@@ -0,0 +1,2628 @@
+/*%0A * Copyright (c) 2010.%0A *%0A * Permission is hereby granted, free of charge, to any person%0A * obtaining a copy of this software and associated documentation%0A * files (the %22Software%22), to deal in the Software without%0A * restriction, including without limitation the rights to use,%0A * copy, modify, merge, publish, distribute, sublicense, and/or sell%0A * copies of the Software, and to permit persons to whom the%0A * Software is furnished to do so, subject to the following%0A * conditions:%0A *%0A * The above copyright notice and this permission notice shall be%0A * included in all copies or substantial portions of the Software.%0A *%0A * THE SOFTWARE IS PROVIDED %22AS IS%22, WITHOUT WARRANTY OF ANY KIND,%0A * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES%0A * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND%0A * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT%0A * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,%0A * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING%0A * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR%0A * THE USE OR OTHER DEALINGS IN THE SOFTWARE.%0A */%0A%0Apackage org.broadinstitute.sting.playground.gatk.walkers;%0A%0Aimport org.broadinstitute.sting.WalkerTest;%0Aimport org.junit.Test;%0A%0Aimport java.util.Arrays;%0A %0Apublic class BeagleIntegrationTest extends WalkerTest %7B%0A%0A    private static final String beagleValidationDataLocation = validationDataLocation + %22/Beagle/%22;%0A    @Test%0A    public void testBeagleOutput() %7B%0A        WalkerTestSpec spec = new WalkerTestSpec(%0A                %22-T BeagleOutputToVCF -R %22 + oneKGLocation + %22reference/human_g1k_v37.fasta %22 +%0A                        %22-B variant,VCF,%22 + beagleValidationDataLocation + %22inttestbgl.input.vcf %22 +%0A                        %22-B beagleR2,BEAGLE,%22 + beagleValidationDataLocation + %22inttestbgl.r2 %22 +%0A                        %22-B beagleProbs,BEAGLE,%22 + beagleValidationDataLocation + %22inttestbgl.gprobs %22 +%0A                        %22-B beaglePhased,BEAGLE,%22 + beagleValidationDataLocation + %22inttestbgl.phased %22 +%0A                        %22-output %25s%22, 1, Arrays.asList(%22e7b9aac20246f26ffcc599850f6cb2a0%22));%0A        executeTest(%22test BeagleOutputToVCF%22, spec);%0A    %7D%0A   %0A    @Test%0A    public void testBeagleInput() %7B%0A        WalkerTestSpec spec = new WalkerTestSpec(%0A                %22-T ProduceBeagleInput -R %22 + oneKGLocation + %22reference/human_g1k_v37.fasta %22 +%0A                        %22-B variant,VCF,%22 + beagleValidationDataLocation + %22inttestbgl.input.vcf %22 +%0A                         %22-beagle %25s%22, 1, Arrays.asList(%22c0d30e5dbe903874f8422a0e63a5118e%22));%0A        executeTest(%22test BeagleInput%22, spec);%0A    %7D%0A%0A%7D

Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker)