0)
{
GenerateSeeds(_pread->length, wp);
if (AlignProcess(ref, _pread, str_align[iam], wp)) naligned++;
}
}
}
#pragma omp single
{
for (int i=0; i<param.ncpu; i++)
{
fout<<str_align[i]; //result write
str_align[i].clear();
}
cerr << readA._index << " reads finished. " << Cal_AllTime() << " secs passed" << endl;
n_aligned += naligned;
}
} //end of if
} //end of while
} //end of parallel part
}
// Convert string seq to binary type
int ReadAlign::ConvertBinaySeq(vector<ReadInf>::iterator &_pread, WorkingPara &wp)
{
int i,j,h,g;
int nxs =0;
bit24_t _a;
string::iterator _sp;
string::reverse_iterator _sq;
// Direct chain
h = _a.a = 0;
for (_sp = _pread->seq.begin(), i = 1; _sp!=_pread->seq.end(); _sp++, i++)
{
_a.a<<=2;
_a.a|=alphabet[*_sp];
// Assign iseq value
wp.iseqquery[i-1] = alphabet[*_sp];
nxs += nvfilter[*_sp];
if (0 == i%12)
{
wp.bseq[h] = _a;
#ifdef DEBUG
cerr<<" h "<<h<<endl;
bitset <24> bs((long)wp.bseq[h].a);
cerr<<" " <<bs<<endl;
bs.reset();
#endif
h++;
_a.a = 0;
}
}
if (nxs >= wp.best_nas) return 1;
if (_pread->length%12)
{
_a.a<<=24-(_pread->length%12)*2;
wp.bseq[h]=_a;
}
// Reverse seq
h = _a.a = 0;
for (_sq=_pread->seq.rbegin(), i=1; _sq != _pread->seq.rend(); _sq++, i++)
{
_a.a<<=2;
_a.a|=rev_alphabet[*_sq];
// Assign ciseq value (reverse strain)
wp.ciseqquery[i-1]=rev_alphabet[*_sq];
if (0 == i%12)
{
wp.cbseq[h] = _a;
h++;
_a.a=0;
}
}
if (_pread->length%12)
{
_a.a<<=24-(_pread->length%12)*2;
wp.cbseq[h] = _a;
}
// test iseq and ciseq (only debug)
#ifdef DEBUG
cerr << endl;
for (i=0; i<_pread->length; i++)
{
cerr << int(iseqquery[i]);
}
cerr << endl;
#endif
return 0;
}
// Get seeds of reads one base one seed
void ReadAlign::GenerateSeeds(int _read_length, WorkingPara &wp)
{
int j(_read_length - param.seed_size + 1);
for (int i=0; i<j; i++)
{
int b = (i%12 + param.seed_size)*2; //some kind of end position
wp.seeds[i] = b<=24? ( wp.bseq[i/12].a>>(24-b))¶m.seed_bits : (wp.bseq[i/12].a<<(b-24)| wp.bseq[i/12+1].a>>48-b)¶m.seed_bits;
wp.cseeds[i] = b<=24? (wp.cbseq[i/12].a>>(24-b))¶m.seed_bits : (wp.cbseq[i/12].a<<(b-24)|wp.cbseq[i/12+1].a>>48-b)¶m.seed_bits;
#ifdef DEBUG
bitset <26> bs2((long)cseeds[i]);
cerr << " " << bs2 << endl;
bs2.reset();
#endif
}
}
// OOP redo
void ReadAlign::AhitCollect(int _read_length, int seedstep, RefSeq &ref, bit32_t *seeds, vector<bit64_t> &Ahit)
{
int temp_loc;
bit32_t m,j,seed;
bit64_t Ta_hit;
ref_id_t *_refid;
ref_loc_t *_refloc;
Hit _hit;
// Seed num of read
bit32_t snum(_read_length - param.seed_size + 1);
for(int i=0; i<snum; i+=seedstep)
{
seed = seeds[i]; // bit32_t
if ((m=ref.index[seed].n) == 0) continue; //no match
// List of seeded reference locations
_refid = ref.index[seed].id;
_refloc = ref.index[seed].loc;
for (j=0; j!= m; j++)
{
// Seed location
_hit.chr = _refid[j];
// Start position of possible alignment to read
temp_loc = _refloc[j] - i;
// Beyond the boundary( ref: 0)
_hit.loc = temp_loc >= 0 ? temp_loc : 0;
// Load refid and location in one 64 bit
Ta_hit = ((bit64_t)_refid[j]<<32)|_hit.loc;
Ahit.push_back(Ta_hit);
}
}
}
// OOP redo
void ReadAlign::HitcansCollect(bit64_t tcc, RefSeq &ref, int _read_length, WorkingPara &wp)
{
int t_loc;
bit32_t ccflag;
bit64_t tcc0;
ref_loc_t ttloc;
Hit_Can Hitcan; //alignment hit sample
ccflag = 0;
for (bit32_t d = 1; d< wp.Ahit.size(); d++)
{
// vary in seed_size length scope
if ((wp.Ahit[d] - tcc) <= param.seed_size)
{
if (ccflag == 0)
{ //get id and loc
Hitcan.chr = tcc>>32;
tcc0 = tcc<<32;
ttloc = tcc0>>32;
t_loc = ttloc - param.seed_size;
// get alignment location info
Hitcan._begin = t_loc > 0 ? t_loc : 0;
// alignlength = read length add 2 folds seedsize
Hitcan._end = ttloc + _read_length + 2*param.seed_size;
if (Hitcan._end > (ref.title[Hitcan.chr].size-1)) Hitcan._end = ref.title[Hitcan.chr].size;
wp._hit_Cans.push_back(Hitcan);
ccflag = 1;
}
}
else
{
tcc = wp.Ahit[d];
ccflag = 0;
}
}
}
// Merge adjoining blocks
void ReadAlign::MergeAdjoiningBlock(WorkingPara &wp)
{
int d;
Hit_Can Hitcan;
// Alignment candidates filtering
if (wp._hit_Cans.size() > 1)
{
Hitcan = wp._hit_Cans[0];
for (d=1; d< wp._hit_Cans.size(); d++)
{
if ((wp._hit_Cans[d].chr!=Hitcan.chr) || (int(Hitcan._end-wp._hit_Cans[d]._begin) < 0))
{
//not same chr, or are apart
wp.perfect_hit.push_back(Hitcan);
Hitcan = wp._hit_Cans[d];
}
else
{
//if overlap, merge to extend it
//ref part length limit MAX_READ
//maybe lost some alignment but it is enough
if ((Hitcan._end - Hitcan._begin) < MAX_READ) Hitcan._end = wp._hit_Cans[d]._end;
}
}
wp.perfect_hit.push_back(Hitcan);
}
else if (wp._hit_Cans.size() == 1)
{
//only one hit
wp.perfect_hit.push_back(wp._hit_Cans[0]);
}
}
// 4-mers checking
void ReadAlign::CreateFourmers(char *iseqquery, int _read_length, WorkingPara &wp)
{
int j, sk, mm,c22;
int lencc = _read_length - 3;
// Get 4-mers value of query
for (sk=0; sk<NAA4; sk++)
{
wp.taap[sk] = 0;
}
for (j=0; j<lencc; j++)
{
c22 = iseqquery[j]*NAA3 + iseqquery[j+1]*NAA2 + iseqquery[j+2]*NAA1 + iseqquery[j+3];
wp.taap[c22]++;
}
// Make index
for (sk=0,mm=0; sk<NAA4; sk++)
{
wp.aap_begin[sk] = mm;
mm += wp.taap[sk];
wp.taap[sk] = 0;
}
for (j=0; j<lencc; j++)
{
c22 = iseqquery[j]*NAA3 + iseqquery[j+1]*NAA2 + iseqquery[j+2]*NAA1 + iseqquery[j+3];
wp.aap_list[wp.aap_begin[c22]+wp.taap[c22]++] = j;
}
}
// Main filtering and alignment part
int ReadAlign::AlignProcess(RefSeq &ref, vector<ReadInf>::iterator &_pread, string &os, WorkingPara &wp)
{
// e-value
int eHSP = expectedHSPlength(mink,_pread->length,ref.sum_length,Hh);
// expect HSP length for e-value computing
int eLengthSeq = effectiveLengthSeq(_pread->length,eHSP,mink);
bit64_t eLengthDB = effectiveLengthDb(ref.sum_length,eHSP,ref.total_num,mink);
double eValue;
double read_identity_d;
int trys;
int seedstep;
int repreports;
int len;
int len1;
int best_sum;
int RefBegin;
int RefEnd;
int alnln;
int tiden_no;
int read_cov;
int read_identity;
int talign_info[5];
// Alignment and filtering
int band_left;
int band_right;
int _RecruitedSignal(0);
int best_score;
Hit_Can Hitcan;
bit24_t *_m;
bit32_t i,j,d,b;
bit64_t tcc;
OutputSort Outputunit;
// Output sorting
vector<OutputSort> Outputlist;
// Get part of ref seq for alignment
char seqjseg[_MaxPartLen];
// Result output container
char _ch[1000];
MerSort Gramunit;
vector< MerSort > Gramsort; //qgrams sorting
seedstep = 1;//speedup using step q-gram of query read
if (_pread->length >= param.lenforstep) seedstep = 2;
// Alignment and 4 mers counting
len = _pread->length;
// 0:both; 1:direct only; 2:complementary only. default=0 direct chain
if ((0 == param.chains) ||(1 == param.chains))
{
AhitCollect(_pread->length, seedstep, ref, wp.seeds, wp.Ahit);
// get alignment candidates
if (wp.Ahit.size() > 1)
{
sort(wp.Ahit.begin(),wp.Ahit.end());
tcc = wp.Ahit[0];
HitcansCollect(tcc, ref, _pread->length, wp);
}
wp.Ahit.resize(0); // Release memory
MergeAdjoiningBlock(wp); // Merge adjoining blocks
wp._hit_Cans.resize(0);
// get 4-mers value of query
CreateFourmers(wp.iseqquery, _pread->length, wp);
// for 4-kmers count filtering and alignment
for (d = 0; d< wp.perfect_hit.size(); d++)
{
Hitcan = wp.perfect_hit[d];
RefEnd = Hitcan._end;
RefBegin = Hitcan._begin;
// candidate alignment length
len1 = RefEnd - RefBegin;
_m = ref.bfa[Hitcan.chr].s;
// get iseq of ref
j = 0;
for (i=RefBegin; i<RefEnd; i++)
{
b = (i%12 + 1)*2;
// seed_bits = 3
seqjseg[j] = b<=24 ? (_m[i/12].a>>(24-b))&3 : (_m[i/12].a<<(b-24)|_m[i/12+1].a>>48-b)&3;
j++;
}
// debug only
#ifdef DEBUG
cerr << "len1 " << len1 << " RefBegin " << RefBegin << " RefEnd " << RefEnd << endl;
#endif
diag_test_aapn_est_circular(seqjseg, len, len1, best_sum, band_left, band_right, wp);
#ifdef DEBUG
cerr << "band_left " << band_left << " band_right " << band_right << endl;
#endif
if (best_sum < wp.best_kmers) continue;
Gramunit.chr = Hitcan.chr;
Gramunit._begin = RefBegin;
Gramunit._end = RefEnd;
Gramunit.qgrams = best_sum;
// location of alignment begin
Gramunit.bandleft = band_left;
//location of alignment end
Gramunit.bandright = band_right;
Gramsort.push_back(Gramunit);
}
// release candidate hits vector memory
wp.perfect_hit.resize(0);
sort(Gramsort.begin(),Gramsort.end());
trys = 0;//try DPs
repreports = 0;//repeats reported
//for dp alignment
for (d = 0; d< Gramsort.size(); d++)
{
Gramunit = Gramsort[d];
RefEnd = Gramunit._end;
RefBegin = Gramunit._begin;
//candidate alignment length
len1 = RefEnd - RefBegin;
_m = ref.bfa[Gramunit.chr].s;
//get iseq of ref
j = 0;
for (i=RefBegin; i<RefEnd; i++)
{
b = (i%12 + 1)*2;
seqjseg[j] = b<=24? (_m[i/12].a>>(24-b))&3 : (_m[i/12].a<<(b-24)|_m[i/12+1].a>>48-b)&3;
j++;
}
// band alignment function
local_band_align2(wp.iseqquery, seqjseg, len, len1, best_score, Gramunit.bandleft, Gramunit.bandright, talign_info, tiden_no, alnln, wp);
read_cov = abs(talign_info[2] - talign_info[1]) + 1;
if (param.global_signal == 1)
{
read_identity = (tiden_no * 100)/_pread->length;
read_identity_d = (double)(tiden_no * 100)/_pread->length;
}
else
{
if (read_cov < wp.align_len)
{
trys++;
if (trys>param.maxtrys) break;
continue;
}
read_identity = (tiden_no * 100)/alnln;
read_identity_d = (double)(tiden_no * 100)/alnln;
}
if (read_identity < param.identity)
{
trys++;
if (trys > param.maxtrys) break;
continue;
}
// get e-value
eValue = rawScoreToExpect(best_score, mink, lamda, eLengthSeq, eLengthDB);
if (eValue > param.evalue)
{
continue;
}
trys = 0;
_RecruitedSignal = 1;
// be recruited
repreports++;
// write alignment output to fout
if (param.report_repeat_hits == 0)
{
if (param.outputformat == 1)
{
//1:PSL fromat
sprintf(_ch, "%d\t%d\t0\t0\t0\t0\t0\t0\t+\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t1\t%d,\t%d,\t%d,\n",
tiden_no, read_cov-tiden_no, _pread->name.c_str(), _pread->length, talign_info[1],\
talign_info[2]+1, ref.title[Gramunit.chr].name.c_str(), ref.title[Gramunit.chr].size,\
RefBegin+talign_info[3], RefBegin+talign_info[4]+1, read_cov,talign_info[1],\
RefBegin+talign_info[3]);
}
else
{
//0:FR-HIT format
sprintf(_ch, "%s\t%dnt\t%.1e\t%d\t%d\t%d\t+\t%0.2f%\t%s\t%d\t%d\n",
_pread->name.c_str(), _pread->length, eValue,read_cov,talign_info[1]+1,\
talign_info[2]+1, read_identity_d, ref.title[Gramunit.chr].name.c_str(), \
RefBegin+talign_info[3]+1, RefBegin+talign_info[4]+1);
}
#pragma omp critical
os.append(_ch);
}
else
{
// for repeats report
if (repreports > param.report_repeat_hits) break;
else
{
Outputunit.eva=eValue;
if (param.outputformat == 1)
{
sprintf(Outputunit.och, "%d\t%d\t0\t0\t0\t0\t0\t0\t+\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t1\t%d,\t%d,\t%d,\n",
tiden_no,read_cov-tiden_no,_pread->name.c_str(),_pread->length,talign_info[1],talign_info[2]+1,\
ref.title[Gramunit.chr].name.c_str(), ref.title[Gramunit.chr].size,RefBegin+talign_info[3],\
RefBegin+talign_info[4]+1, read_cov, talign_info[1], RefBegin+talign_info[3]);
}
else
{
sprintf(Outputunit.och, "%s\t%dnt\t%.1e\t%d\t%d\t%d\t+\t%0.2f%\t%s\t%d\t%d\n", \
_pread->name.c_str(),_pread->length,eValue,read_cov,talign_info[1]+1,talign_info[2]+1,\
read_identity_d,ref.title[Gramunit.chr].name.c_str(),RefBegin+talign_info[3]+1,\
RefBegin+talign_info[4]+1);
}
Outputlist.push_back(Outputunit);
}
}
}// end dp alignment
Gramsort.resize(0);
}
// Random recruited finished
//if ((param.report_repeat_hits == 0)&&(_RecruitedSignal == 1)) return 1;
//complementary chain | done
if ((0 == param.chains) || (2 == param.chains))
{
AhitCollect(_pread->length, seedstep, ref, wp.cseeds, wp.Ahit);
// get alignment candidates
if (wp.Ahit.size() > 1)
{
sort(wp.Ahit.begin(),wp.Ahit.end());//sort Ahit
tcc = wp.Ahit[0];
HitcansCollect(tcc, ref, _pread->length, wp);
}// end get alignment candidates
wp.Ahit.resize(0);//release initial seeds hits vector memory
MergeAdjoiningBlock(wp);// Merge adjoining blocks
wp._hit_Cans.resize(0);
// Get 4-mers value of query
CreateFourmers(wp.ciseqquery, _pread->length, wp);
// analysis hits for 4-kmers count filter and alignment
for (d = 0; d< wp.perfect_hit.size(); d++)
{
Hitcan = wp.perfect_hit[d];
RefEnd = Hitcan._end;
RefBegin = Hitcan._begin;
len1 = RefEnd - RefBegin; // candidate alignment length
_m = ref.bfa[Hitcan.chr].s; // get reference
// get iseq of ref
j = 0;
for (i=RefBegin; i<RefEnd; i++)
{
b = (i%12 + 1)*2;
//seed_bits
seqjseg[j] = b<=24? (_m[i/12].a>>(24-b))&3 : (_m[i/12].a<<(b-24)|_m[i/12+1].a>>48-b)&3;
j++;
}
diag_test_aapn_est_circular(seqjseg, len, len1, best_sum, band_left, band_right, wp);
// filtering using 4-mers
if (best_sum < wp.best_kmers) continue;
Gramunit.chr = Hitcan.chr;
Gramunit._begin = RefBegin;
Gramunit._end = RefEnd;
Gramunit.qgrams = best_sum;
// location of alignment begin
Gramunit.bandleft = band_left;
// location of alignment end
Gramunit.bandright = band_right;
Gramsort.push_back(Gramunit);
}
wp.perfect_hit.resize(0);
sort(Gramsort.begin(),Gramsort.end());
trys = 0; //try DPs
repreports = 0; //repeats reported
//for dp alignment
for (d = 0; d< Gramsort.size(); d++)
{
Gramunit = Gramsort[d];
RefEnd = Gramunit._end;
RefBegin = Gramunit._begin;
// candidate alignment length
len1 = RefEnd - RefBegin;
_m = ref.bfa[Gramunit.chr].s;
// get iseq of ref
j = 0;
for (i=RefBegin; i<RefEnd; i++)
{
b = (i%12 + 1)*2;
//seed_bits
seqjseg[j] = b<=24? (_m[i/12].a>>(24-b))& 3: (_m[i/12].a<<(b-24)|_m[i/12+1].a>>48-b)&3;
j++;
}
// band DP alignment
local_band_align2(wp.ciseqquery,seqjseg,len,len1,best_score,Gramunit.bandleft,Gramunit.bandright,talign_info,tiden_no,alnln,wp);
// the alignment length of read
read_cov = abs(talign_info[2] - talign_info[1]) + 1;
if (param.global_signal == 1)
{
read_identity = (tiden_no * 100)/_pread->length;
read_identity_d = (double)(tiden_no * 100)/_pread->length;
}
else
{
if (read_cov < wp.align_len)
{
trys++;
if (trys>param.maxtrys) break;
continue;
}
read_identity = (tiden_no * 100)/alnln;
read_identity_d = (double)(tiden_no * 100)/alnln;
}
if (read_identity < param.identity)
{
trys++;
if (trys>param.maxtrys) break;
continue;
}
// get evalue
eValue = rawScoreToExpect(best_score,mink,lamda,eLengthSeq,eLengthDB);
if (eValue > param.evalue) continue;
trys = 0;
// be recruited
_RecruitedSignal = 1;
repreports++;
// write alignment output to fout
if (param.report_repeat_hits == 0)
{
if (param.outputformat == 1)
{
//1:PSL fromat
sprintf(_ch, "%d\t%d\t0\t0\t0\t0\t0\t0\t-\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t1\t%d,\t%d,\t%d,\n",
tiden_no,read_cov-tiden_no,_pread->name.c_str(),_pread->length,_pread->length-talign_info[2]-1,\
_pread->length-talign_info[1],ref.title[Gramunit.chr].name.c_str(),ref.title[Gramunit.chr].size,\
RefBegin+talign_info[3],RefBegin+talign_info[4]+1,read_cov,talign_info[1],\
RefBegin+talign_info[3]);
}
else
{
//0:FR-HIT format
sprintf(_ch, "%s\t%dnt\t%.1e\t%d\t%d\t%d\t-\t%0.2f%\t%s\t%d\t%d\n", _pread->name.c_str(),\
_pread->length,eValue,read_cov,_pread->length-talign_info[1],_pread->length-talign_info[2],\
read_identity_d, ref.title[Gramunit.chr].name.c_str(),RefBegin+talign_info[3]+1,\
RefBegin+talign_info[4]+1);
}
#pragma omp critical
os.append(_ch);
}
else
{
// for repeats report, only random one
if (repreports > param.report_repeat_hits) break;
else
{
Outputunit.eva=eValue;
if (param.outputformat == 1)
{
sprintf(Outputunit.och, "%d\t%d\t0\t0\t0\t0\t0\t0\t-\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t1\t%d,\t%d,\t%d,\n",
tiden_no,read_cov-tiden_no,_pread->name.c_str(),_pread->length, _pread->length-talign_info[2]-1,\
_pread->length-talign_info[1],ref.title[Gramunit.chr].name.c_str(),ref.title[Gramunit.chr].size,\
RefBegin+talign_info[3],RefBegin+talign_info[4]+1,read_cov,talign_info[1],RefBegin+talign_info[3]);
}
else
{
sprintf(Outputunit.och, "%s\t%dnt\t%.1e\t%d\t%d\t%d\t-\t%0.2f%\t%s\t%d\t%d\n", _pread->name.c_str(),\
_pread->length,eValue,read_cov,_pread->length-talign_info[1],_pread->length-talign_info[2],\
read_identity_d,ref.title[Gramunit.chr].name.c_str(),RefBegin+talign_info[3]+1,\
RefBegin+talign_info[4]+1);
}
Outputlist.push_back(Outputunit);
}
} //end if
} // end 4-mers filtering and alignment
Gramsort.resize(0);//release candidate hits vector memory
} //end complementary chain processing
//output N best top hits
if (param.report_repeat_hits != 0)
if (Outputlist.size()>0)
{
sort(Outputlist.begin(),Outputlist.end());
j = Outputlist.size();
if (j>param.report_repeat_hits) j = param.report_repeat_hits;
#pragma omp critical
{
for (i=0; i<j; i++)
os.append(Outputlist[i].och);
}
Outputlist.resize(0);
}
return _RecruitedSignal;
}
//filtering HSP fasta//len1:reads length, len2:ref seq segment len, iseq2:ref seq segment binary
int ReadAlign::diag_test_aapn_est_circular(char iseq2[],int len1,int len2, int &best_sum,int &band_left, int &band_right,WorkingPara &wp)
{
int i, j, k;
int nall = len1 + len2 - 1;
int *pp = wp.diag_score;
for (i=nall; i; i--) *pp++=0;
int len22 = len2 - 3;
int i1 = len1 - 1;
for (i=0; i<len22; i++, i1++, iseq2++)
{
int c22 = iseq2[0]*NAA3 + iseq2[1]*NAA2 + iseq2[2]*NAA1 + iseq2[3];
if ((j = wp.taap[c22]) == 0) continue;
pp = wp.aap_list+ wp.aap_begin[c22];
for (; j; j--, pp++)
{
wp.diag_score[i1 - *pp]++;
}
}
// find the best band range
int required_aa1 = wp.best_nas;
int band_b = required_aa1 >= 1 ? required_aa1-1:0;
int band_e = nall - required_aa1;