diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java new file mode 100755 index 000000000..05aa20716 --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java @@ -0,0 +1,36 @@ +package org.broadinstitute.sting.playground.gatk.walkers.reducereads; + +import org.broadinstitute.sting.WalkerTest; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.util.Arrays; + +public class ReduceReadsIntegrationTest extends WalkerTest { + final static String REF = b37KGReference; + final String BAM = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam"; + final String L = "20:10,100,000-10,200,000"; + + private void RRTest(String args, String md5) { + String base = String.format("-T ReduceReads -R %s -I %s -L %s", REF, BAM, L) + " -o %s"; + WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5)); + executeTest("testReduceReads1: args=" + args, spec); + } + + @Test() + public void testReduceReadsBase() { + RRTest("", "6c34409f19ba2e5b21f3bfe6847dadda"); + } + + @Test() + public void testReduceReads50MaxReads() { + RRTest(" -mravs 50", "3a896ac6e2ea0fc0a3fb4348d31313b6"); + } + + @Test() + public void testReduceReadsMinBasesForConsensus10000() { + RRTest(" -mbrc 10000", "d8edbc04fd47cd1d64f2ce08459f7dae"); + } + +} +