htsjdk.tribble.example.IndexToTable Maven / Gradle / Ivy
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package htsjdk.tribble.example;
import htsjdk.tribble.index.IndexFactory;
import htsjdk.tribble.index.linear.LinearIndex;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
public class IndexToTable {
/**
* this class:
* 1) checks to see that the feature file exists
* 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk
* 3) Converts the index to a human readable table
* @see htsjdk.tribble.index.linear.LinearIndex#writeTable(java.io.PrintStream)
*
* @param args 2 parameters:
* 1) The path of the file to index
* 2) The output file path
*/
public static void main(String[] args) {
// check yourself before you wreck yourself - we require one arg, the input file
if (args.length != 2)
printUsage();
//LinearIndex.enableAdaptiveIndexing = false;
LinearIndex idx = (LinearIndex) IndexFactory.loadIndex(new File(args[0]).getAbsolutePath());
try {
idx.writeTable(new PrintStream(new FileOutputStream(new File(args[1]))));
} catch ( FileNotFoundException e ) {
e.printStackTrace();
System.exit(1);
}
}
/**
* print usage information
*/
public static void printUsage() {
System.err.println("Usage: java -jar IndexToTable.jar index.file output.table");
System.exit(1);
}
}