88 lines
3.1 KiB
Java
88 lines
3.1 KiB
Java
package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.junit.Assert;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import java.io.*;
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/**
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* @author aaron
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* <p/>
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* Class rodDbSNPUnitTest
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class rodDbSNPUnitTest extends BaseTest {
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private static IndexedFastaSequenceFile seq;
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@BeforeClass
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public static void beforeTests() {
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try {
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seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
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} catch (FileNotFoundException e) {
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throw new StingException("unable to load the sequence dictionary");
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}
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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public BufferedReader openFile(String filename) {
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try {
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return new BufferedReader(new FileReader(filename));
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} catch (FileNotFoundException e) {
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throw new StingException("Couldn't open file " + filename);
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}
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}
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@Test
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// count the number of SNP's between 10M and 11M on chr1 in dbSNP
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public void testDBSNPInput() {
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BufferedReader stream = openFile("/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod");
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int snpCount = 0;
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int indelCount = 0;
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try {
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String line = stream.readLine();
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rodDbSNP rod = new rodDbSNP("db");
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boolean stop = false;
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while (line != null && !stop) {
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rod.parseLine(null,line.split("\t"));
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rodDbSNP var = (rodDbSNP)rod;
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if (rod.isSNP()) {
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// quick check, if we're not triallelic, make sure the ref is right
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if (var.getReferenceForSNP() == var.refBases.charAt(0) || var.getAlternativeBaseForSNP() == var.refBases.charAt(0))
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// also make sure the ref is a single character
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if (var.refBases.length() == 1)
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Assert.assertTrue(var.refBases.charAt(0)==var.getReferenceForSNP());
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if (var.getLocation().getContig().equals("1") &&
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var.getLocation().getStart() >= 10000000 &&
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var.getLocation().getStart() <= 11000000) {
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if (var.isSNP()) {
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snpCount++;
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}
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}
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}
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if (rod.isIndel())
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indelCount++;
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stop = (var.getLocation().getContig().equals("1") && var.getLocation().getStart() > 11000000);
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line = stream.readLine();
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}
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Assert.assertEquals(3615,snpCount);
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Assert.assertEquals(9902,indelCount);
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} catch (IOException e) {
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e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
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}
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}
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}
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