org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.snpEffect.testCases.unity;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

import org.junit.Test;
import org.snpeff.fileIterator.SeekableBufferedReader;
import org.snpeff.util.Gpr;

import junit.framework.Assert;

/**
 * Seekable file reader test case
 *
 * @author pcingola
 */
public class TestCasesSeekableReader extends TestCasesBase {

	/**
	 * Calculate a simple hash using SeekableBufferedReader
	 * @param fileName
	 * @return
	 * @throws IOException
	 */
	long calcHash(String fileName) throws IOException {
		SeekableBufferedReader sbr = new SeekableBufferedReader(fileName);
		String line;
		long hash = 0;
		while ((line = sbr.readLine()) != null) {
			hash += line.hashCode();
		}

		sbr.close();
		return hash;
	}

	/**
	 * Same as calc hash, but using BufferedReader
	 * @param fileName
	 * @return
	 * @throws IOException
	 */
	long calcHashBufferedReader(String fileName) throws IOException {
		BufferedReader br = new BufferedReader(new FileReader(new File(fileName)));
		String line;
		long hash = 0;
		while ((line = br.readLine()) != null) {
			hash += line.hashCode();
		}
		br.close();
		return hash;
	}

	@Test
	public void test_00() throws IOException {
		Gpr.debug("Test");
		String fileName = path("testLukas.vcf");
		long hashExp = calcHashBufferedReader(fileName);
		long hash = calcHash(fileName);
		System.out.println(String.format("%016x\t%016x\t%s", hashExp, hash, fileName));

		Assert.assertEquals(hashExp, hash);
	}

	/**
	 * Basic parsing
	 * @throws IOException
	 */
	@Test
	public void test_01() throws IOException {
		Gpr.debug("Test");
		String fileName = path("testLukas.vcf");
		long hashExp = calcHashBufferedReader(fileName);
		long hash = calcHash(fileName);
		System.out.println(String.format("%016x\t%016x\t%s", hashExp, hash, fileName));
		Assert.assertEquals(hashExp, hash);
	}
}