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/******************************************************************************
* Copyright © 2009-2016 -- LIRMM/CNRS *
* (Laboratoire d'Informatique, de Robotique et de *
* Microélectronique de Montpellier / *
* Centre National de la Recherche Scientifique) *
* LIFL/INRIA *
* (Laboratoire d'Informatique Fondamentale de *
* Lille / Institut National de Recherche en *
* Informatique et Automatique) *
* LITIS *
* (Laboratoire d'Informatique, du Traitement de *
* l'Information et des Systèmes). *
* *
* Copyright © 2011-2016 -- IRB/INSERM *
* (Institut de Recherches en Biothérapie / *
* Institut National de la Santé et de la Recherche *
* Médicale). *
* *
* Copyright © 2015-2016 -- AxLR/SATT *
* (Lanquedoc Roussilon / *
* Societe d'Acceleration de Transfert de *
* Technologie). *
* *
* Programmeurs/Progammers: *
* Nicolas PHILIPPE <nphilippe.resear@gmail.com> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Jérôme Audoux <jerome.audoux@gmail.com> *
* with additional contribution for the packaging of: *
* Alban MANCHERON <alban.mancheron@lirmm.fr> *
* *
* Contact: CRAC list <crac-bugs@lists.gforge.inria.fr> *
* Paper: CRAC: An integrated RNA-Seq read analysis *
* Philippe N., Salson M., Commes T., Rivals E. *
* Genome Biology 2013; 14:R30. *
* *
* ------------------------------------------------------------------------- *
* *
* This File is part of the CRAC program. *
* *
* This program 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. This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
* *
******************************************************************************/
#include "BreakList.h"
#include <cassert>
// #include <iostream>
// using namespace std;
BreakList::BreakList(SupportBreak **breaks, size_t nb_breaks):vector<SupportBreak *>(nb_breaks, NULL) {
for (size_t i = 0; i < nb_breaks; i++) {
// cout << breaks[i] << endl;
(*this)[i] = breaks[i];
}
if (nb_breaks)
parameters = breaks[0]->getParameters();
}
/**
* @return the length between the breaks of index i and j
* @pre 0 <= i < size() && 0 <= j < size() && i != j
*/
size_t BreakList::getGapSize(size_t i, size_t j) const{
assert (0 <= i && i < size() && 0 <= j && j < size() && i != j);
if (j < i)
return getGapSize(j, i);
return (*this)[j]->getPositionStartBreak() - (*this)[i]->getPositionEndBreak() - 1;
}
size_t BreakList::getGapSize(size_t i) const{
return getGapSize(i, i+1);
}
size_t BreakList::getTotalBreakSize(size_t i, size_t j) const{
assert (0 <= i && i < size() && 0 <= j && j < size() && i != j);
if (j < i)
return getTotalBreakSize(j, i);
return (*this)[j]->getPositionEndBreak() - (*this)[i]->getPositionStartBreak() + 1;
}
size_t BreakList::getTotalBreakSize(size_t i) const{
return getTotalBreakSize(i, i+1);
}
bool BreakList::hasShortBreakSpan(size_t i, size_t j) const {
return getTotalBreakSize(i, j) <= parameters->max_nb_overlapping_breaks * ((*this)[i])->getThreshold();
}
bool BreakList::hasShortGapBetweenBreaks(size_t i, size_t j) const {
return getGapSize(i, j) <= parameters->max_bases_randomly_matched;
}
void BreakList::merge(size_t i, size_t j) {
assert (0 <= i && i < size() && 0 <= j && j < size() && i != j);
if (j < i)
merge(j, i);
else {
SupportBreak *first_break = (*this)[i];
SupportBreak *second_break = (*this)[j];
SupportBreak *final_break = new SupportBreak(*first_break, *second_break);
this->erase(this->begin() + j);
(*this)[i] = final_break;
delete first_break;
delete second_break;
}
}
void BreakList::merge(size_t i) {
assert (0 <= i && i < size()-1);
merge(i, i+1);
}
size_t BreakList::conditional_neighbor_merge(size_t i, std::function <bool(size_t, size_t)> f) {
if (i > 0 && f(i-1, i)) {
merge(i-1);
return i-1;
} else if (i < size() - 1 && f(i, i+1)) {
merge(i);
return i;
}
return ~0;
}
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