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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 "SNPInfo.h"
#include "libSSA/utils.h"
SNPInfo::SNPInfo(ChrPosition chrPos, uint position,
float score, bool is_duplicated,
char actual_nuc, char expected_nuc):
chrPos(chrPos), score(score),
is_duplicated(is_duplicated),
actual_nuc(actual_nuc),
expected_nuc(expected_nuc)
{
setPosition(position);
if (actual_nuc == 0) {
if (expected_nuc == 0) {
type = SNP_UNKNOWN;
} else {
type = SNP_DELETION;
}
} else {
if (expected_nuc == 0) {
type = SNP_INSERTION;
} else {
type = SNP_SUBSTITUTION;
}
}
}
SNPInfo::~SNPInfo() {
}
char SNPInfo::getActualNucleotide(int strand) {
if (getSNPType() == SNP_UNKNOWN || getSNPType() == SNP_DELETION)
return '?';
return (strand == 1) ? actual_nuc : complementDNA(actual_nuc);;
}
char SNPInfo::getExpectedNucleotide(int strand) {
if (getSNPType() == SNP_UNKNOWN || getSNPType() == SNP_INSERTION)
return '?';
return (strand == 1) ? expected_nuc : complementDNA(expected_nuc);
}
ChrPosition &SNPInfo::getChrPosition() {
return chrPos;
}
float SNPInfo::getScore() {
return score;
}
snp_type SNPInfo::getSNPType() {
return type;
}
bool SNPInfo::isDuplicated() {
return is_duplicated;
}
void SNPInfo::output(ostream &os) {
os << *this;
}
void SNPInfo::samOutput(ostream &os, int strand) {
os << "SNP:" << getScore() << ":" << getPosition(strand) << ":" << getChrPosition()
<< ":" << getExpectedNucleotide(strand) << ":" << getActualNucleotide(strand);
}
cigar_type SNPInfo::getCigarInfo() {
cigar_type cigar;
cigar.nb = 1;
cigar.type = 0; // Just initializing so that gcc is happy
if (getSNPType() == SNP_SUBSTITUTION) {
cigar.type = 'X';
} else if (getSNPType() == SNP_DELETION) {
cigar.type = 'D';
} else if (getSNPType() == SNP_INSERTION) {
cigar.type = 'I';
}
return cigar;
}
ostream &operator<<(ostream &os, SNPInfo& i) {
if (i.isDuplicated()){
os << "duplicate ";
}else{
os << "single ";
}
os << i.getChrPosition()
<< " pos_SNV="<<i.getPosition()
<< " ";
if (i.getSNPType() == SNP_UNKNOWN)
os << "?->?";
else {
if (i.getSNPType() == SNP_INSERTION)
os << "?";
else
os << i.getExpectedNucleotide() ;
os << "->";
if (i.getSNPType() == SNP_DELETION)
os << "?";
else
os << i.getActualNucleotide();
os << " score=" << i.getScore() ;
}
return os;
}
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