88 lines
2.6 KiB
C++
88 lines
2.6 KiB
C++
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/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <iostream>
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#include "presets.h"
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#include "opts.h"
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using namespace std;
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void PresetsV0::apply(
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const std::string& preset,
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std::string& policy,
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EList<std::pair<int, std::string> >& opts)
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{
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// Presets: Same as:
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// For --end-to-end:
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// --very-fast -M 5 -R 1 -N 0 -L 22 -i S,1,2.50
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// --fast -M 10 -R 2 -N 0 -L 22 -i S,1,2.50
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// --sensitive -M 15 -R 2 -N 0 -L 22 -i S,1,1.15
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// --very-sensitive -M 25 -R 3 -N 0 -L 19 -i S,1,0.50
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if(preset == "very-fast") {
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policy += ";SEED=0,22";
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policy += ";DPS=5";
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policy += ";ROUNDS=1";
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policy += ";IVAL=S,0,2.50";
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} else if(preset == "fast") {
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policy += ";SEED=0,22";
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policy += ";DPS=10";
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policy += ";ROUNDS=2";
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policy += ";IVAL=S,0,2.50";
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} else if(preset == "sensitive") {
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policy += ";SEED=0,22";
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policy += ";DPS=15";
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policy += ";ROUNDS=2";
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policy += ";IVAL=S,1,1.15";
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} else if(preset == "very-sensitive") {
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policy += ";SEED=0,20";
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policy += ";DPS=20";
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policy += ";ROUNDS=3";
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policy += ";IVAL=S,1,0.50";
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}
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// For --local:
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// --very-fast-local -M 1 -N 0 -L 25 -i S,1,2.00
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// --fast-local -M 2 -N 0 -L 22 -i S,1,1.75
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// --sensitive-local -M 2 -N 0 -L 20 -i S,1,0.75 (default)
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// --very-sensitive-local -M 3 -N 0 -L 20 -i S,1,0.50
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else if(preset == "very-fast-local") {
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policy += ";SEED=0,25";
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policy += ";DPS=5";
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policy += ";ROUNDS=1";
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policy += ";IVAL=S,1,2.00";
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} else if(preset == "fast-local") {
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policy += ";SEED=0,22";
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policy += ";DPS=10";
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policy += ";ROUNDS=2";
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policy += ";IVAL=S,1,1.75";
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} else if(preset == "sensitive-local") {
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policy += ";SEED=0,20";
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policy += ";DPS=15";
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policy += ";ROUNDS=2";
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policy += ";IVAL=S,1,0.75";
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} else if(preset == "very-sensitive-local") {
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policy += ";SEED=0,20";
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policy += ";DPS=20";
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policy += ";ROUNDS=3";
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policy += ";IVAL=S,1,0.50";
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}
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else {
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cerr << "Unknown preset: " << preset.c_str() << endl;
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}
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}
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