gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java

package org.broadinstitute.sting.gatk.walkers;

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

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
 *
 * @Author chartl
 * @Date Feb 25, 2010
 */
public class DepthOfCoverageIntegrationTest extends WalkerTest {

    private boolean RUN_TESTS = true;
    private String root = "-T DepthOfCoverage ";
    private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
    private String b36 = "/broad/1KG/reference/human_b36_both.fasta";

    private String buildRootCmd(String ref, List<String> bams, List<String> intervals) {
        StringBuilder bamBuilder = new StringBuilder();
        do {
            bamBuilder.append(" -I ");
            bamBuilder.append(bams.remove(0));
        } while ( bams.size() > 0 );

        StringBuilder intervalBuilder = new StringBuilder();
        do {
            intervalBuilder.append(" -L ");
            intervalBuilder.append(intervals.remove(0));
        } while ( intervals.size() > 0 );


        return root + "-R "+ref+bamBuilder.toString()+intervalBuilder.toString();
    }

    private void execute(String name, WalkerTestSpec spec) {
        if ( RUN_TESTS ) {
            executeTest(name,spec);
        }
    }

    @Test
    public void testBaseOutputNoFiltering() {
        // our base file
        File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
        this.setOutputFileLocation(baseOutputFile);

        String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
        String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};

        String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -both --outputFormat csv";
        WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());

        // now add the expected files that get generated
        spec.addAuxFile("f53ddf25c2b71e46381f9c434402d88d", baseOutputFile);
        spec.addAuxFile("925cc5b49286e0222bce6251d1baafc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
        spec.addAuxFile("d9e812398d778f28ed12d7f3d18628e2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
        spec.addAuxFile("80577bf378de570f84d91b0ef6004102", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics"));
        spec.addAuxFile("3a059ad82d945643dc4e03239c4041f5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary_statistics"));
        spec.addAuxFile("f3315551081331bc322c53b11412d707", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
        spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
        spec.addAuxFile("fd29fe0c14351e934a6fef9df1f38f7b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
        spec.addAuxFile("111261f0e8ccf8c456d0b2a9482bc32c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics"));
        spec.addAuxFile("cc7ee5075a932dba486e78824ca34202", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
        spec.addAuxFile("e1653480daa2d96f7c584ed4cd20c147", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
        
        execute("testBaseOutputNoFiltering",spec);
    }

    public File createTempFileFromBase(String name) {
        File fl = new File(name);
        fl.deleteOnExit();
        return fl;
    }
}