PileupReader.cpp

00001 #include <stdexcept>
00002 /*
00003  *  Copyright (C) 2010  Regents of the University of Michigan
00004  *
00005  *   This program is free software: you can redistribute it and/or modify
00006  *   it under the terms of the GNU General Public License as published by
00007  *   the Free Software Foundation, either version 3 of the License, or
00008  *   (at your option) any later version.
00009  *
00010  *   This program is distributed in the hope that it will be useful,
00011  *   but WITHOUT ANY WARRANTY; without even the implied warranty of
00012  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00013  *   GNU General Public License for more details.
00014  *
00015  *   You should have received a copy of the GNU General Public License
00016  *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
00017  */
00018 
00019 
00020 #include "PileupReader.h"
00021 
00022 bool ReadBase::set(SamRecord &samRecord, int basePosition)
00023 {
00024     throw std::logic_error("ReadBase::set unimplemented");
00025     _samRecord = &samRecord;
00026     return false;
00027 }
00028 
00029 bool SequenceCoverageReader::getBases(
00030     int referenceID,
00031     uint32_t position,
00032     std::vector<ReadBase> &readBases,
00033     bool &basesInserted)
00034 {
00035     throw std::logic_error("SequenceCoverageReader::getBases unimplemented");
00036     return true;
00037 }
00038 
00039 bool SequenceCoverageReader::getInsertedBases(
00040     int referenceID,
00041     uint32_t position,
00042     std::vector<ReadInsertion> &readInsertions
00043     )
00044 {
00045     abort();
00046     return true;
00047 }