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splice_site_new.cpp
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/*
* Copyright 2013, Daehwan Kim <[email protected]>
*
* This file is part of Bowtie 2.
*
* Bowtie 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.
*
* Bowtie 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include "edit.h"
#include "splice_site.h"
#include "aligner_report.h"
#include "aligner_result.h"
#if defined(NEW_PROB_MODEL)
#include "splice_site_mem.h"
#else
float donor_prob[4][donor_len] = {
{0.340f, 0.604f, 0.092f, 0.001f, 0.001f, 0.526f, 0.713f, 0.071f, 0.160f},
{0.363f, 0.129f, 0.033f, 0.001f, 0.001f, 0.028f, 0.076f, 0.055f, 0.165f},
{0.183f, 0.125f, 0.803f, 1.000f, 0.001f, 0.419f, 0.118f, 0.814f, 0.209f},
{0.114f, 0.142f, 0.073f, 0.001f, 1.000f, 0.025f, 0.093f, 0.059f, 0.462f}
};
float acceptor_prob[4][acceptor_len] = {
{0.090f, 0.084f, 0.075f, 0.068f, 0.076f, 0.080f, 0.097f, 0.092f, 0.076f, 0.078f, 0.237f, 0.042f, 1.000f, 0.001f, 0.239f},
{0.310f, 0.310f, 0.307f, 0.293f, 0.326f, 0.330f, 0.373f, 0.385f, 0.410f, 0.352f, 0.309f, 0.708f, 0.001f, 0.001f, 0.138f},
{0.125f, 0.115f, 0.106f, 0.104f, 0.110f, 0.113f, 0.113f, 0.085f, 0.066f, 0.064f, 0.212f, 0.003f, 0.001f, 1.000f, 0.520f},
{0.463f, 0.440f, 0.470f, 0.494f, 0.471f, 0.463f, 0.408f, 0.429f, 0.445f, 0.504f, 0.240f, 0.246f, 0.001f, 0.001f, 0.104f}
};
float donor_prob_sum[1 << (donor_len << 1)];
float acceptor_prob_sum1[1 << (acceptor_len1 << 1)];
float acceptor_prob_sum2[1 << (acceptor_len2 << 1)];
#endif
void init_junction_prob()
{
#if !defined(NEW_PROB_MODEL)
for(size_t i = 0; i < donor_len; i++) {
ASSERT_ONLY(float sum = 0.0f);
for(size_t j = 0; j < 4; j++) {
float prob = donor_prob[j][i];
assert_gt(prob, 0.0f);
ASSERT_ONLY(sum += prob);
donor_prob[j][i] = log(prob / background_prob[j]);
}
assert_range(0.9f, 1.05f, sum);
}
for(size_t i = 0; i < acceptor_len; i++) {
ASSERT_ONLY(float sum = 0.0f);
for(size_t j = 0; j < 4; j++) {
float prob = acceptor_prob[j][i];
assert_gt(prob, 0.0f);
ASSERT_ONLY(sum += prob);
acceptor_prob[j][i] = log(prob / background_prob[j]);
}
assert_range(0.9f, 1.05f, sum);
}
const size_t donor_elms = 1 << (donor_len << 1);
for(size_t i = 0; i < donor_elms; i++) {
float sum = 0.0f;
for(size_t j = 0; j < donor_len; j++) {
int base = (i >> (j << 1)) & 0x3;
sum += donor_prob[base][donor_len - j - 1];
}
donor_prob_sum[i] = exp(-sum);
}
const size_t acceptor_elms1 = 1 << (acceptor_len1 << 1);
for(size_t i = 0; i < acceptor_elms1; i++) {
float sum = 0.0f;
for(size_t j = 0; j < acceptor_len1; j++) {
int base = (i >> (j << 1)) & 0x3;
sum += acceptor_prob[base][acceptor_len1 - j - 1];
}
acceptor_prob_sum1[i] = exp(-sum);
}
const size_t acceptor_elms2 = 1 << (acceptor_len2 << 1);
for(size_t i = 0; i < acceptor_elms2; i++) {
float sum = 0.0f;
for(size_t j = 0; j < acceptor_len2; j++) {
int base = (i >> (j << 1)) & 0x3;
sum += acceptor_prob[base][acceptor_len - j - 1];
}
acceptor_prob_sum2[i] = exp(-sum);
}
#endif
}
ostream& operator<<(ostream& out, const SpliceSite& s)
{
out << s.ref() << "\t"
<< s.left() << "\t"
<< s.right() << "\t"
<< (s.fw() ? "+" : "-") << endl;
return out;
}
#if defined(SPLIT_DB)
static const uint64_t ref_segment_size = 1 << 24;
SpliceSiteDB::SpliceSiteDB(
const BitPairReference& refs,
const EList<string>& refnames,
bool threadSafe,
bool write,
bool read) :
_numRefs(refs.numRefs()),
_refnames(refnames),
_write(write),
_read(read),
_threadSafe(threadSafe),
_empty(true)
{
assert_gt(_numRefs, 0);
assert_eq(_numRefs, _refnames.size());
for(uint64_t i = 0; i < _numRefs; i++) {
uint64_t reflen = refs.approxLen(i);
assert_gt(reflen, 0);
uint64_t numsegs = (reflen + ref_segment_size - 1) / ref_segment_size;
assert_gt(numsegs, 0);
_fwIndex.expand();
_bwIndex.expand();
for(uint64_t j = 0; j < numsegs; j++) {
_fwIndex.back().push_back(new RedBlack<SpliceSitePos, uint32_t>(16 << 10, CA_CAT));
_bwIndex.back().push_back(new RedBlack<SpliceSitePos, uint32_t>(16 << 10, CA_CAT));
}
_pool.expand();
_pool.back().resize(numsegs);
_spliceSites.expand();
_spliceSites.back().resize(numsegs);
_mutex.expand();
for(uint64_t j = 0; j < numsegs; j++) {
_mutex.back().push_back(MUTEX_T());
}
}
donorstr.resize(donor_exonic_len + donor_intronic_len);
acceptorstr.resize(acceptor_intronic_len + acceptor_exonic_len);
}
SpliceSiteDB::~SpliceSiteDB() {
assert_eq(_fwIndex.size(), _bwIndex.size());
assert_eq(_fwIndex.size(), _pool.size());
for(uint64_t i = 0; i < _numRefs; i++) {
assert_eq(_fwIndex[i].size(), _bwIndex[i].size());
for(uint64_t j = 0; j < _fwIndex[i].size(); j++) {
delete _fwIndex[i][j];
delete _bwIndex[i][j];
}
_fwIndex[i].clear();
_bwIndex[i].clear();
ELList<Pool*>& pool = _pool[i];
for(size_t j = 0; j < pool.size(); j++) {
for(size_t k = 0; k < pool[j].size(); k++) {
delete pool[j][k];
}
}
}
}
#if 0
size_t SpliceSiteDB::size(uint64_t ref) const {
if(!_read) return 0;
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
assert_lt(ref, _fwIndex.size());
assert_eq(_fwIndex.size(), _bwIndex.size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref]), _threadSafe && _write);
return _fwIndex.size();
}
bool SpliceSiteDB::empty(uint64_t ref) const {
return size(ref) == 0;
}
#endif
bool SpliceSiteDB::addSpliceSite(
const Read& rd,
const AlnRes& rs,
uint32_t minAnchorLen)
{
if(!_write) return false;
if(rs.trimmed5p(true) + rs.trimmed3p(true) > 0) return false;
_empty = false;
Coord coord = rs.refcoord();
uint64_t ref = coord.ref();
assert_lt(ref, _numRefs);
const EList<Edit>& edits = rs.ned();
if(!coord.orient()) {
Edit::invertPoss(const_cast<EList<Edit>&>(edits), rd.length(), false);
}
SpliceSitePos ssp;
uint32_t refoff = coord.off();
uint32_t leftAnchorLen = 0, rightAnchorLen = 0;
size_t eidx = 0;
size_t last_eidx = 0;
for(size_t i = 0; i < rd.length(); i++, refoff++) {
while(eidx < edits.size() && edits[eidx].pos == i) {
if(edits[eidx].isReadGap()) {
refoff++;
} else if(edits[eidx].isRefGap()) {
assert_gt(refoff, 0);
refoff--;
}
if(edits[eidx].isSpliced()) {
assert_gt(refoff, 0);
if(ssp.inited()) {
assert(edits[last_eidx].isSpliced());
assert_lt(edits[last_eidx].pos, edits[eidx].pos);
rightAnchorLen = edits[eidx].pos - edits[last_eidx].pos;
if(leftAnchorLen >= minAnchorLen && rightAnchorLen >= minAnchorLen) {
bool added = false;
uint64_t ref_seg = ssp.left() / ref_segment_size;
uint64_t ref_seg2 = ssp.right() / ref_segment_size;
assert_leq(ref_seg, ref_seg2);
assert_lt(ref, _mutex.size());
assert_lt(ref_seg, _mutex[ref].size());
assert_lt(ref_seg2, _mutex[ref].size());
ThreadSafe t(&_mutex[ref][ref_seg], _threadSafe && _write);
ThreadSafe t2(&_mutex[ref][ref_seg2], _threadSafe && _write && ref_seg != ref_seg2);
assert_lt(ref, _fwIndex.size());
assert_lt(ref_seg, _fwIndex[ref].size());
assert(_fwIndex[ref][ref_seg] != NULL);
Node *cur = _fwIndex[ref][ref_seg]->add(pool(ref, ref_seg), ssp, &added);
if(added) {
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
_spliceSites[ref][ref_seg].expand();
_spliceSites[ref][ref_seg].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref][ref_seg].back()._readid = rd.rdid;
assert(cur != NULL);
cur->payload = _spliceSites[ref][ref_seg].size() - 1;
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
assert_lt(ref, _bwIndex.size());
assert_lt(ref_seg2, _bwIndex[ref].size());
assert(_bwIndex[ref][ref_seg2] != NULL);
cur = _bwIndex[ref][ref_seg2]->add(pool(ref, ref_seg2), rssp, &added);
assert(added);
assert(cur != NULL);
if(ref_seg != ref_seg2) {
_spliceSites[ref][ref_seg2].expand();
_spliceSites[ref][ref_seg2].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref][ref_seg2].back()._readid = rd.rdid;
}
cur->payload = _spliceSites[ref][ref_seg2].size() - 1;
} else {
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
assert_lt(cur->payload, _spliceSites[ref][ref_seg].size());
if(rd.rdid < _spliceSites[ref][ref_seg][cur->payload]._readid) {
_spliceSites[ref][ref_seg][cur->payload]._readid = rd.rdid;
}
if(ref_seg != ref_seg2) {
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
cur = _bwIndex[ref][ref_seg2]->add(pool(ref, ref_seg2), rssp, &added);
assert(cur != NULL);
assert(!added);
if(rd.rdid < _spliceSites[ref][ref_seg2][cur->payload]._readid) {
_spliceSites[ref][ref_seg2][cur->payload]._readid = rd.rdid;
}
}
}
}
leftAnchorLen = rightAnchorLen;
rightAnchorLen = 0;
} else {
leftAnchorLen = edits[eidx].pos;
}
bool fw = (edits[eidx].splDir == EDIT_SPL_FW || edits[eidx].splDir == EDIT_SPL_UNKNOWN);
bool canonical = (edits[eidx].splDir != EDIT_SPL_UNKNOWN);
ssp.init(coord.ref(), refoff - 1, refoff + edits[eidx].splLen, fw, canonical);
refoff += edits[eidx].splLen;
last_eidx = eidx;
}
eidx++;
}
}
if(ssp.inited()) {
assert(edits[last_eidx].isSpliced());
assert_lt(edits[last_eidx].pos, rd.length());
rightAnchorLen = rd.length() - edits[last_eidx].pos;
if(leftAnchorLen >= minAnchorLen && rightAnchorLen >= minAnchorLen) {
bool added = false;
uint64_t ref_seg = ssp.left() / ref_segment_size;
uint64_t ref_seg2 = ssp.right() / ref_segment_size;
assert_leq(ref_seg, ref_seg2);
assert_lt(ref, _mutex.size());
assert_lt(ref_seg, _mutex[ref].size());
assert_lt(ref_seg2, _mutex[ref].size());
ThreadSafe t(&_mutex[ref][ref_seg], _threadSafe && _write);
ThreadSafe t2(&_mutex[ref][ref_seg2], _threadSafe && _write && ref_seg != ref_seg2);
assert_lt(ref, _fwIndex.size());
assert_lt(ref_seg, _fwIndex[ref].size());
assert(_fwIndex[ref][ref_seg] != NULL);
Node *cur = _fwIndex[ref][ref_seg]->add(pool(ref, ref_seg), ssp, &added);
if(added) {
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
_spliceSites[ref][ref_seg].expand();
_spliceSites[ref][ref_seg].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref][ref_seg].back()._readid = rd.rdid;
assert(cur != NULL);
cur->payload = _spliceSites[ref][ref_seg].size() - 1;
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
assert_lt(ref, _bwIndex.size());
assert_lt(ref_seg2, _bwIndex[ref].size());
assert(_bwIndex[ref][ref_seg2] != NULL);
cur = _bwIndex[ref][ref_seg2]->add(pool(ref, ref_seg2), rssp, &added);
assert(added);
assert(cur != NULL);
if(ref_seg != ref_seg2) {
_spliceSites[ref][ref_seg2].expand();
_spliceSites[ref][ref_seg2].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref][ref_seg2].back()._readid = rd.rdid;
}
cur->payload = _spliceSites[ref][ref_seg2].size() - 1;
} else {
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
assert_lt(cur->payload, _spliceSites[ref][ref_seg].size());
if(rd.rdid < _spliceSites[ref][ref_seg][cur->payload]._readid) {
_spliceSites[ref][ref_seg][cur->payload]._readid = rd.rdid;
}
if(ref_seg != ref_seg2) {
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
cur = _bwIndex[ref][ref_seg2]->add(pool(ref, ref_seg2), rssp, &added);
assert(cur != NULL);
assert(!added);
if(rd.rdid < _spliceSites[ref][ref_seg2][cur->payload]._readid) {
_spliceSites[ref][ref_seg2][cur->payload]._readid = rd.rdid;
}
}
}
}
}
if(!coord.orient()) {
Edit::invertPoss(const_cast<EList<Edit>&>(edits), rd.length(), false);
}
return true;
}
bool SpliceSiteDB::getSpliceSite(SpliceSite& ss) const
{
if(!_read) return false;
uint64_t ref = ss.ref();
uint64_t ref_seg = ss.left() / ref_segment_size;
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
assert_lt(ref_seg, _mutex[ref].size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref][ref_seg]), _threadSafe && _write);
assert_lt(ref, _fwIndex.size());
assert_lt(ref_seg, _fwIndex[ref].size());
assert(_fwIndex[ref][ref_seg] != NULL);
const Node *cur = _fwIndex[ref][ref_seg]->lookup(ss);
if(cur == NULL) return false;
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
ss = _spliceSites[ref][ref_seg][cur->payload];
return true;
}
void SpliceSiteDB::getLeftSpliceSites(uint32_t ref, uint32_t left, uint32_t range, EList<SpliceSite>& spliceSites) const
{
if(!_read) return;
spliceSites.clear();
assert_lt(ref, _numRefs);
assert_gt(range, 0);
assert_geq(left + 1, range);
uint32_t begin = left + 1 - range, end = left;
for(uint32_t i = begin / ref_segment_size; i <= end / ref_segment_size; i++) {
assert_lt(ref, _mutex.size());
assert_lt(i, _mutex[ref].size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref][i]), _threadSafe && _write);
assert_lt(ref, _bwIndex.size());
assert_lt(i, _bwIndex[ref].size());
assert(_bwIndex[ref][i] != NULL);
const Node *cur = _bwIndex[ref][i]->root();
if(cur != NULL) getSpliceSites_recur(cur, _spliceSites[ref][i], ref, begin, end, spliceSites);
}
}
void SpliceSiteDB::getRightSpliceSites(uint32_t ref, uint32_t right, uint32_t range, EList<SpliceSite>& spliceSites) const
{
if(!_read) return;
spliceSites.clear();
assert_lt(ref, _numRefs);
assert_gt(range, 0);
assert_gt(right + range, range);
uint32_t begin = right, end = right + range - 1;
for(uint32_t i = begin / ref_segment_size; i <= end / ref_segment_size; i++) {
assert_lt(ref, _mutex.size());
assert_lt(i, _mutex[ref].size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref][i]), _threadSafe && _write);
assert_lt(ref, _fwIndex.size());
assert_lt(i, _fwIndex[ref].size());
assert(_fwIndex[ref][i] != NULL);
const Node *cur = _fwIndex[ref][i]->root();
if(cur != NULL) getSpliceSites_recur(cur, _spliceSites[ref][i], ref, begin, end, spliceSites);
}
}
void SpliceSiteDB::getSpliceSites_recur(
const RedBlackNode<SpliceSitePos, uint32_t> *node,
const EList<SpliceSite>& spliceSites_db,
uint32_t ref,
uint32_t left,
uint32_t right,
EList<SpliceSite>& spliceSites) const
{
assert(node != NULL);
bool goleft = true, goright = true;
if((node->key.ref() > ref) ||
(node->key.ref() == ref && node->key.left() > right)) {
goright = false;
}
if((node->key.ref() < ref) ||
(node->key.ref() == ref && node->key.left() < left)) {
goleft = false;
}
if(goleft && node->left != NULL) {
getSpliceSites_recur(
node->left,
spliceSites_db,
ref,
left,
right,
spliceSites);
}
if(node->key.ref() == ref &&
node->key.left() >= left && node->key.left() <= right) {
assert_lt(node->payload, spliceSites_db.size());
#ifndef NDEBUG
const SpliceSite& ss = spliceSites_db[node->payload];
assert_eq(ss.ref(), node->key.ref());
assert(ss.left() == node->key.left() ||
ss.right() == node->key.left());
#endif
spliceSites.push_back(spliceSites_db[node->payload]);
}
if(goright && node->right != NULL) {
getSpliceSites_recur(
node->right,
spliceSites_db,
ref,
left,
right,
spliceSites);
}
}
void SpliceSiteDB::print(ofstream& out)
{
EList<SpliceSitePos> ss_list;
for(uint64_t i = 0; i < _fwIndex.size(); i++) {
for(uint64_t j = 0; j < _fwIndex[i].size(); j++) {
assert(_fwIndex[i][j] != NULL);
const Node *root = _fwIndex[i][j]->root();
if(root != NULL) print_recur(root, out, ss_list);
}
}
print_impl(out, ss_list);
}
void SpliceSiteDB::print_recur(
const RedBlackNode<SpliceSitePos, uint32_t> *node,
ofstream& out,
EList<SpliceSitePos>& ss_list)
{
if(node == NULL) return;
print_recur(node->left, out, ss_list);
print_impl(out, ss_list, &(node->key));
print_recur(node->right, out, ss_list);
}
void SpliceSiteDB::print_impl(
ofstream& out,
EList<SpliceSitePos>& ss_list,
const SpliceSitePos* ss)
{
size_t i = 0;
while(i < ss_list.size()) {
const SpliceSitePos& tmp_ss = ss_list[i];
bool do_print = true;
if(ss != NULL) {
if(tmp_ss.ref() == ss->ref()) {
assert_leq(tmp_ss.left(), ss->left());
if(ss->left() < tmp_ss.left() + 10) {
do_print = false;
if((int)ss->left() - (int)tmp_ss.left() == (int)ss->right() - (int)tmp_ss.right()) {
if(!tmp_ss.canonical() && ss->canonical()) {
ss_list.erase(i);
ss_list.push_back(*ss);
}
return;
}
}
}
}
if(!do_print) {
i++;
continue;
}
assert_lt(tmp_ss.ref(), _refnames.size());
out << _refnames[tmp_ss.ref()] << "\t"
<< tmp_ss.left() << "\t"
<< tmp_ss.right() << "\t"
<< (tmp_ss.canonical() ? (tmp_ss.fw() ? "+" : "-") : ".") << endl;
ss_list.erase(i);
}
if(ss != NULL) ss_list.push_back(*ss);
}
void SpliceSiteDB::read(ifstream& in, bool novel)
{
_empty = false;
assert_eq(_numRefs, _refnames.size());
while(!in.eof()) {
string refname;
uint32_t left = 0, right = 0;
char fw = 0;
in >> refname >> left >> right >> fw;
uint32_t ref = 0;
for(; ref < _refnames.size(); ref++) {
if(_refnames[ref] == refname) break;
}
if(ref >= _numRefs) continue;
uint64_t ref_seg = left / ref_segment_size;
assert_lt(ref, _spliceSites.size());
assert_lt(ref_seg, _spliceSites[ref].size());
_spliceSites[ref][ref_seg].expand();
_spliceSites[ref][ref_seg].back().init(ref, left, right, fw == '+' || fw == '.', fw != '.');
_spliceSites[ref][ref_seg].back()._fromfile = true;
assert_gt(_spliceSites[ref][ref_seg].size(), 0);
bool added = false;
assert_lt(ref, _fwIndex.size());
assert_lt(ref_seg, _fwIndex[ref].size());
assert(_fwIndex[ref][ref_seg] != NULL);
Node *cur = _fwIndex[ref][ref_seg]->add(pool(ref, ref_seg), _spliceSites[ref][ref_seg].back(), &added);
assert(added);
assert(cur != NULL);
cur->payload = _spliceSites[ref][ref_seg].size() - 1;
added = false;
uint64_t ref_seg2 = right / ref_segment_size;
SpliceSitePos rssp(ref, right, left, fw == '+' || fw == '.', fw != '.');
assert_lt(ref, _bwIndex.size());
assert_lt(ref_seg2, _bwIndex.size());
assert(_bwIndex[ref][ref_seg2] != NULL);
cur = _bwIndex[ref][ref_seg2]->add(pool(ref, ref_seg2), rssp, &added);
assert(added);
assert(cur != NULL);
if(ref_seg != ref_seg2) {
_spliceSites[ref][ref_seg2].expand();
_spliceSites[ref][ref_seg2].back().init(ref, left, right, fw == '+' || fw == '.', fw != '.');
_spliceSites[ref][ref_seg2].back()._fromfile = true;
}
cur->payload = _spliceSites[ref][ref_seg2].size() - 1;
}
}
Pool& SpliceSiteDB::pool(uint64_t ref, uint64_t ref_seg) {
assert_lt(ref, _numRefs);
assert_lt(ref, _pool.size());
assert_lt(ref_seg, _pool[ref].size());
if(_pool[ref][ref_seg].size() <= 0 || _pool[ref][ref_seg].back()->full()) {
_pool[ref][ref_seg].push_back(new Pool(1 << 18 /* 256KB */, 16 << 10 /* 16KB */, CA_CAT));
}
assert(_pool[ref][ref_seg].back() != NULL);
return *_pool[ref][ref_seg].back();
}
#else
SpliceSiteDB::SpliceSiteDB(
const BitPairReference& refs,
const EList<string>& refnames,
bool threadSafe,
bool write,
bool read) :
_numRefs(refs.numRefs()),
_refnames(refnames),
_write(write),
_read(read),
_threadSafe(threadSafe),
_empty(true)
{
assert_gt(_numRefs, 0);
assert_eq(_numRefs, _refnames.size());
for(uint64_t i = 0; i < _numRefs; i++) {
_fwIndex.push_back(new RedBlack<SpliceSitePos, uint32_t>(16 << 10, CA_CAT));
_bwIndex.push_back(new RedBlack<SpliceSitePos, uint32_t>(16 << 10, CA_CAT));
_pool.expand();
_spliceSites.expand();
_mutex.push_back(MUTEX_T());
}
donorstr.resize(donor_exonic_len + donor_intronic_len);
acceptorstr.resize(acceptor_intronic_len + acceptor_exonic_len);
}
SpliceSiteDB::~SpliceSiteDB() {
assert_eq(_fwIndex.size(), _bwIndex.size());
assert_eq(_fwIndex.size(), _pool.size());
for(uint64_t i = 0; i < _numRefs; i++) {
delete _fwIndex[i];
delete _bwIndex[i];
EList<Pool*>& pool = _pool[i];
for(size_t j = 0; j < pool.size(); j++) {
delete pool[j];
}
}
}
size_t SpliceSiteDB::size(uint64_t ref) const {
if(!_read) return 0;
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
assert_lt(ref, _fwIndex.size());
assert_eq(_fwIndex.size(), _bwIndex.size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref]), _threadSafe && _write);
return _fwIndex.size();
}
bool SpliceSiteDB::empty(uint64_t ref) const {
return size(ref) == 0;
}
bool SpliceSiteDB::addSpliceSite(
const Read& rd,
const AlnRes& rs,
uint32_t minAnchorLen)
{
if(!_write) return false;
if(rs.trimmed5p(true) + rs.trimmed3p(true) > 0) return false;
_empty = false;
Coord coord = rs.refcoord();
uint64_t ref = coord.ref();
assert_lt(ref, _numRefs);
const EList<Edit>& edits = rs.ned();
if(!coord.orient()) {
Edit::invertPoss(const_cast<EList<Edit>&>(edits), rd.length(), false);
}
SpliceSitePos ssp;
uint32_t refoff = coord.off();
uint32_t leftAnchorLen = 0, rightAnchorLen = 0;
size_t eidx = 0;
size_t last_eidx = 0;
uint32_t mm = 0;
for(size_t i = 0; i < rd.length(); i++, refoff++) {
while(eidx < edits.size() && edits[eidx].pos == i) {
if(edits[eidx].isReadGap()) {
refoff++;
} else if(edits[eidx].isRefGap()) {
assert_gt(refoff, 0);
refoff--;
}
if(edits[eidx].isGap() || edits[eidx].isMismatch()) mm++;
if(edits[eidx].isSpliced()) {
assert_gt(refoff, 0);
if(ssp.inited()) {
assert(edits[last_eidx].isSpliced());
assert_lt(edits[last_eidx].pos, edits[eidx].pos);
rightAnchorLen = edits[eidx].pos - edits[last_eidx].pos;
uint32_t minLeftAnchorLen = minAnchorLen + mm * 2 + (edits[eidx].splDir == EDIT_SPL_UNKNOWN ? 6 : 0);
uint32_t mm2 = 0;
for(size_t j = eidx + 1; j < edits.size(); j++) {
if(edits[j].isGap() || edits[j].isMismatch()) mm2++;
}
uint32_t minRightAnchorLen = minAnchorLen + mm2 * 2 + (edits[eidx].splDir == EDIT_SPL_UNKNOWN ? 6 : 0);
if(leftAnchorLen >= minLeftAnchorLen && rightAnchorLen >= minRightAnchorLen) {
bool added = false;
assert_lt(ref, _mutex.size());
ThreadSafe t(&_mutex[ref], _threadSafe && _write);
assert_lt(ref, _fwIndex.size());
assert(_fwIndex[ref] != NULL);
Node *cur = _fwIndex[ref]->add(pool(ref), ssp, &added);
if(added) {
assert_lt(ref, _spliceSites.size());
_spliceSites[ref].expand();
_spliceSites[ref].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref].back()._readid = rd.rdid;
_spliceSites[ref].back()._leftext = leftAnchorLen;
_spliceSites[ref].back()._rightext = rightAnchorLen;
_spliceSites[ref].back()._numreads = 1;
assert(cur != NULL);
cur->payload = _spliceSites[ref].size() - 1;
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
assert_lt(ref, _bwIndex.size());
assert(_bwIndex[ref] != NULL);
cur = _bwIndex[ref]->add(pool(ref), rssp, &added);
assert(added);
assert(cur != NULL);
cur->payload = _spliceSites[ref].size() - 1;
assert_eq(_fwIndex[ref]->size(), _bwIndex[ref]->size());
} else {
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
assert_lt(cur->payload, _spliceSites[ref].size());
if(leftAnchorLen > _spliceSites[ref][cur->payload]._leftext) _spliceSites[ref][cur->payload]._leftext = leftAnchorLen;
if(rightAnchorLen > _spliceSites[ref][cur->payload]._rightext) _spliceSites[ref][cur->payload]._rightext = rightAnchorLen;
_spliceSites[ref][cur->payload]._numreads += 1;
if(rd.rdid < _spliceSites[ref][cur->payload]._readid) {
_spliceSites[ref][cur->payload]._readid = rd.rdid;
}
}
}
leftAnchorLen = rightAnchorLen;
rightAnchorLen = 0;
} else {
leftAnchorLen = edits[eidx].pos;
}
bool fw = (edits[eidx].splDir == EDIT_SPL_FW || edits[eidx].splDir == EDIT_SPL_UNKNOWN);
bool canonical = (edits[eidx].splDir != EDIT_SPL_UNKNOWN);
ssp.init(coord.ref(), refoff - 1, refoff + edits[eidx].splLen, fw, canonical);
refoff += edits[eidx].splLen;
last_eidx = eidx;
}
eidx++;
}
}
if(ssp.inited()) {
assert(edits[last_eidx].isSpliced());
assert_lt(edits[last_eidx].pos, rd.length());
rightAnchorLen = rd.length() - edits[last_eidx].pos;
uint32_t minLeftAnchorLen = minAnchorLen + mm * 2 + (edits[last_eidx].splDir == EDIT_SPL_UNKNOWN ? 6 : 0);
uint32_t mm2 = 0;
for(size_t j = last_eidx + 1; j < edits.size(); j++) {
if(edits[j].isGap() || edits[j].isMismatch()) mm2++;
}
uint32_t minRightAnchorLen = minAnchorLen + mm2 * 2 + (edits[last_eidx].splDir == EDIT_SPL_UNKNOWN ? 6 : 0);
if(leftAnchorLen >= minLeftAnchorLen && rightAnchorLen >= minRightAnchorLen) {
bool added = false;
assert_lt(ref, _mutex.size());
ThreadSafe t(&_mutex[ref], _threadSafe && _write);
assert_lt(ref, _fwIndex.size());
assert(_fwIndex[ref] != NULL);
Node *cur = _fwIndex[ref]->add(pool(ref), ssp, &added);
if(added) {
assert_lt(ref, _spliceSites.size());
_spliceSites[ref].expand();
_spliceSites[ref].back().init(ssp.ref(), ssp.left(), ssp.right(), ssp.fw(), ssp.canonical());
_spliceSites[ref].back()._readid = rd.rdid;
_spliceSites[ref].back()._leftext = leftAnchorLen;
_spliceSites[ref].back()._rightext = rightAnchorLen;
_spliceSites[ref].back()._numreads = 1;
assert(cur != NULL);
cur->payload = _spliceSites[ref].size() - 1;
SpliceSitePos rssp(ssp.ref(), ssp.right(), ssp.left(), ssp.fw(), ssp.canonical());
assert_lt(ref, _bwIndex.size());
assert(_bwIndex[ref] != NULL);
cur = _bwIndex[ref]->add(pool(ref), rssp, &added);
assert(added);
assert(cur != NULL);
cur->payload = _spliceSites[ref].size() - 1;
assert_eq(_fwIndex[ref]->size(), _bwIndex[ref]->size());
} else {
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
assert_lt(cur->payload, _spliceSites[ref].size());
if(leftAnchorLen > _spliceSites[ref][cur->payload]._leftext) _spliceSites[ref][cur->payload]._leftext = leftAnchorLen;
if(rightAnchorLen > _spliceSites[ref][cur->payload]._rightext) _spliceSites[ref][cur->payload]._rightext = rightAnchorLen;
_spliceSites[ref][cur->payload]._numreads += 1;
if(rd.rdid < _spliceSites[ref][cur->payload]._readid) {
_spliceSites[ref][cur->payload]._readid = rd.rdid;
}
}
}
}
if(!coord.orient()) {
Edit::invertPoss(const_cast<EList<Edit>&>(edits), rd.length(), false);
}
return true;
}
bool SpliceSiteDB::getSpliceSite(SpliceSite& ss) const
{
if(!_read) return false;
uint64_t ref = ss.ref();
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref]), _threadSafe && _write);
assert_lt(ref, _fwIndex.size());
assert(_fwIndex[ref] != NULL);
const Node *cur = _fwIndex[ref]->lookup(ss);
if(cur == NULL) return false;
assert(cur != NULL);
assert_lt(ref, _spliceSites.size());
ss = _spliceSites[ref][cur->payload];
return true;
}
void SpliceSiteDB::getLeftSpliceSites(uint32_t ref, uint32_t left, uint32_t range, EList<SpliceSite>& spliceSites) const
{
if(!_read) return;
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref]), _threadSafe && _write);
assert_gt(range, 0);
assert_geq(left + 1, range);
assert_lt(ref, _bwIndex.size());
assert(_bwIndex[ref] != NULL);
const Node *cur = _bwIndex[ref]->root();
if(cur != NULL) getSpliceSites_recur(cur, ref, left + 1 - range, left, spliceSites);
}
void SpliceSiteDB::getRightSpliceSites(uint32_t ref, uint32_t right, uint32_t range, EList<SpliceSite>& spliceSites) const
{
if(!_read) return;
assert_lt(ref, _numRefs);
assert_lt(ref, _mutex.size());
ThreadSafe t(const_cast<MUTEX_T*>(&_mutex[ref]), _threadSafe && _write);
assert_gt(range, 0);
assert_gt(right + range, range);
assert_lt(ref, _fwIndex.size());
assert(_fwIndex[ref] != NULL);
const Node *cur = _fwIndex[ref]->root();
if(cur != NULL) getSpliceSites_recur(cur, ref, right, right + range - 1, spliceSites);
}
void SpliceSiteDB::getSpliceSites_recur(
const RedBlackNode<SpliceSitePos, uint32_t> *node,
uint32_t ref,
uint32_t left,
uint32_t right,
EList<SpliceSite>& spliceSites) const
{
assert(node != NULL);
bool goleft = true, goright = true;
if((node->key.ref() > ref) ||
(node->key.ref() == ref && node->key.left() > right)) {
goright = false;
}
if((node->key.ref() < ref) ||
(node->key.ref() == ref && node->key.left() < left)) {
goleft = false;
}
if(goleft && node->left != NULL) {
getSpliceSites_recur(
node->left,
ref,
left,
right,
spliceSites);
}
if(node->key.ref() == ref &&
node->key.left() >= left && node->key.left() <= right) {
assert_lt(ref, _spliceSites.size());
assert_lt(node->payload, _spliceSites[ref].size());
#ifndef NDEBUG
const SpliceSite& ss = _spliceSites[ref][node->payload];
assert_eq(ss.ref(), node->key.ref());
assert(ss.left() == node->key.left() ||
ss.right() == node->key.left());
#endif
spliceSites.push_back(_spliceSites[ref][node->payload]);
}
if(goright && node->right != NULL) {
getSpliceSites_recur(
node->right,
ref,
left,
right,
spliceSites);
}
}
void calculate_splicesite_read_dist_impl(const RedBlackNode<SpliceSitePos, uint32_t> *node,
const EList<SpliceSite> &spliceSites,
EList<int64_t>& splicesite_read_dist) {
if(node == NULL) return;
calculate_splicesite_read_dist_impl(node->left, spliceSites, splicesite_read_dist);
assert_lt(node->payload, spliceSites.size());
const SpliceSite& ss = spliceSites[node->payload];
if(ss.numreads() < splicesite_read_dist.size())
splicesite_read_dist[ss.numreads()] += 1;
else
splicesite_read_dist.back() += 1;
calculate_splicesite_read_dist_impl(node->right, spliceSites, splicesite_read_dist);
}
uint32_t calculate_splicesite_read_dist(const EList<RedBlack<SpliceSitePos, uint32_t>* >& fwIndex,
const ELList<SpliceSite> &spliceSites,
EList<int64_t>& splicesite_read_dist) {
for(size_t i = 0; i < fwIndex.size(); i++) {
assert(fwIndex[i] != NULL);
const RedBlackNode<SpliceSitePos, uint32_t> *root = fwIndex[i]->root();
assert_lt(i, spliceSites.size());
if(root != NULL) calculate_splicesite_read_dist_impl(root, spliceSites[i], splicesite_read_dist);
}
for(size_t i = 1; i < splicesite_read_dist.size(); i++) {
splicesite_read_dist[i] += splicesite_read_dist[i-1];
}
for(size_t i = 0; i < splicesite_read_dist.size(); i++) {
float cmf_i = float(splicesite_read_dist[i]) / splicesite_read_dist.back();
if(cmf_i > 0.7)
return i;
}
return 0;
}
void SpliceSiteDB::print(ofstream& out)
{
EList<int64_t> splicesite_read_dist;
for(size_t i = 0; i < 100; i++) {
splicesite_read_dist.push_back(0);
}
uint32_t numreads_cutoff = calculate_splicesite_read_dist(_fwIndex, _spliceSites, splicesite_read_dist);
EList<SpliceSite> ss_list;
for(size_t i = 0; i < _fwIndex.size(); i++) {
assert(_fwIndex[i] != NULL);
const Node *root = _fwIndex[i]->root();
if(root != NULL) print_recur(root, out, numreads_cutoff, ss_list);
}
print_impl(out, ss_list);
}
void SpliceSiteDB::print_recur(
const RedBlackNode<SpliceSitePos, uint32_t> *node,
ofstream& out,
const uint32_t numreads_cutoff,
EList<SpliceSite>& ss_list)
{
if(node == NULL) return;
print_recur(node->left, out, numreads_cutoff, ss_list);
const SpliceSitePos& ssp = node->key;
assert_lt(ssp.ref(), _spliceSites.size());
assert_lt(node->payload, _spliceSites[ssp.ref()].size());
const SpliceSite& ss = _spliceSites[ssp.ref()][node->payload];
if(ss.numreads() >= numreads_cutoff) print_impl(out, ss_list, &ss);
print_recur(node->right, out, numreads_cutoff, ss_list);
}