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/*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* HISAT 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef REPEAT_H_
#define REPEAT_H_
#include <iostream>
#include <fstream>
#include <limits>
#include <map>
#include "assert_helpers.h"
#include "word_io.h"
#include "mem_ids.h"
#include "ref_coord.h"
#include "alt.h"
using namespace std;
template <typename index_t>
class RepeatCoord {
public:
bool operator< (const RepeatCoord<index_t>& o) const {
if(joinedOff != o.joinedOff)
return joinedOff < o.joinedOff;
if(fw != o.fw)
return fw;
if(alleleID != o.alleleID)
return alleleID < o.alleleID;
return false;
}
public:
RepeatCoord() {};
RepeatCoord(index_t l_tid, index_t l_toff, index_t l_joinedOff, bool l_fw, index_t l_alleleID) :
tid(l_tid), toff(l_toff), joinedOff(l_joinedOff), fw(l_fw) {};
index_t tid;
index_t toff;
index_t joinedOff;
bool fw;
index_t alleleID;
};
template <typename index_t>
class RepeatAllele {
public:
RepeatAllele() {
reset();
}
void init(index_t allelePos_,
index_t alleleLen_) {
allelePos = allelePos_;
alleleLen = alleleLen_;
}
void reset() {
allelePos = 0;
alleleLen = 0;
}
bool operator< (const RepeatAllele& o) const {
if(allelePos != o.allelePos)
return allelePos < o.allelePos;
return alleleLen < o.alleleLen;
}
#ifndef NDEBUG
bool repOk() const {
return true;
}
#endif
bool write(ofstream& f_out, bool bigEndian) const {
writeU16(f_out, allelePos, bigEndian);
writeU16(f_out, alleleLen, bigEndian);
return true;
}
bool read(ifstream& f_in, bool bigEndian) {
allelePos = readU16(f_in, bigEndian);
alleleLen = readU16(f_in, bigEndian);
return true;
}
bool compatible(index_t left, index_t right) const {
if(left < allelePos || right > allelePos + alleleLen)
return false;
return true;
}
public:
uint16_t allelePos;
uint16_t alleleLen;
};
// sorting functions
template <typename index_t>
struct sort_pair_loci {
bool operator()(const pair<RepeatCoord<index_t>, index_t>& a, const pair<RepeatCoord<index_t>, index_t>& b) {
return a.first.joinedOff < b.first.joinedOff;
}
};
template <typename index_t>
struct sort_pair_loci_by_index {
bool operator()(const pair<RepeatCoord<index_t>, index_t>& a, const pair<RepeatCoord<index_t>, index_t>& b) {
return a.second < b.second;
}
};
template <typename index_t>
class Repeat {
public:
void init(const string& repName_,
index_t repID_,
index_t repPos_,
index_t repLen_) {
repName = repName_;
repID = repID_;
repPos = repPos_;
repLen = repLen_;
}
bool write(ofstream& f_out, bool bigEndian) const {
writeIndex<index_t>(f_out, repID, bigEndian);
writeIndex<index_t>(f_out, repPos, bigEndian);
writeIndex<index_t>(f_out, repLen, bigEndian);
writeIndex<index_t>(f_out, alleles.size(), bigEndian);
for(index_t i = 0; i < alleles.size(); i++) {
alleles[i].write(f_out, bigEndian);
}
writeIndex<index_t>(f_out, positions.size(), bigEndian);
for(index_t i = 0; i < positions.size(); i++) {
writeIndex<index_t>(f_out, positions[i].joinedOff, bigEndian);
writeU8(f_out, positions[i].fw);
writeIndex<index_t>(f_out, positions[i].alleleID, bigEndian);
}
return true;
}
bool read(ifstream& f_in, bool bigEndian) {
repID = readIndex<index_t>(f_in, bigEndian);
repPos = readIndex<index_t>(f_in, bigEndian);
repLen = readIndex<index_t>(f_in, bigEndian);
index_t numAlleles = readIndex<index_t>(f_in, bigEndian);
alleles.resizeExact(numAlleles);
for(index_t i = 0; i < numAlleles; i++) {
alleles[i].read(f_in, bigEndian);
}
index_t numPositions = readIndex<index_t>(f_in, bigEndian);
positions.resizeExact(numPositions);
for(index_t i = 0; i < numPositions; i++) {
positions[i].tid = 0;
positions[i].toff = 0;
positions[i].joinedOff = readIndex<index_t>(f_in, bigEndian);
positions[i].fw = readU8(f_in);
positions[i].alleleID = readIndex<index_t>(f_in, bigEndian);
assert_lt(positions[i].alleleID, alleles.size());
}
return true;
}
public:
string repName;
index_t repID;
index_t repPos;
index_t repLen;
EList<RepeatAllele<index_t> > alleles;
EList<RepeatCoord<index_t> > positions;
};
template <typename index_t>
class RepeatDB {
public:
RepeatDB() {}
virtual ~RepeatDB() {}
bool empty() const { return _repeats.size() == 0; }
EList<Repeat<index_t> >& repeats() { return _repeats; }
const EList<Repeat<index_t> >& repeats() const { return _repeats; }
const ELList<pair<index_t, index_t> >& repeatMap() const { return _repeatMap; }
void write(ofstream& f_out, bool bigEndian) const {
if(_repeats.size() <= 0) {
writeIndex<index_t>(f_out, 0, bigEndian);
return;
}
EList<index_t> repeatGroup;
for(index_t i = 0; i < _repeats.size(); i++) {
#ifndef NDEBUG
if(i + 1 < _repeats.size()) {
assert_leq(_repeats[i].repID, _repeats[i+1].repID);
}
#endif
if(_repeats[i].repID > repeatGroup.size()) {
repeatGroup.push_back(i);
assert_eq(_repeats[i].repID, repeatGroup.size());
}
}
repeatGroup.push_back(_repeats.size());
assert_eq(_repeats.back().repID + 1, repeatGroup.size());
writeIndex<index_t>(f_out, repeatGroup.size(), bigEndian);
streampos filepos = f_out.tellp();
EList<streampos> repeatFilePos;
for(index_t i = 0; i < repeatGroup.size(); i++) {
writeIndex<uint64_t>(f_out, 0, bigEndian);
}
for(index_t i = 0; i < repeatGroup.size(); i++) {
index_t begin = (i == 0 ? 0 : repeatGroup[i-1]);
index_t end = repeatGroup[i];
writeIndex<index_t>(f_out, end - begin, bigEndian);
for(index_t j = begin; j < end; j++) {
_repeats[j].write(f_out, bigEndian);
}
repeatFilePos.push_back(f_out.tellp());
}
assert_eq(repeatFilePos.size(), repeatGroup.size());
streampos origpos = f_out.tellp();
f_out.seekp(filepos);
for(index_t i = 0; i < repeatFilePos.size(); i++) {
writeIndex<uint64_t>(f_out, repeatFilePos[i], bigEndian);
}
f_out.seekp(origpos);
}
void read(ifstream& f_in, bool bigEndian, const EList<uint8_t>& includeRepeat) {
index_t numRepeatGroup = readIndex<index_t>(f_in, bigEndian);
EList<streampos> filePos; filePos.resizeExact(numRepeatGroup);
for(index_t i = 0; i < numRepeatGroup; i++) {
filePos[i] = readIndex<uint64_t>(f_in, bigEndian);
}
assert_eq(numRepeatGroup, includeRepeat.size());
for(index_t i = 0, repID = 0; i < numRepeatGroup; i++) {
if(!includeRepeat[i])
continue;
if(i > 0) {
f_in.seekg(filePos[i-1]);
}
index_t numRepeats = readIndex<index_t>(f_in, bigEndian);
index_t repeat_size = _repeats.size();
_repeats.resizeExact(repeat_size + numRepeats);
for(index_t j = 0; j < numRepeats; j++) {
_repeats[repeat_size+j].read(f_in, bigEndian);
_repeats[repeat_size+j].repID = repID;
}
repID++;
}
f_in.seekg(filePos.back());
}
// Build an internal table to enable rapid search of repeats
// and converts joined offsets to chromosome IDs (tid) and loci (toff)
void construct(const index_t* rstarts, index_t rlen) {
_repeatMap.clear();
if(_repeats.empty())
return;
for(index_t r = 0; r < _repeats.size(); r++) {
if(_repeats[r].repID >= _repeatMap.size()) {
_repeatMap.expand();
_repeatMap.back().clear();
}
EList<pair<index_t, index_t> >& repeatMap = _repeatMap.back();
repeatMap.expand();
if(repeatMap.size() == 1) {
repeatMap.back().first = _repeats[r].repLen;
} else {
repeatMap.back().first = repeatMap[repeatMap.size() - 2].first + _repeats[r].repLen;
}
repeatMap.back().second = r;
}
EList<pair<RepeatCoord<index_t>, index_t> > joinedOffList;
for(index_t r = 0; r < _repeats.size(); r++) {
Repeat<index_t>& repeat = _repeats[r];
EList<RepeatCoord<index_t> >& positions = repeat.positions;
for(index_t p = 0; p < positions.size(); p++) {
joinedOffList.expand();
joinedOffList.back().first.joinedOff = positions[p].joinedOff;
joinedOffList.back().first.tid = 0;
joinedOffList.back().first.toff = 0;
joinedOffList.back().first.fw = positions[p].fw;
joinedOffList.back().first.alleleID = positions[p].alleleID;
joinedOffList.back().second = joinedOffList.size() - 1;
}
}
sort(joinedOffList.begin(), joinedOffList.end(), sort_pair_loci<index_t>());
index_t j = 0, r = 0;
while(j < joinedOffList.size() && r < rlen) {
index_t off = joinedOffList[j].first.joinedOff;
index_t lower = rstarts[r*3];
index_t upper;
if(r == rlen - 1) {
upper = numeric_limits<index_t>::max();
} else {
upper = rstarts[(r+1)*3];
}
assert_gt(upper, lower);
if(off >= upper) {
r++;
continue;
}
assert_geq(off, lower);
joinedOffList[j].first.tid = rstarts[(r*3)+1];
joinedOffList[j].first.toff = off - lower + rstarts[(r*3)+2];
j++;
}
sort(joinedOffList.begin(), joinedOffList.end(), sort_pair_loci_by_index<index_t>());
index_t count = 0;
for(index_t r = 0; r < _repeats.size(); r++) {
Repeat<index_t>& repeat = _repeats[r];
EList<RepeatCoord<index_t> >& positions = _repeats[r].positions;
for(index_t p = 0; p < positions.size(); p++) {
assert_lt(count, joinedOffList.size());
assert_eq(positions[p].joinedOff, joinedOffList[count].first.joinedOff);
positions[p] = joinedOffList[count].first;
RepeatAllele<index_t>& allele = repeat.alleles[positions[p].alleleID];
if(positions[p].fw) {
positions[p].joinedOff -= allele.allelePos;
positions[p].toff -= allele.allelePos;
} else {
assert_leq(allele.allelePos + allele.alleleLen, repeat.repLen);
index_t subLen = repeat.repLen - allele.allelePos - allele.alleleLen;
positions[p].joinedOff -= subLen;
positions[p].toff -= subLen;
}
count++;
}
}
}
bool repeatExist(index_t repID, index_t left, index_t right) const {
if(repID >= _repeatMap.size())
return false;
// Find a repeat corresponding to a given location (left, right)
const EList<pair<index_t, index_t> >& repeatMap = _repeatMap[repID];
pair<index_t, index_t> repeat(left, numeric_limits<index_t>::max());
index_t repeatIdx = repeatMap.bsearchLoBound(repeat);
assert_lt(repeatIdx, repeatMap.size());
if(right > repeatMap[repeatIdx].first)
return false;
return true;
}
bool getCoords(index_t repID,
index_t left, // left offset in the repeat sequence
index_t right, // right offset
const EList<index_t>& snpIDs, // SNP IDs
const ALTDB<index_t>& altdb,
EList<pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >& near_positions,
index_t max_positions = numeric_limits<index_t>::max()) const {
near_positions.clear();
if(repID >= _repeatMap.size())
return false;
// Find a repeat corresponding to a given location (left, right)
const EList<pair<index_t, index_t> >& repeatMap = _repeatMap[repID];
pair<index_t, index_t> repeat(left, numeric_limits<index_t>::max());
index_t repeatIdx = repeatMap.bsearchLoBound(repeat);
assert_lt(repeatIdx, repeatMap.size());
if(right > repeatMap[repeatIdx].first)
return false;
index_t repeatIdx_ = repeatMap[repeatIdx].second;
assert_lt(repeatIdx_, _repeats.size());
const EList<RepeatAllele<index_t> >& alleles = _repeats[repeatIdx_].alleles;
index_t adjLeft = left, adjRight = right;
if(repeatIdx > 0) {
adjLeft -= repeatMap[repeatIdx-1].first;
adjRight -= repeatMap[repeatIdx-1].first;
}
const EList<RepeatCoord<index_t> >& positions = _repeats[repeatIdx_].positions;
for(index_t p = 0; p < positions.size(); p++) {
const RepeatCoord<index_t>& position = positions[p];
assert_lt(position.alleleID, alleles.size());
const RepeatAllele<index_t>& allele = alleles[position.alleleID];
if(!allele.compatible(adjLeft, adjRight))
continue;
near_positions.expand();
near_positions.back().first = position;
if(positions[p].fw) {
near_positions.back().first.joinedOff += adjLeft;
near_positions.back().first.toff += adjLeft;
} else {
const index_t len = right - left;
assert_leq(adjLeft + len, _repeats[repeatIdx_].repLen);
index_t rc_adjLeft = _repeats[repeatIdx_].repLen - adjLeft - len;
near_positions.back().first.joinedOff += rc_adjLeft;
near_positions.back().first.toff += rc_adjLeft;
}
if(near_positions.size() >= max_positions)
break;
}
return near_positions.size() > 0;
}
bool findCoords(index_t anchor_left,
index_t anchor_right,
index_t repID,
index_t left, // left offset in the repeat sequence
index_t right, // right offset
const EList<index_t>& snpIDs, // SNP IDs
const ALTDB<index_t>& altdb,
EList<pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >& near_positions,
index_t max_positions = numeric_limits<index_t>::max(),
index_t dist = 1000) const {
near_positions.clear();
if(repID >= _repeatMap.size())
return false;
// Find a repeat corresponding to a given location (left, right)
const EList<pair<index_t, index_t> >& repeatMap = _repeatMap[repID];
pair<index_t, index_t> repeat(left, numeric_limits<index_t>::max());
index_t repeatIdx = repeatMap.bsearchLoBound(repeat);
assert_lt(repeatIdx, repeatMap.size());
if(right > repeatMap[repeatIdx].first)
return false;
index_t repeatIdx_ = repeatMap[repeatIdx].second;
assert_lt(repeatIdx_, _repeats.size());
const EList<RepeatAllele<index_t> >& alleles = _repeats[repeatIdx_].alleles;
index_t adjLeft = left, adjRight = right;
if(repeatIdx > 0) {
adjLeft -= repeatMap[repeatIdx-1].first;
adjRight -= repeatMap[repeatIdx-1].first;
}
const EList<RepeatCoord<index_t> >& positions = _repeats[repeatIdx_].positions;
RepeatCoord<index_t> cmp;
cmp.joinedOff = (anchor_left >= dist ? anchor_left - dist : 0);
index_t p = positions.bsearchLoBound(cmp);
for(; p < positions.size(); p++) {
const RepeatCoord<index_t>& position = positions[p];
index_t pos = positions[p].joinedOff + adjLeft;
if(pos + dist < anchor_left)
continue;
if(anchor_right + dist < pos)
break;
assert_lt(position.alleleID, alleles.size());
const RepeatAllele<index_t>& allele = alleles[position.alleleID];
if(!allele.compatible(adjLeft, adjRight))
continue;
near_positions.expand();
near_positions.back().first = position;
if(positions[p].fw) {
near_positions.back().first.joinedOff += adjLeft;
near_positions.back().first.toff += adjLeft;
} else {
const index_t len = right - left;
assert_leq(adjLeft + len, _repeats[repeatIdx_].repLen);
index_t rc_adjLeft = _repeats[repeatIdx_].repLen - adjLeft - len;
near_positions.back().first.joinedOff += rc_adjLeft;
near_positions.back().first.toff += rc_adjLeft;
}
if(near_positions.size() >= max_positions)
break;
}
return near_positions.size() > 0;
}
bool findCommonCoords(index_t repID,
index_t left, // left offset in the repeat sequence
index_t right, // right offset
const EList<index_t>& snpIDs, // SNP IDs
index_t repID2,
index_t left2, // left offset 2 in the repeat sequence
index_t right2, // right offset 2
const EList<index_t>& snpIDs2, // SNP IDs
const ALTDB<index_t>& altdb,
EList<pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >& common_positions,
index_t max_positions = numeric_limits<index_t>::max(),
index_t dist = 1000) const {
common_positions.clear();
if(repID >= _repeatMap.size() || repID2 >= _repeatMap.size())
return false;
// Find a repeat corresponding to a given location (left, right)
const EList<pair<index_t, index_t> >& repeatMap = _repeatMap[repID];
assert_lt(left, right);
pair<index_t, index_t> repeat(left, numeric_limits<index_t>::max());
index_t repeatIdx = repeatMap.bsearchLoBound(repeat);
assert_lt(repeatIdx, repeatMap.size());
if(right > repeatMap[repeatIdx].first)
return false;
index_t repeatIdx_ = repeatMap[repeatIdx].second;
assert_lt(repeatIdx_, _repeats.size());
const EList<RepeatAllele<index_t> >& alleles = _repeats[repeatIdx_].alleles;
index_t adjLeft = left, adjRight = right;
if(repeatIdx > 0) {
adjLeft -= repeatMap[repeatIdx-1].first;
adjRight -= repeatMap[repeatIdx-1].first;
}
// Find a repeat cooresponding to a given location (left2, right2)
const EList<pair<index_t, index_t> >& repeatMap2 = _repeatMap[repID2];
assert_lt(left2, right2);
pair<index_t, index_t> repeat2(left2, numeric_limits<index_t>::max());
index_t repeatIdx2 = repeatMap2.bsearchLoBound(repeat2);
assert_lt(repeatIdx2, repeatMap2.size());
if(right2 > repeatMap2[repeatIdx2].first)
return false;
index_t repeatIdx2_ = repeatMap2[repeatIdx2].second;
assert_lt(repeatIdx2_, _repeats.size());
const EList<RepeatAllele<index_t> >& alleles2 = _repeats[repeatIdx2_].alleles;
index_t adjLeft2 = left2, adjRight2 = right2;
if(repeatIdx2 > 0) {
adjLeft2 -= repeatMap2[repeatIdx2-1].first;
adjRight2 -= repeatMap2[repeatIdx2-1].first;
}
const EList<RepeatCoord<index_t> >& positions = _repeats[repeatIdx_].positions;
const EList<RepeatCoord<index_t> >& positions2 = _repeats[repeatIdx2_].positions;
index_t jsave = 0;
for(index_t i = 0; i < positions.size(); i++) {
const RepeatAllele<index_t>& allele = alleles[positions[i].alleleID];
if(!allele.compatible(adjLeft, adjRight))
continue;
index_t i_pos = positions[i].joinedOff + adjLeft;
for(index_t j = jsave; j < positions2.size(); j++) {
index_t j_pos = positions2[j].joinedOff + adjLeft2;
if(j_pos + dist < i_pos) {
jsave = j + 1;
continue;
}
if(i_pos + dist < j_pos)
break;
const RepeatAllele<index_t>& allele2 = alleles2[positions2[j].alleleID];
if(!allele2.compatible(adjLeft2, adjRight2))
continue;
common_positions.expand();
common_positions.back().first = positions[i];
if(positions[i].fw) {
common_positions.back().first.joinedOff += adjLeft;
common_positions.back().first.toff += adjLeft;
} else {
const index_t len = right - left;
assert_leq(adjLeft + len, _repeats[repeatIdx_].repLen);
index_t rc_adjLeft = _repeats[repeatIdx_].repLen - adjLeft - len;
common_positions.back().first.joinedOff += rc_adjLeft;
common_positions.back().first.toff += rc_adjLeft;
}
common_positions.back().second = positions2[j];
if(positions2[j].fw) {
common_positions.back().second.toff += adjLeft2;
common_positions.back().second.joinedOff += adjLeft2;
} else {
const index_t len = right2 - left2;
assert_leq(adjLeft2 + len, _repeats[repeatIdx2_].repLen);
index_t rc_adjLeft2 = _repeats[repeatIdx2_].repLen - adjLeft2 - len;
common_positions.back().second.joinedOff += rc_adjLeft2;
common_positions.back().second.toff += rc_adjLeft2;
}
if(common_positions.size() >= max_positions)
break;
}
if(common_positions.size() >= max_positions)
break;
}
return common_positions.size() > 0;
}
private:
pair<index_t, index_t> get_alt_range(const ALTDB<index_t>& altdb,
index_t left,
index_t right) const {
pair<index_t, index_t> alt_range;
ALT<index_t> cmp_alt;
cmp_alt.pos = left;
alt_range.first = alt_range.second = (index_t)altdb.alts().bsearchLoBound(cmp_alt);
for(; alt_range.second < altdb.alts().size(); alt_range.second++) {
const ALT<index_t>& alt = altdb.alts()[alt_range.second];
if(alt.left > right) break;
}
return alt_range;
}
private:
EList<Repeat<index_t> > _repeats;
ELList<pair<index_t, index_t> > _repeatMap; // pos to repeat id
};
#endif /*ifndef REPEAT_H_*/
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