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alu_insert.cpp
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alu_insert.cpp
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#define SEQAN_HAS_ZLIB 1
#include "insert_utils.h"
ParametersAluInsert p_alu;
struct REALIGNS
{
int rid, pos_key, aBegin, aEnd;
string qName;
};
void alu_mate_flag( BamFileHandler * bam_fh, string fn_output, string &header, map <string, int> & rg_to_idx, map <int, EmpiricalPdf *> pdf_rg)
{
ofstream fout (fn_output.c_str() );
fout << header ;
seqan::BamAlignmentRecord record;
while ( bam_fh -> fetch_a_read(record) )
{
if ( ! QC_insert_read(record) ) continue;
// not allow pair to be mapped to decoy
if ( ! key_exists(bam_fh->rID_chrn, record.rID) or ! key_exists(bam_fh->rID_chrn, record.rNextId) )
continue;
int rgIdx = get_rgIdx(rg_to_idx, record); // if not exists, return 0
if ( pdf_rg[rgIdx]->RG_mate_pair )
continue;
int len_seq = length(record.seq);
// bp that is not 'M', this may cause bias ==> fewer short insert_len reads are counted
if ( count_non_match(record) >= CLIP_BP or len_seq < 60 ) continue;
if ( record.rID < record.rNextId or
( record.rID == record.rNextId and record.beginPos < record.pNext
and abs(record.tLen) > DISCORDANT_LEN + pdf_rg[rgIdx]->max_len ) )
fout << record.qName << " " << record.rID << " " << record.rNextId << " " << record.beginPos << " "
<< record.pNext << " " << hasFlagRC(record) << " " << hasFlagNextRC(record) << " " << len_seq
<< " " << rgIdx << endl;
}
fout.close();
}
int get_type_cnts(map <int, set <string> > & type_cnts, int key)
{
if ( type_cnts.find(key) == type_cnts.end()) return 0;
return type_cnts[key].size();
}
void parse_line1(string &line, int pos, int offset, vector <int> & clipls, vector <int> & cliprs)
{
stringstream ss;
ss.str(line);
string pn, tmpv;
int clipLen, p;
ss >> pn >> clipLen >> p;
if ( abs( p - pos) <= offset )
{
if (clipLen < 0 ) clipls.push_back(p);
else cliprs.push_back(p);
}
}
int parse_line3( string &line, int & pos)
{
int lr_num, rr_num;
stringstream ss;
ss.str(line);
ss >> pos >> lr_num >> rr_num;
return lr_num + rr_num;
}
void get_scan_pos(string fn, list <int> & pos_to_scan, int combine_bp)
{
pos_to_scan.clear();
stringstream ss;
string line, qname;
int this_rID, this_pos, len_read, previous_end;
bool this_isRC;
ifstream fin( fn.c_str());
assert(fin); // init, 700 * 30 /100 = 210
getline(fin, line);
while (pos_to_scan.empty())
{
getline(fin, line);
ss.clear(); ss.str(line);
ss >> qname >> this_rID >> this_pos >> this_isRC >> len_read;
if ( this_pos > ::p_alu.scan_win_len ) pos_to_scan.push_back(this_pos);
}
while (getline(fin, line))
{
previous_end = this_pos + len_read;
ss.clear(); ss.str(line);
ss >> qname >> this_rID >> this_pos >> this_isRC >> len_read;
if (this_pos - previous_end > 3 * combine_bp) pos_to_scan.push_back(previous_end + combine_bp);
if (this_pos - pos_to_scan.back() > 2 * combine_bp) pos_to_scan.push_back(this_pos - combine_bp);
}
}
// need smarter way to combine positions ==> minimum number of regions to cover all reads info
void join_location(string file1, string file2, int pos_dif, int max_region_len)
{
ifstream fin( file1.c_str());
assert(fin);
string line;
getline(fin, line); // skip header
getline(fin, line);
int pos, pos_pre;
int nowCount = parse_line3(line, pos_pre);
//cout << "nowC " << nowCount << endl;
int maxCount = nowCount;
vector<int> maxCount_pos;
maxCount_pos.push_back(pos_pre);
stringstream sout;
while (getline(fin, line))
{
nowCount = parse_line3(line, pos);
if ( pos - pos_pre <= pos_dif and pos - (*maxCount_pos.begin()) <= max_region_len)
{// same block
if ( nowCount > maxCount)
{
maxCount = nowCount;
maxCount_pos.clear();
maxCount_pos.push_back(pos);
}
else if ( nowCount == maxCount)
{
maxCount_pos.push_back(pos);
}
}
else
{ // create new block
sout << maxCount << " " << maxCount_pos.front() << " " << maxCount_pos.back() << endl;
maxCount_pos.clear();
maxCount_pos.push_back(pos);
maxCount = nowCount;
}
pos_pre = pos;
}
fin.close();
ofstream fout( file2.c_str());
fout << sout.str();
fout.close();
}
void alumate_counts_filter(string & path0, string pn, string fn_suffix_input, string fn_suffix_output, string fn_suffix_output2, vector<string> &chrns, int th_cnt)
{
int lr_num, rr_num, this_rID, this_pos, len_read;
string line, qname;
bool this_isRC;
stringstream ss;
for (vector<string>::iterator ci = chrns.begin(); ci != chrns.end(); ci++)
{
string chrn = *ci;
string f_input = path0 + chrn + "/" + pn + fn_suffix_input;
string f_output = path0 + chrn + "/" + pn + fn_suffix_output;
string f_output2 = path0 + chrn + "/" + pn + fn_suffix_output2;
list <int> pos_to_scan;
get_scan_pos(f_input, pos_to_scan, 8); // no big diff when change 8 to 20
// cout << f_input << " " << pos_to_scan.size() << endl;
list< READ_INFO *> lr_reads;
ifstream fin ( f_input.c_str());
assert(fin);
ofstream fout( f_output.c_str());
fout << "check_pos lr_num rr_num\n";
getline(fin, line); // skip header
getline(fin, line);
ss.clear(); ss.str(line);
ss >> qname >> this_rID >> this_pos >> this_isRC >> len_read;
lr_reads.push_back(new READ_INFO(this_pos, len_read, !this_isRC, ""));
bool readable = true;
while ( readable and pos_to_scan.size())
{
int check_pos = pos_to_scan.front();
pos_to_scan.pop_front();
while (readable and (lr_reads.empty() or lr_reads.back()-> endPos < check_pos + ::p_alu.scan_win_len) )
{
if (getline(fin, line))
{
ss.clear(); ss.str(line);
ss >> qname >> this_rID >> this_pos >> this_isRC >> len_read;
if ( len_read > 50)
lr_reads.push_back(new READ_INFO(this_pos, len_read, !this_isRC, ""));
}
else
readable = false;
}
if (lr_reads.empty()) continue;
lr_num = 0; rr_num = 0;
list< READ_INFO *>::iterator ri = lr_reads.begin();
while (ri != lr_reads.end() )
{
if ( (*ri)->beginPos < check_pos - ::p_alu.scan_win_len )
{
delete *ri;
ri = lr_reads.erase(ri); // <==> lr_reads.erase(ri++)
continue;
}
if ( (*ri)->endPos < check_pos and (*ri)->should_be_left) lr_num++;
else if ( (*ri)->beginPos > check_pos and !(*ri)->should_be_left ) rr_num++;
ri++;
if ( (*ri)->endPos >= check_pos + ::p_alu.scan_win_len ) break;
}
if (lr_num + rr_num >= th_cnt) fout << check_pos << " " << lr_num << " " << rr_num << endl;
}
fin.close();
fout.close();
join_location(f_output, f_output2, MAX_POS_DIF,::p_alu.max_len_region);
cout << "done " << f_output << endl;
}
}
void filter_location_rep(string path0, string pn, string file1_suffix, string file2_suffix, vector<string> &chrns, RepMaskPos *repmaskPos)
{
for (vector<string>::iterator ci = chrns.begin(); ci != chrns.end(); ci++)
{
string chrn = *ci;
ifstream fin( (path0 + chrn + "/" + pn + file1_suffix).c_str());
assert(fin);
ofstream fout( (path0 + chrn + "/" + pn + file2_suffix).c_str());
string line;
stringstream ss;
int readCnt, pos_left, pos_right;
vector<int>::iterator bi = repmaskPos->beginP[chrn].begin();
vector<int>::iterator ei = repmaskPos->endP[chrn].begin();
int bei = 0;
int be_size = repmaskPos->beginP[chrn].size();
while ( getline(fin, line) )
{
ss.clear(); ss.str( line );
ss >> readCnt >> pos_left >> pos_right;
if (pos_right <= 0) continue;
while ( pos_left >= (*ei) and bei < be_size)
{ bi++; ei++; bei++; }
if ( min(*ei, pos_right) - max(*bi, pos_left) < 0) // NB: < 0, not <= 0
fout << line << endl; // not in Alu
}
fin.close();
fout.close();
}
}
int read_sort_by_col(string fn, int coln, bool has_header, list< IntString> &rows_list)
{
string line, tmpv;
int pos;
stringstream ss;
ifstream fin( fn.c_str());
assert(fin);
rows_list.clear();
if (has_header) getline(fin, line);
size_t rown = 0;
while (getline(fin, line))
{
rown++;
ss.clear(); ss.str( line );
for (int i = 0; i < coln-1; i++) ss >> tmpv;
ss >> pos;
rows_list.push_back( make_pair(pos, line) );
}
fin.close();
rows_list.sort(compare_IntString);
if (rows_list.size() != rown ) cerr << "ERROR: " << fn << endl;
return rows_list.size();
}
// qname A_chr B_chr A_beginPos B_beginPos A_isRC B_isRC len_read
void read_match_rid(string fn, int col_val, list< AlumateINFO *> & alumate_list)
{
string line, qname;
int rid1, rid2, pos1, pos2, len_read, rgIdx;
bool rc1, rc2;
stringstream ss;
ifstream fin( fn.c_str());
if (!fin)
{
cerr << "ERROR: " << fn << " is missing\n";
exit(0);
}
getline(fin, line);
while (getline(fin, line))
{
ss.clear(); ss.str( line );
ss >> qname >> rid1 >> rid2 >> pos1 >> pos2 >> rc1 >> rc2 >> len_read >> rgIdx;
if (rid1 == col_val)
alumate_list.push_back(new AlumateINFO(qname, len_read, rid2, rid1, pos2, pos1, rgIdx, rc2, rc1));
if (rid2 == col_val)
alumate_list.push_back(new AlumateINFO(qname, len_read, rid1, rid2, pos1, pos2, rgIdx, rc1, rc2));
}
}
void keep_alu_mate(BamFileHandler * bam_fh, int alu_rid, string file1, MapFO & fileMap, string file_alu)
{
const int ALU_MIN_LEN = 50; // min overlap in alu region
list< AlumateINFO *> alumate_list;
read_match_rid(file1, alu_rid, alumate_list);
alumate_list.sort(AlumateINFO::sort_pos2);
cout << "alu file " << file_alu << endl;
AluRefPos *alurefpos = new AluRefPos(file_alu, 100, 100); // combine nearby positions, considered as Alu
int bei = 0, n_alu = 0;
int be_size = alurefpos->db_size - 1; // -1 ! otherwise seg fault
int left_pos;
for (list< AlumateINFO *>::iterator ri = alumate_list.begin(); ri != alumate_list.end(); ri++)
{
assert ( (*ri)->rid2 == alu_rid );
left_pos = (*ri)->pos2;
while ( ( left_pos >= alurefpos->get_endP() ) and bei < be_size)
{ alurefpos->nextdb(); bei++; }
if ( min( alurefpos->get_endP(), left_pos + (*ri)->len_read ) - max( alurefpos->get_beginP(), left_pos) > ALU_MIN_LEN and
key_exists(bam_fh->rID_chrn, (*ri)->rid1) and n_alu++)
*(fileMap[(*ri)->rid1]) << (*ri)->qname << " " << (*ri)->rid1 << " " << (*ri)->pos1 << " " << (*ri)->RC1 << " " << (*ri)->len_read
<< " " << (*ri)->rid2 << " " << left_pos << " " << (*ri)->RC2 << " " << (*ri)->rgIdx << " " << alurefpos->get_type() << endl ;
}
////// about 18% err counts are mapped to Alu region(normal chrns)
cout << file1 << " err counts: " << alumate_list.size() << ", alu mate: " << n_alu << endl;
AlumateINFO::delete_list(alumate_list);
delete alurefpos;
}
bool write_tmpFile_all_loci( vector<string> &fn_inputs, vector <string> & fn_idx, string fn_output)
{
stringstream ss;
string line;
ofstream fout;
vector<string>::iterator di;
if (!fn_idx.empty()) di = fn_idx.begin();
//cout << "####write to " << fn_output << " " << fn_inputs.size() << " " << fn_idx.size() << endl;
fout.open(fn_output.c_str());
for (vector<string>::iterator fi = fn_inputs.begin(); fi != fn_inputs.end(); fi ++ )
{
ifstream fin( (*fi).c_str());
if (!fin)
{
cerr << "ERROR: " << *fi << " does not exists! skip it\n";
continue;
}
if ( fn_idx.empty() )
{
while (getline(fin, line))
fout << line << endl;
}
else
{
while (getline(fin, line))
fout << line << " " << *di << endl; di++;
}
fin.close();
}
fout.close();
// sorting
list< IntString> rows_list;
read_sort_by_col(fn_output, 2, false, rows_list);
fout.open(fn_output.c_str());
for (list< IntString>::iterator ri = rows_list.begin(); ri!=rows_list.end(); ri++)
fout << (*ri).second << endl;
fout.close();
rows_list.clear();
return true;
}
void join_all_loci(string f_in, string f_out, int block_dist, int block_len)
{
string line, pn;
int cnt, sum_cnt, pa, pb, pa_block, pb_block;
set <string> pns;
ifstream fin(f_in.c_str());
assert(fin);
ofstream fout(f_out.c_str());
stringstream ss;
getline(fin, line);
ss.str(line);
ss >> cnt >> pa_block >> pb_block;
while (ss >> pn) pns.insert(pn);
sum_cnt = cnt;
while ( getline(fin, line) )
{
ss.clear(); ss.str( line );
ss >> cnt >> pa >> pb;
if ( pa <= pb_block + block_dist and // same block
( pa <= pa_block + block_len or pa <= pb_block) )
{
pb_block = min( pa_block + block_len, max(pb_block, pb) );
sum_cnt += cnt;
}
else
{ // new block
if (pb_block > 0)
{
fout << sum_cnt << " " << pa_block << " " << pb_block;
for (set<string>::iterator si = pns.begin(); si != pns.end(); si++ ) fout << " " << *si;
fout << endl;
}
pns.clear();
pa_block = pa;
pb_block = pb;
sum_cnt = cnt;
}
while (ss >> pn) pns.insert(pn);
}
fout << sum_cnt << " " << pa_block << " " << pb_block;
for (set<string>::iterator si = pns.begin(); si != pns.end(); si++ ) fout << " " << *si;
fout << endl;
fin.close();
fout.close();
}
void combine_fn(vector<string> & fn_inputs, string fn_output, vector<string> & fn_idx)
{
write_tmpFile_all_loci(fn_inputs, fn_idx, fn_output + ".tmp");
join_all_loci(fn_output + ".tmp", fn_output, MAX_POS_DIF, 2 *::p_alu.max_len_region);
system( ("rm " + fn_output + ".tmp").c_str() );
}
bool combine_pn_pos(string chrn, map <int, string> &id_pn_map, string tmpn, string output_prefix, int group_size, string path0)
{
string fn_prefix = output_prefix + chrn ; // some random names
// first iteration
map <string, vector<string> > fnOut_fnInput;
map <string, vector<string> >::iterator fni;
map <string, vector<string> > fnOut_pns;
string fnOut, fnInput_prefix, pn;
int i, j, n_size, n_group;
n_size = id_pn_map.size();
n_group = (int)(n_size / group_size);
for (i = 0; i < n_group; i++)
{
fnOut = (n_size <= group_size) ? fn_prefix : (fn_prefix + "." + int_to_string(i) + ".tmp0");
for ( j = 0; j < group_size; j++)
{
pn = id_pn_map[ i*group_size+j ];
fnOut_fnInput[fnOut].push_back(path0 + chrn + "/" + pn + tmpn);
fnOut_pns[fnOut].push_back(pn);
}
}
fnOut = (n_size <= group_size) ? fn_prefix : (fn_prefix + "." + int_to_string(n_group) + ".tmp0");
for ( j = n_group * group_size; j < n_size; j++)
{
pn = id_pn_map[ j ];
fnOut_fnInput[fnOut].push_back(path0 + chrn + "/" + pn + tmpn);
fnOut_pns[fnOut].push_back(pn);
}
for (fni = fnOut_fnInput.begin(); fni != fnOut_fnInput.end(); fni ++)
combine_fn(fni->second, fni->first, fnOut_pns[fni->first]);
fnOut_pns.clear();
if ( fnOut_fnInput.size() <= 1) return true;
vector<string> empty_vec;
int fn_idx = 0;
while ( true )
{
n_size = fnOut_fnInput.size();
n_group = (int)( n_size / group_size);
fnOut_fnInput.clear();
for (i = 0; i < n_group; i++)
{
fnOut = (n_size <= group_size) ? fn_prefix : (fn_prefix + "."+ int_to_string(i) + ".tmp"+ int_to_string(fn_idx+1) );
for ( j = 0; j < group_size; j++) fnOut_fnInput[fnOut].push_back( fn_prefix + "." + int_to_string(i*group_size+j) + ".tmp"+ int_to_string(fn_idx) );
}
fnOut = (n_size <= group_size) ? fn_prefix : (fn_prefix+ "." + int_to_string(n_group) + ".tmp"+ int_to_string(fn_idx+1) );
for ( j = n_group * group_size; j < n_size; j++) fnOut_fnInput[fnOut].push_back( fn_prefix + "." + int_to_string(j) + ".tmp" + int_to_string(fn_idx) );
for (fni = fnOut_fnInput.begin(); fni != fnOut_fnInput.end(); fni ++)
combine_fn(fni->second, fni->first, empty_vec);
fn_idx++;
if ( fnOut_fnInput.size() <= 1) break;
}
return true;
}
// scan candidate regions, write down clipReads if one of the following is valid (1) mate is discordant (2) partly aligned to consensus alu
// write down anyway if not sure
bool clipreads_at_insertPos(string pn, string chrn, BamFileHandler *bam_fh, string fin_pos, string fout_reads, AluconsHandler *alucons_fh)
{
const int MAX_REGION_LEN = 400;
ifstream fin( (fin_pos).c_str());
if (!fin) return false;
string line, numAluRead, _pn;
ofstream fout(fout_reads.c_str());
fout << "pn regionBegin regionEnd left_right clipPos qName cigar flag\n" ;
stringstream ss, ss_header;
int regionBegin, regionEnd, refBegin, refEnd;
int regionBegin0, regionEnd0;
while (getline(fin, line))
{
ss.clear(); ss.str( line );
ss >> numAluRead >> regionBegin >> regionEnd;
refBegin = regionBegin - ::p_alu.scan_win_len;
refEnd = regionEnd + ::p_alu.scan_win_len;
int _tmpwin = ( MAX_REGION_LEN - regionEnd + regionBegin) / 2;
regionBegin0 = regionBegin - _tmpwin;
regionEnd0 = regionEnd + _tmpwin;
bool pn_has_alumate = false;
while ( ss >> _pn )
if ( _pn == pn)
{ pn_has_alumate=true; break;}
if (! pn_has_alumate) continue;
if (! bam_fh->jump_to_region(chrn, refBegin, refEnd) ) continue;
ss_header.clear(); ss_header.str("");
ss_header << pn << " " << regionBegin << " " << regionEnd << " " ;
seqan::BamAlignmentRecord record;
map<int, int> confidentPos; // resolution of 10
while ( true )
{
string read_status = bam_fh->fetch_a_read(chrn, refBegin, refEnd, record);
if (read_status == "stop" ) break; // allow one pair is clipped, one pair is alu_read. More reads considered
if (read_status == "skip" or !QC_insert_read_qual(record)) continue;
/////if (!qname_match(record, "FCD1YM9ACXX:2:1114:6796:44598#GCTTAATG")) continue;
//bool s1 = has_soft_last(record, CLIP_BP); // endPos
//bool s2 = has_soft_first(record, CLIP_BP); // beginPos
bool s1 = has_soft_last(record, 5); // endPos
bool s2 = has_soft_first(record, 5); // beginPos
//if (record.rID != record.rNextId) cerr << "alu " << regionBegin << " " << refEnd << " " << record.beginPos << endl;
//if (s1 or s2) cerr << get_cigar(record) << " " << regionBegin << " " << refEnd << " " << record.beginPos << endl;
if (s1 and s2) continue;
if (!s1 and !s2) continue;
if (!aluclip_RC_match(record, s1, s2) ) continue; // RC flag should be right if it is alu mate
int beginPos = record.beginPos;
int endPos = beginPos + getAlignmentLengthInRef(record);
int _cliplen;
seqan::CharString _qualSeq;
bool use_this_read = false;
if ( s1 and endPos >= regionBegin0 and endPos < regionEnd0 )
use_this_read = trim_clip_soft_last(record, _cliplen, _qualSeq, ::p_alu.clip_q);
if ( s2 and beginPos >= regionBegin0 and beginPos < regionEnd0 )
use_this_read = trim_clip_soft_first(record, _cliplen, _qualSeq, ::p_alu.clip_q);
if ( abs(_cliplen) < CLIP_BP or !use_this_read) continue;
string output_direct = s1 ? "L " : "R ";
int output_pos = s1 ? endPos : beginPos;
int output_pos_division = round_by_division(output_pos, 10);
if (record.rID != record.rNextId or abs(record.tLen) >= DISCORDANT_LEN)
{
fout << ss_header.str() << output_direct << output_pos << " " << record.qName << " " << get_cigar(record) << " mate\n";
add3key(confidentPos, output_pos_division);
continue;
}
if ( confidentPos.find(output_pos_division) != confidentPos.end() )
{
fout << ss_header.str() << output_direct << output_pos << " " << record.qName << " " << get_cigar(record) << " previous\n";
continue;
}
string alu_type;
float sim_rate;
seqan::CharString clipped;
//cout << "cliplen " << _cliplen << " " << length(_qualSeq) << " " << get_cigar(record) << endl;
if ( s1 ) clipped = infix(_qualSeq, length(_qualSeq) - abs(_cliplen), length(_qualSeq));
else clipped = infix(_qualSeq, 0, abs(_cliplen));
alu_type = align_alu_cons_call(clipped, alucons_fh, sim_rate, 0.8, true);
if (!alu_type.empty())
{
add3key(confidentPos, output_pos_division);
fout << ss_header.str() << output_direct << output_pos << " " << record.qName << " " << get_cigar(record) << " aligned\n";
}
else
{
fout << ss_header.str() << output_direct << output_pos << " " << record.qName << " " << get_cigar(record) << " false\n";
}
}
}
fin.close();
fout.close();
return true;
}
// for each insertion region, combine reads from different pns
void combine_clipreads_by_pos(std::set<string> &pns_used, string path0, string path1)
{
map< pair<string, string>, vector<string> > regionPos_lines;
for (std::set<string>::iterator pi = pns_used.begin(); pi != pns_used.end(); pi ++ )
{
string file_input_clip = path0 + *pi;
ifstream fin(file_input_clip.c_str());
if (!fin)
{
cout << "error " << file_input_clip << " missing \n";
continue;
}
stringstream ss;
string line, pn, regionBegin, regionEnd;
getline(fin, line); // read header
while ( getline(fin, line) )
{
string flag = line.substr(line.size() - 5, line.size());
if ( flag == "false" ) continue; // false clip reads
ss.clear(); ss.str(line);
ss >> pn >> regionBegin >> regionEnd;
regionPos_lines[make_pair(regionBegin, regionEnd)].push_back(line);
}
fin.close();
}
map< pair<string, string>, vector<string> >::iterator ri;
for (ri = regionPos_lines.begin(); ri != regionPos_lines.end(); ri ++)
{
string file_output_clip = path1 + (ri->first).first + "_" + (ri->first).second;
ofstream fout(file_output_clip.c_str() );
for (vector<string>::iterator ii = (ri->second).begin(); ii != (ri->second).end(); ii++)
fout << *ii << endl;
fout.close();
}
}
string pos_to_fn( pair<int, int> ps)
{
return int_to_string(ps.first) + "_" + int_to_string(ps.second);
}
bool nonempty_files_sorted(string & path1, std::set < pair<int, int> > & regionPos_set)
{
DIR *d;
struct dirent *dir;
d = opendir(path1.c_str());
string fn;
int regionBegin, regionEnd;
string s_regionBegin, s_regionEnd;
if (d)
{
while ( (dir = readdir(d))!=NULL )
{
fn = dir->d_name;
if (fn[0] == '.' or check_file_size( path1 + fn)<=0 ) continue;
split_by_sep(fn, s_regionBegin, s_regionEnd, '_');
seqan::lexicalCast2(regionBegin, s_regionBegin);
seqan::lexicalCast2(regionEnd, s_regionEnd);
regionPos_set.insert( make_pair(regionBegin, regionEnd));
}
closedir(d);
return true;
}
return false;
}
void addcnt_if_pos_match( map <int, float> & clipLeft_cnt, int pos, int match_offset, float inc_val)
{
int match_key = 0;
for ( map <int, float>::iterator mi = clipLeft_cnt.begin(); mi != clipLeft_cnt.end(); mi ++)
{
if ( abs(mi->first - pos) <= match_offset )
{
match_offset = abs(mi->first - pos);
match_key = mi->first;
}
}
if ( match_key == 0)
{
addKey(clipLeft_cnt, pos, inc_val);
}
else
{
if (match_key > pos)
{ // previously add clipRight
float cnt = clipLeft_cnt[match_key] + inc_val;
clipLeft_cnt.erase(match_key);
clipLeft_cnt[pos] = cnt;
// cout << "offset " << match_key << " " << pos << endl;
}
else
{
addKey(clipLeft_cnt, match_key, inc_val);
}
}
}
void region_pos_vote( string fn, int & cl1, int & cl2, int & cr1, int & cr2 )
{
const float MIN_VOTE_FREQ = 0.4;
const int MIN_PN_CLIP_CNT = 2; // otherwise ignore this pn
cl1 = 0; cl2 = 0; cr1 = 0; cr2 = 0;
ifstream fin(fn.c_str());
assert(fin);
stringstream ss;
string line, pn;
char left_right;
int region_begin, region_end, clipPos;
map <string, vector <pair<char, int> > > pn_splitori_pos;
while ( getline(fin, line))
{
ss.clear(); ss.str( line );
ss >> pn >> region_begin >> region_end >> left_right >> clipPos;
pn_splitori_pos[pn].push_back( make_pair( left_right, clipPos) );
}
fin.close();
vector < int > cls, crs;
map <string, vector <pair<char, int> > >::iterator psi;
vector <pair<char, int> >::iterator si;
for ( psi = pn_splitori_pos.begin(); psi != pn_splitori_pos.end(); psi++)
{
int pl1 = 0, pl2 = 0, pr1 = 0, pr2 = 0;
vector<int> pls, prs;
for (si = (psi->second).begin(); si != (psi->second).end(); si ++ )
{
if ( (*si).first == 'L') pls.push_back( (*si).second );
else prs.push_back( (*si).second );
}
int fl1, fl2;
if ( (int)pls.size() >= MIN_PN_CLIP_CNT)
major_two_keys(pls, pl1, pl2, fl1, fl2, CLIP_BP, MIN_VOTE_FREQ - 0.1); // each pn 2 votes
int fr1, fr2;
if ( (int)prs.size() >= MIN_PN_CLIP_CNT)
major_two_keys(prs, pr1, pr2, fr1, fr2, CLIP_BP, MIN_VOTE_FREQ - 0.1);
if ( fl1 <= 1 and fr1 <= 1 and abs(pl1 - pr1) > MAX_POS_DIF )
{
pl1 = 0; pr1 = 0;
}
if (pl1 > 0)
{
cls.push_back(pl1);
if (pl2 > 0) cls.push_back(pl2);
else cls.push_back(pl1);
}
if (pr1 > 0)
{
crs.push_back(pr1);
if (pr2 > 0) crs.push_back(pr2);
else crs.push_back(pr1);
}
}
int fc1, fc2;
major_two_keys(cls, cl1, cl2, fc1, fc2, CLIP_BP, MIN_VOTE_FREQ);
if ( cl1 and fc1 <= 2 and fc1 / (float) cls.size() < 0.99 ) cl1 = 0;
if ( fc2 <= 2) cl2 = 0;
major_two_keys(crs, cr1, cr2, fc1, fc2, CLIP_BP, MIN_VOTE_FREQ);
if ( cr1 and fc1 <= 2 and fc1 / (float) crs.size() < 0.99 ) cr1 = 0;
////////if ( fc1 <= 2 ) cr1 = 0;
if ( fc2 <= 2 ) cr2 = 0;
//if (!cls.empty() and !crs.empty())
// cout << "##1 " << region_begin << " " << cls.size() << " " << crs.size() << " " << cl1 << " " << cr1 << endl;
}
string get_pos_pair(int cl1, int cl2, int cr1, int cr2)
{
if ( !cl1 and !cr1) return "";
std::set <int> cms;
cms.insert(0);
cms.insert(cl1);
cms.insert(cl2);
cms.insert(cr1);
cms.insert(cr2);
cms.erase(0);
std::set <int>::iterator ci = cms.begin();
stringstream ss;
int pre_pos = *ci;
ci++;
for (; ci != cms.end(); ci++)
{
if ( abs(*ci - pre_pos) < MAX_POS_DIF )
{
pre_pos = (*ci + pre_pos)/2;
}
else
{
ss << " " << pre_pos;
pre_pos = *ci;
}
}
ss << " " << pre_pos;
return ss.str();
}
void regions_pos_vote( string path1, std::set < pair<int, int> > & regionPos_set, string fn_output)
{
ofstream fout(fn_output.c_str());
fout << "region_begin region_end clipMid\n";
for (std::set < pair <int, int> >::iterator ri = regionPos_set.begin(); ri != regionPos_set.end(); ri++ )
{
int cl1, cl2, cr1, cr2;
region_pos_vote(path1 + pos_to_fn(*ri), cl1, cl2, cr1, cr2) ; // at least two reads to vote for this position
// if ( cl1 + cl2 + cr1 + cr2 > 0 )
// cout << pos_to_fn(*ri) << " " << cl1 << " " << cl2 << " " << cr1 << " " << cr2 << endl;
string cs = get_pos_pair(cl1, cl2, cr1, cr2);
if ( cs.size() > 3 )
fout << (*ri).first << " " << (*ri).second << cs << endl;
}
}
void neighbor_pos_filename(std::set < pair<int,int> > & regionPos_set, std::set <pair <int, int> > & fns, int clipLeft)
{
const int FLANK_REGION_LEN = 80;
std::set < pair<int,int> >::iterator ri;
ri = regionPos_set.find( * (fns.begin()) );
while ( ri != regionPos_set.begin() and (*ri).first + FLANK_REGION_LEN >= clipLeft)
fns.insert( *ri-- );
ri = regionPos_set.find( * (fns.rbegin()) );
while ( ri !=regionPos_set.end() and (*ri).second - FLANK_REGION_LEN <= clipLeft )
fns.insert( *ri++ );
}
int approximate_pos_pns(string path1, string fn_input, string fn_output, std::set < pair<int,int> > & regionPos_set, int pos_dif)
{
ifstream fin;
fin.open(fn_input.c_str());
assert(fin);
map< int, std::set <pair<int, int> > > clipLeft_fn0;
map< int, std::set <pair<int, int> > > clipLeft_fn;
stringstream ss;
string line;
int region_begin, region_end, pos2, pos1;
getline(fin,line);
while (getline(fin,line))
{
ss.clear(); ss.str( line );
ss >> region_begin >> region_end;
while ( ss >> pos2) // in each region, several potential breakpoints
clipLeft_fn0[pos2].insert( make_pair(region_begin, region_end)) ;
}
fin.close();
if (clipLeft_fn0.empty() ) return 0;
map< int, std::set <pair<int, int> > >::iterator ci = clipLeft_fn0.begin();
int pos0 = ci->first;
clipLeft_fn[pos0].swap(ci->second);
ci ++;
for (; ci != clipLeft_fn0.end(); ci++)
{
pos2 = ci->first;
if ( pos2 - pos0 <= pos_dif )
{
pos1 = (pos2 + pos0) / 2;
clipLeft_fn[pos1].swap(clipLeft_fn[pos0]);
clipLeft_fn.erase(pos0);
pos2 = pos1;
for ( std::set <pair<int, int> >::iterator fi = (ci->second).begin(); fi != (ci->second).end(); fi++ )
clipLeft_fn[pos2].insert(*fi);
}
else
{
clipLeft_fn[pos2].swap(ci->second);
}
pos0 = pos2;
}
//cout << "size0 " << clipLeft_fn0.size() << " " << clipLeft_fn.size() << endl;
clipLeft_fn0.clear();
ofstream fout(fn_output.c_str());
fout << "clipMid pn(count)\n";
for (map< int, std::set < pair<int, int> > >::iterator pi = clipLeft_fn.begin(); pi != clipLeft_fn.end(); pi++ )
{
int clipLeft = pi->first;
map <string, std::set<string> > pn_qName;
std::set < pair<int, int> > fns;
size_t fns_size = (pi->second).size() ; // num of regions voted for this clip pos
fns.swap(pi->second);
neighbor_pos_filename(regionPos_set, fns, clipLeft); // add more regions to fns
assert ( fns.size() >= fns_size );
for ( std::set < pair<int, int> >::iterator fi = fns.begin(); fi != fns.end(); fi++ )
{
fin.open( (path1 + pos_to_fn(*fi) ).c_str());
string line, pn, qName, tmp1, tmp2, tmp3;
while (getline(fin, line))
{
ss.clear(); ss.str( line );
int _p;
ss >> pn >> tmp1 >> tmp2 >> tmp3 >> _p >> qName;
if ( abs( _p - clipLeft ) <= MAX_POS_DIF)
pn_qName[pn].insert(qName); // some reads appear more than once
}
fin.close();
}
if ( pn_qName.empty() )
continue;
fout << clipLeft; // clipRight unknown for now
for (map <string, std::set<string> >::iterator pi = pn_qName.begin(); pi != pn_qName.end(); pi++)
fout << " " << pi->first << "," << (pi->second).size() ;
fout << endl;
}
fout.close();
return 1;
}
void vote_clipPos(int clip0, int & clipl, int & clipr, string path0, map <string, int> & pn_cnt, float freq_th)
{
clipl = clipr = 0;
vector <int> clipls, cliprs;
for (map <string, int>::iterator pi = pn_cnt.begin(); pi != pn_cnt.end(); pi++ )
{
ifstream fin( (path0 + pi->first).c_str() );
assert(fin);
string line, tmpv0;
char left_right;
int adj_clipPos, tmpv1, tmpv2;
stringstream ss;
getline(fin, line);
while ( getline(fin, line) )
{
ss.clear(); ss.str( line );
ss >> tmpv0 >> tmpv1 >> tmpv2 >> left_right >> adj_clipPos;
//cout << clip0 << " " << tmpv2 << " " << adj_clipPos << endl;
if ( clip0 + 300 < tmpv2 ) break;
if ( abs(clip0 - adj_clipPos) <= MAX_POS_DIF )
{
pi->second += 1;
if ( left_right == 'L' ) clipls.push_back(adj_clipPos);
else if ( left_right == 'R' ) cliprs.push_back(adj_clipPos);
}
}
fin.close();
}
//cout << "vote " << clip0 << " " << clipls.size() << " " << cliprs.size() << endl;
////if ( major_key_freq(clipls, clipl, MAX_POS_DIF, freq_th, 3) >= 2 // eg: freq_th = 0.7, at least 3 clip read exact the same
major_key_freq(clipls, clipl, MAX_POS_DIF, freq_th, 3); // eg: freq_th = 0.7, at least 3 clip read exact the same
major_key_freq(cliprs, clipr, MAX_POS_DIF, freq_th, 3);
}
void exact_pos_pns(string path0, string fn_input, string fn_output, float freq_th )
{
ifstream fin(fn_input.c_str());
assert(fin);
ofstream fout(fn_output.c_str());
stringstream ss;
string line, pn, cnt, tmpv;
int clip0, clipl, clipr;
getline(fin,line);
fout << "clipLeft clipRight pn(count)\n";
while (getline(fin, line))
{
ss.clear(); ss.str(line);
ss >> clip0;
map <string, int> pn_cnt;
while ( ss >> tmpv )
{
split_by_sep (tmpv, pn, cnt, ',');
pn_cnt[pn] = 0;
}
int tmpcnt;
seqan::lexicalCast2(tmpcnt, cnt);
if (pn_cnt.size() <= 1 and tmpcnt <= 2 ) continue; // at least 2 reads to support
vote_clipPos(clip0, clipl, clipr, path0, pn_cnt, freq_th);
//cout << clip0 << " " << pn_cnt.size() << " " << clipl << " " << clipr << endl;
if (!clipl and !clipr ) continue;
fout << clipl << " " << clipr;
for (map <string, int>::iterator pi = pn_cnt.begin(); pi != pn_cnt.end(); pi++ )
fout << " " << pi->first;
fout << endl;
}
fin.close();
fout.close();
}
string classify_read(map<int, int> & confidentPos, seqan::BamAlignmentRecord & record, int clipLeft, int clipRight,
int & clipLen, seqan::CharString & clipSeq)
{
assert (clipLeft > 0 );
assert (clipRight > 0 );
bool s1 = has_soft_last(record, CLIP_BP);
bool s2 = has_soft_first(record, CLIP_BP);
if (s1 and s2 ) return "bad_read"; // ignore this pair
if ( (s1 or s2) and !aluclip_RC_match(record, s1, s2)) return "bad_read";
int thisEnd = record.beginPos + (int)getAlignmentLengthInRef(record);
int output_pos = s1 ? thisEnd : record.beginPos;
int output_pos_division = round_by_division(output_pos, 3); // very strict
if (record.rID != record.rNextId or abs(record.tLen) >= DISCORDANT_LEN)
{
if ( ( s1 and trim_clip_soft_last(record, clipLen, clipSeq, 10) ) or
( s2 and trim_clip_soft_first(record, clipLen, clipSeq, 10 )) )
{
add3key(confidentPos, output_pos_division);
return "alu_clip";
}
if ( !hasFlagRC(record) and thisEnd < clipLeft + MAX_POS_DIF ) return "alu_read"; // this read is left_read
if ( hasFlagRC(record) and record.beginPos > clipRight - MAX_POS_DIF ) return "alu_read";
return "bad_read";
}
bool read_is_left = left_read(record);
// otherwise only look at proper mapped reads
if ( hasFlagRC(record) == hasFlagNextRC(record) or read_is_left == hasFlagRC(record) ) return "bad_read";
seqan::CharString clipped;
if ( s1 and trim_clip_soft_last(record, clipLen, clipSeq, ::p_alu.clip_q) and abs( output_pos - clipLeft) < MAX_POS_DIF )
{
if ( confidentPos.find(output_pos_division) != confidentPos.end() ) return "clip_read";
clipped = infix(clipSeq, length(clipSeq) - abs(clipLen), length(clipSeq));
}
if ( s2 and trim_clip_soft_first(record, clipLen, clipSeq, ::p_alu.clip_q) and abs( output_pos - clipRight ) < MAX_POS_DIF )
{
if ( confidentPos.find(output_pos_division) != confidentPos.end() ) return "clip_read";
clipped = infix(clipSeq, 0, abs(clipLen));
}
if ( length(clipped) > 10 )
// no need to re-align to alu consensus, one of them has been aligned
//string alu_type = align_alu_cons_call(clipped, alucons_fh, sim_rate, 0.8, true);
//if (!alu_type.empty())
{
add3key(confidentPos, output_pos_division);
return "clip_read";
}
int trimb, trime;