Adding Unit test for Haplotype class. Used in HC's genotype given alleles mode.
This commit is contained in:
Ryan Poplin
parent
9b53250bef
commit
f6905630bb
|
|
@ -0,0 +1,163 @@
|
|||
/*
|
||||
* 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 org.broadinstitute.sting.utils;
|
||||
|
||||
|
||||
import net.sf.samtools.Cigar;
|
||||
import net.sf.samtools.CigarElement;
|
||||
import net.sf.samtools.CigarOperator;
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.BeforeClass;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* Basic unit test for Haplotype Class
|
||||
*/
|
||||
public class HaplotypeUnitTest extends BaseTest {
|
||||
@BeforeClass
|
||||
public void init() {
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSimpleInsertionAllele() {
|
||||
final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
|
||||
basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSimpleDeletionAllele() {
|
||||
final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
|
||||
basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSimpleSNPAllele() {
|
||||
final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "AGTGGTCAACTGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("C", "G", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCTACTGGTCAACTGGTCAACTGGTCA";
|
||||
basicInsertTest("A", "T", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ACTGGTCAACTGGTCAAATGGTCAACTGGTCA";
|
||||
basicInsertTest("C", "A", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testComplexInsertionAllele() {
|
||||
final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(10, CigarOperator.I));
|
||||
h1CigarList.add(new CigarElement(8, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(3, CigarOperator.D));
|
||||
h1CigarList.add(new CigarElement(7, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC";
|
||||
basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testComplexDeletionAllele() {
|
||||
final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(10, CigarOperator.I));
|
||||
h1CigarList.add(new CigarElement(8, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(3, CigarOperator.D));
|
||||
h1CigarList.add(new CigarElement(7, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC";
|
||||
basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testComplexSNPAllele() {
|
||||
final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
|
||||
final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(10, CigarOperator.I));
|
||||
h1CigarList.add(new CigarElement(8, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(3, CigarOperator.D));
|
||||
h1CigarList.add(new CigarElement(7, CigarOperator.M));
|
||||
h1CigarList.add(new CigarElement(4, CigarOperator.M));
|
||||
final Cigar h1Cigar = new Cigar(h1CigarList);
|
||||
String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("T", "G", 1, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCTATCG" + "AGGGGGA" + "AGGC";
|
||||
basicInsertTest("G", "T", 7, h1Cigar, bases, h1bases);
|
||||
h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGCGGGA" + "AGGC";
|
||||
basicInsertTest("G", "C", 17, h1Cigar, bases, h1bases);
|
||||
}
|
||||
|
||||
private void basicInsertTest(String ref, String alt, int loc, Cigar cigar, String hap, String newHap) {
|
||||
final int INDEL_PADDING_BASE = (ref.length() == alt.length() ? 0 : 1);
|
||||
final Haplotype h = new Haplotype(hap.getBytes());
|
||||
final Allele h1refAllele = Allele.create(ref, true);
|
||||
final Allele h1altAllele = Allele.create(alt, false);
|
||||
final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE, 0, cigar) );
|
||||
final Haplotype h1expected = new Haplotype(newHap.getBytes());
|
||||
Assert.assertEquals(h1, h1expected);
|
||||
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue