From 46b470cc69939e7e8b676ebbc6cee22fba04ffb1 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 6 Mar 2012 10:14:45 -0500 Subject: [PATCH] Minor misc updates --- .../sting/utils/HaplotypeUnitTest.java | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java index 25bd7a2eb..86bc2d59b 100644 --- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java @@ -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 * 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(8, CigarOperator.M)); h1CigarList.add(new CigarElement(3, CigarOperator.D)); - h1CigarList.add(new CigarElement(7, CigarOperator.M)); - h1CigarList.add(new CigarElement(4, CigarOperator.M)); + h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; 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(8, CigarOperator.M)); h1CigarList.add(new CigarElement(3, CigarOperator.D)); - h1CigarList.add(new CigarElement(7, CigarOperator.M)); - h1CigarList.add(new CigarElement(4, CigarOperator.M)); + h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; 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(8, CigarOperator.M)); h1CigarList.add(new CigarElement(3, CigarOperator.D)); - h1CigarList.add(new CigarElement(7, CigarOperator.M)); - h1CigarList.add(new CigarElement(4, CigarOperator.M)); + h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; 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 h1expected = new Haplotype(newHap.getBytes()); Assert.assertEquals(h1, h1expected); - } }