From 0892f2b8b2196a779bb9eb433b73854168c3fb3b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 3 Sep 2012 20:18:56 -0400 Subject: [PATCH] Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference -- Confirmed that reads spanning off the end of the chromosome don't cause an exception by adding integration test for a single read that starts 7 bases from the end of chromosome 1 and spans 90 bases or so off. Added pileup integration test to ensure this behavior continues to work --- .../walkers/PileupWalkerIntegrationTest.java | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java index 9d9b91872..667b325ed 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java @@ -5,15 +5,7 @@ import org.testng.annotations.Test; import java.util.Arrays; -/** - * Created by IntelliJ IDEA. - * User: chartl - * Date: Dec 1, 2009 - * Time: 9:03:34 AM - * To change this template use File | Settings | File Templates. - */ public class PileupWalkerIntegrationTest extends WalkerTest { - @Test public void testGnarleyFHSPileup() { String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam " @@ -23,4 +15,14 @@ public class PileupWalkerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5)); executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec); } + + @Test + public void testSingleReadAligningOffChromosome1() { + String gatk_args = "-T Pileup " + + " -I " + privateTestDir + "readOffb37contig1.bam" + + " -R " + b37KGReference + + " -o %s"; + WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList("4a45fe1f85aaa8c4158782f2b6dee2bd")); + executeTest("Testing single read spanning off chromosome 1", spec); + } }