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Minor misc updates

This commit is contained in:
Ryan Poplin 2012-03-06 10:14:45 -05:00
parent 0702ee1587
commit 46b470cc69
1 changed files with 4 additions and 8 deletions
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12
public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
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@ -1,5 +1,5 @@
/* /*
* Copyright (c) 2010 The Broad Institute * Copyright (c) 2012 The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
@ -99,8 +99,7 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(10, CigarOperator.I)); h1CigarList.add(new CigarElement(10, CigarOperator.I));
h1CigarList.add(new CigarElement(8, CigarOperator.M)); h1CigarList.add(new CigarElement(8, CigarOperator.M));
h1CigarList.add(new CigarElement(3, CigarOperator.D)); h1CigarList.add(new CigarElement(3, CigarOperator.D));
h1CigarList.add(new CigarElement(7, CigarOperator.M)); h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
h1CigarList.add(new CigarElement(4, CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList); final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases); basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
@ -119,8 +118,7 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(10, CigarOperator.I)); h1CigarList.add(new CigarElement(10, CigarOperator.I));
h1CigarList.add(new CigarElement(8, CigarOperator.M)); h1CigarList.add(new CigarElement(8, CigarOperator.M));
h1CigarList.add(new CigarElement(3, CigarOperator.D)); h1CigarList.add(new CigarElement(3, CigarOperator.D));
h1CigarList.add(new CigarElement(7, CigarOperator.M)); h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
h1CigarList.add(new CigarElement(4, CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList); final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases); basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
@ -139,8 +137,7 @@ public class HaplotypeUnitTest extends BaseTest {
h1CigarList.add(new CigarElement(10, CigarOperator.I)); h1CigarList.add(new CigarElement(10, CigarOperator.I));
h1CigarList.add(new CigarElement(8, CigarOperator.M)); h1CigarList.add(new CigarElement(8, CigarOperator.M));
h1CigarList.add(new CigarElement(3, CigarOperator.D)); h1CigarList.add(new CigarElement(3, CigarOperator.D));
h1CigarList.add(new CigarElement(7, CigarOperator.M)); h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
h1CigarList.add(new CigarElement(4, CigarOperator.M));
final Cigar h1Cigar = new Cigar(h1CigarList); final Cigar h1Cigar = new Cigar(h1CigarList);
String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
basicInsertTest("T", "G", 1, h1Cigar, bases, h1bases); basicInsertTest("T", "G", 1, h1Cigar, bases, h1bases);
@ -158,6 +155,5 @@ public class HaplotypeUnitTest extends BaseTest {
final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE, 0, cigar) ); final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE, 0, cigar) );
final Haplotype h1expected = new Haplotype(newHap.getBytes()); final Haplotype h1expected = new Haplotype(newHap.getBytes());
Assert.assertEquals(h1, h1expected); Assert.assertEquals(h1, h1expected);
} }
} }