package org.broadinstitute.sting.gatk.walkers.indels;

import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

import java.util.ArrayList;

public class IndelRealignerPerformanceTest extends WalkerTest {
    @Test
    public void testRealigner() {
        WalkerTestSpec spec1 = new WalkerTestSpec(

                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
                        " -T IndelRealigner" +
                        " -LOD 5" +
                        " -maxConsensuses 100" +
                        " -greedy 100" +
                        " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                        " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                        " -L chr1:1-5,650,000" +
                        " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals",
                 0,
                new ArrayList<String>(0));
        executeTest("testIndelRealignerWholeGenome", spec1);

        WalkerTestSpec spec2 = new WalkerTestSpec(
                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
                        " -T IndelRealigner" +
                        " -LOD 5" +
                        " -maxConsensuses 100" +
                        " -greedy 100" +
                        " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                        " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                        " -L chr1:1-150,000,000" +
                        " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals",
                 0,
                new ArrayList<String>(0));
        executeTest("testIndelRealignerWholeExome", spec2);
    }
}
@@ -802,32 +802,88 @@
 :1-5,650,000%22 +%0A
+                        %22 --realignReadsWithBadMates%22 +%0A
                 
@@ -1657,32 +1657,88 @@
 -150,000,000%22 +%0A
+                        %22 --realignReadsWithBadMates%22 +%0A
                 

Fix performance tests