83 lines
2.8 KiB
Java
83 lines
2.8 KiB
Java
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/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 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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* HISAT 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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import java.util.Map;
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import java.util.HashMap;
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import java.util.List;
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import java.util.ArrayList;
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public class HT2ModuleExample {
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public static void main(String[] args) {
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HT2Module module = null;
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Map<String, Integer> ht2Options = null;
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String indexPath = "../../evaluation/indexes/HISAT2_22/22_rep";
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//String indexPath = "../../evaluation/indexes/HISAT2/genome_rep";
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try {
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module = new HT2Module();
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// Get Default Options
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//ht2Options = module.InitOption();
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// or
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ht2Options = new HashMap<>();
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//ht2Options.put("gVerbose", 1);
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//ht2Options.put("startVerbose", 1);
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//ht2Options.put("sanityCheck", 1);
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System.out.println(ht2Options);
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module.initLibrary(indexPath, ht2Options);
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//module.initLibrary(indexPath);
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System.out.println("CHR_ID 0: " + module.getRefNameById(0));
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// in 22_rep, OutOfIndex
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System.out.println("CHR_ID 1: " + module.getRefNameById(1));
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List<String> refnames = module.getRefNames();
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System.out.println("Refnames size:" + refnames.size());
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for(String name: refnames) {
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System.out.println(name);
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}
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// repeat for 22_rep
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List<HT2Module.HT2Position> positions = module.repeatExpand("rep100-300", 8308, 100);
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// repeat for genome_rep
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//List<HT2Module.HT2Position> positions = module.repeatExpand("rep100-300", 2446692, 100);
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System.out.println("Repeat expand size: " + positions.size());
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for(HT2Module.HT2Position pos: positions) {
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String chrName = refnames.get(pos.chr_id).split(" ")[0];
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String direction = pos.direction == 0 ? "+":"-";
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System.out.println(chrName + ":" + pos.position + ":" + direction);
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}
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} finally {
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if(module != null) {
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module.cleanup();
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}
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}
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}
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}
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