Final updates to integration tests for BCF2
-- Fully working version -- Use -generateShadowBCF to write out foo.bcf as well as foo.vcf anywhere you use -o foo.vcf -- Moved MedianUnitTest to its proper home in Utils -- Added reportng to ivy and testng, so build/report/X/html/ is a nicely formatted output for Unit and Integration tests. From this website it's easy to see md5 diffs, etc. This is a vastly better way to manage unit and integration test output
This commit is contained in:
Mark DePristo
parent
ade1843818
commit
e9c22b9aad
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@ -1140,7 +1140,7 @@
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verbose="2"
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workingDir="${basedir}"
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useDefaultListeners="false"
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listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
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listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
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<jvmarg value="-Xmx${test.maxmemory}" />
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<jvmarg value="-ea" />
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<jvmarg value="-Djava.awt.headless=true" />
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1
ivy.xml
1
ivy.xml
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@ -83,6 +83,7 @@
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<!-- testing and evaluation dependencies -->
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<dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
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<dependency org="org.uncommons" name="reportng" rev="1.1.2" conf="test" />
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<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
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<!-- Contracts for Java and dependencies -->
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@ -105,7 +105,7 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
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// if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
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// TODO -- remove me when argument generateShadowBCF is removed
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if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
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final File bcfFile = new File(file.getAbsolutePath() + ".bcf");
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final File bcfFile = new File(file.getAbsolutePath().replace(".vcf", ".bcf"));
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VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
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writer = new TestWriter(writer, bcfWriter);
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}
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@ -215,7 +215,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
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vcfHeader.addMetaDataLine(commandLineArgHeaderLine);
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}
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vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
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//vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
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}
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outputTracker.getStorage(this).writeHeader(vcfHeader);
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@ -87,7 +87,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
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rodList = this.getToolkit().getRodDataSources();
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for (ReferenceOrderedDataSource rod : rodList) {
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out.println(rod.getName() + DIVIDER + rod.getType());
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out.println(rod.getName() + DIVIDER + rod.getFile());
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out.println(rod.getName() + DIVIDER + rod.getFile().getName());
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out.println(rod.getName() + DIVIDER + md5sum(rod.getFile()));
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}
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out.println("Data:");
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@ -9,6 +9,7 @@ import org.broadinstitute.sting.commandline.CommandLineUtils;
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import org.broadinstitute.sting.utils.crypt.CryptUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.io.IOUtils;
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import org.testng.Reporter;
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import java.io.File;
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import java.io.IOException;
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@ -254,4 +255,13 @@ public abstract class BaseTest {
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file.deleteOnExit();
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return file;
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}
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/**
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* Log this message so that it shows up inline during output as well as in html reports
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*
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* @param message
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*/
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public static void log(final String message) {
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Reporter.log(message, true);
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}
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}
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@ -171,12 +171,13 @@ public class MD5DB {
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}
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public static class MD5Match {
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final String md5;
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final String actualMD5, expectedMD5;
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final String failMessage;
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boolean failed;
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public MD5Match(final String md5, final String failMessage, final boolean failed) {
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this.md5 = md5;
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public MD5Match(final String actualMD5, final String expectedMD5, final String failMessage, final boolean failed) {
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this.actualMD5 = actualMD5;
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this.expectedMD5 = expectedMD5;
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this.failMessage = failMessage;
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this.failed = failed;
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}
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@ -191,20 +192,20 @@ public class MD5DB {
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* @return The calculated MD5.
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*/
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public static MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
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final String filemd5sum = testFileMD5(name, resultsFile, expectedMD5, parameterize);
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final String actualMD5 = testFileMD5(name, resultsFile, expectedMD5, parameterize);
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String failMessage = null;
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boolean failed = false;
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if (parameterize || expectedMD5.equals("")) {
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// Don't assert
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} else if ( filemd5sum.equals(expectedMD5) ) {
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System.out.println(String.format(" => %s PASSED (expected=%s)", name, expectedMD5));
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} else if ( actualMD5.equals(expectedMD5) ) {
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//BaseTest.log(String.format(" => %s PASSED (expected=%s)", name, expectedMD5));
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} else {
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failed = true;
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failMessage = String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, filemd5sum);
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failMessage = String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, actualMD5);
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}
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return new MD5Match(filemd5sum, failMessage, failed);
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return new MD5Match(actualMD5, expectedMD5, failMessage, failed);
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}
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@ -230,8 +231,7 @@ public class MD5DB {
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updateMD5Db(filemd5sum, resultsFile);
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if (parameterize || expectedMD5.equals("")) {
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System.out.println(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
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name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
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BaseTest.log(String.format("PARAMETERIZATION: file %s has md5 = %s", resultsFile, filemd5sum));
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} else {
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//System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
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//System.out.flush();
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@ -242,16 +242,23 @@ public class MD5DB {
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System.out.printf("##### Test %s is going to fail #####%n", name);
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String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
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String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]");
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System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);
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System.out.printf("##### Path to calculated file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
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System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
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BaseTest.log(String.format("expected %s at %s", expectedMD5, pathToExpectedMD5File));
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BaseTest.log(String.format("calculated %s at %s", filemd5sum, pathToFileMD5File));
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BaseTest.log(String.format("diff %s %s", pathToExpectedMD5File, pathToFileMD5File));
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// inline differences
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DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0);
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// TODO -- capture output and put in log
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final ByteArrayOutputStream baos = new ByteArrayOutputStream();
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final PrintStream ps = new PrintStream(baos);
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DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0);
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boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
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if ( success )
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if ( success ) {
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final String content = baos.toString();
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BaseTest.log(content);
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System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
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pathToExpectedMD5File, pathToFileMD5File);
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}
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ps.close();
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}
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}
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@ -0,0 +1,63 @@
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/*
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* Copyright (c) 2012, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting;
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import java.util.Collections;
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import java.util.List;
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/**
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* Assertion failure representing an MD5 mismatch between expected and actual
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*
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* @author Your Name
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* @since Date created
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*/
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public class MD5Mismatch extends Exception {
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final List<String> actuals, expecteds;
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public MD5Mismatch(final String actual, final String expected) {
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this(Collections.singletonList(actual), Collections.singletonList(expected));
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}
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public MD5Mismatch(final List<String> actuals, final List<String> expecteds) {
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super(formatMessage(actuals, expecteds));
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this.actuals = actuals;
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this.expecteds = expecteds;
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}
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@Override
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public String toString() {
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return formatMessage(actuals, expecteds);
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}
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private final static String formatMessage(final List<String> actuals, final List<String> expecteds) {
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final StringBuilder b = new StringBuilder("MD5 mismatch: ");
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for ( int i = 0; i < actuals.size(); i++ ) {
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if ( i > 1 ) b.append("\t\t\n");
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b.append("actual ").append(actuals.get(i));
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b.append(" expected ").append(expecteds.get(i));
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}
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return b.toString();
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}
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}
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@ -43,7 +43,6 @@ import org.testng.Assert;
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import org.testng.annotations.BeforeMethod;
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import java.io.File;
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import java.io.IOException;
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import java.util.*;
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public class WalkerTest extends BaseTest {
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@ -61,7 +60,7 @@ public class WalkerTest extends BaseTest {
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}
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public void validateOutputBCFIfPossible(final String name, final File resultFile) {
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final File bcfFile = new File(resultFile.getAbsolutePath() + ".bcf");
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final File bcfFile = new File(resultFile.getAbsolutePath().replace(".vcf", ".bcf"));
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if ( bcfFile.exists() ) {
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logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile);
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try {
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@ -105,17 +104,23 @@ public class WalkerTest extends BaseTest {
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if ( ! result.failed ) {
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validateOutputIndex(name, resultFiles.get(i));
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validateOutputBCFIfPossible(name, resultFiles.get(i));
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md5s.add(result.md5);
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md5s.add(result.expectedMD5);
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} else {
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fails.add(result);
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}
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}
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if ( ! fails.isEmpty() ) {
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List<String> actuals = new ArrayList<String>();
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List<String> expecteds = new ArrayList<String>();
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for ( final MD5DB.MD5Match fail : fails ) {
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actuals.add(fail.actualMD5);
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expecteds.add(fail.expectedMD5);
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logger.warn("Fail: " + fail.failMessage);
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}
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Assert.fail("Test failed: " + name);
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final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds);
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Assert.fail(failure.toString(), failure);
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}
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return md5s;
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@ -335,10 +340,10 @@ public class WalkerTest extends BaseTest {
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gotAnException = true;
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if ( expectedException != null ) {
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// we expect an exception
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System.out.println(String.format("Wanted exception %s, saw %s", expectedException, e.getClass()));
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//System.out.println(String.format("Wanted exception %s, saw %s", expectedException, e.getClass()));
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if ( expectedException.isInstance(e) ) {
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// it's the type we expected
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System.out.println(String.format(" => %s PASSED", name));
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//System.out.println(String.format(" => %s PASSED", name));
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} else {
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if ( e.getCause() != null )
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e.getCause().printStackTrace(System.out); // must print to stdout to see the message
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@ -368,5 +373,5 @@ public class WalkerTest extends BaseTest {
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File fl = new File(name);
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fl.deleteOnExit();
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return fl;
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}
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}
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}
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@ -79,7 +79,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
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@Test
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// in this test, the index exists, but is out of date.
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public void testBuilderIndexUnwriteable() {
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File vcfFile = new File(testDir + "/ROD_validation/read_only/relic.vcf");
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/relic.vcf");
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try {
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builder.loadIndex(vcfFile, new VCF3Codec());
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} catch (IOException e) {
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@ -96,7 +96,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
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// sure we don't do this
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@Test
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public void testDirIsLockedIndexFromDisk() {
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File vcfFile = new File(testDir + "/ROD_validation/read_only/good_index.vcf");
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/good_index.vcf");
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File vcfFileIndex = Tribble.indexFile(vcfFile);
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Index ind = null;
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try {
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@ -112,7 +112,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
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@Test
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public void testBuilderIndexDirectoryUnwritable() {
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File vcfFile = new File(testDir + "/ROD_validation/read_only/no_index.vcf");
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf");
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File vcfFileIndex = Tribble.indexFile(vcfFile);
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Index ind = null;
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@ -131,7 +131,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
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@Test
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public void testGenerateIndexForUnindexedFile() {
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File vcfFile = new File(testDir + "/ROD_validation/always_reindex.vcf");
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File vcfFile = new File(validationDataLocation + "/ROD_validation/always_reindex.vcf");
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File vcfFileIndex = Tribble.indexFile(vcfFile);
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// if we can't write to the directory, don't fault the tester, just pass
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@ -157,7 +157,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
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// test to make sure we get a full sequence dictionary from the VCF (when we set the dictionary in the builder)
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@Test
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public void testBuilderIndexSequenceDictionary() {
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File vcfFile = createCorrectDateIndexFile(new File(testDir + "/ROD_validation/newerTribbleTrack.vcf"));
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File vcfFile = createCorrectDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
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Long indexTimeStamp = Tribble.indexFile(vcfFile).lastModified();
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try {
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Index idx = builder.loadIndex(vcfFile, new VCFCodec());
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|
|
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@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
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"--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
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"--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
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"--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
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"-o %s --no_cmdline_in_header", 1, Arrays.asList("6d0f213918e3b9ea33bc2f8a51a462f1"));
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"-o %s --no_cmdline_in_header", 1, Arrays.asList("93962cac4c308908bd20df8c5763d5e2"));
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executeTest("test BeagleOutputToVCF", spec);
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}
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|
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@ -31,7 +31,7 @@ import org.testng.annotations.Test;
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import java.util.Arrays;
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public class VariantEvalIntegrationTest extends WalkerTest {
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private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval";
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private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval/";
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private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
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private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
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private static String fundamentalTestSNPsSplit1of2VCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf";
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|
|
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@ -18,7 +18,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
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1,
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Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
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Arrays.asList("b3df647811b5f13aa8eac080705c1be9")
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);
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spec.disableShadowBCF();
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executeTest("testComplexSelection--" + testfile, spec);
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|
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@ -32,7 +32,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
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1,
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Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd")
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Arrays.asList("64f0f3fc7297c21325f76222ccb48b1d")
|
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);
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spec.disableShadowBCF();
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|
|
@ -46,7 +46,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("5085a2f8cddfeae9f6274f905025184f")
|
||||
Arrays.asList("20936f028bd073224f0adcdb0b9a8dfe")
|
||||
);
|
||||
|
||||
executeTest("testRepeatedLineSelection--" + testfile, spec);
|
||||
|
|
@ -59,7 +59,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("929bbb96381541c162dc7e5462e26ea2")
|
||||
Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -73,7 +73,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5")
|
||||
Arrays.asList("9fb54ed003234a5847c565ffb6767b95")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -87,7 +87,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
|
||||
Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -101,7 +101,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("e0b12c0b47a8a7a988b3587b47bfa8cf")
|
||||
Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b")
|
||||
);
|
||||
|
||||
executeTest("testVariantTypeSelection--" + testFile, spec);
|
||||
|
|
@ -114,7 +114,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("167a1265df820978a74c267df44d5c43")
|
||||
Arrays.asList("a8a26c621018142c9cba1080cbe687a8")
|
||||
);
|
||||
|
||||
executeTest("testUsingDbsnpName--" + testFile, spec);
|
||||
|
|
@ -127,7 +127,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("0fd8e52bdcd1f4b921d8fb5c689f196a")
|
||||
Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff")
|
||||
);
|
||||
|
||||
executeTest("testRegenotype--" + testFile, spec);
|
||||
|
|
@ -140,7 +140,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("ffa2524380d84a870d2e4a33d9f3d31a")
|
||||
Arrays.asList("6ff686a64e98fc1be2cde9b034d4a43a")
|
||||
);
|
||||
|
||||
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
|
||||
|
|
@ -153,14 +153,14 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("f17885e5cbd5387edb99112047ea43c1")
|
||||
Arrays.asList("b96a09ae32cc3aa300adfba3b5ee71ce")
|
||||
);
|
||||
|
||||
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParallelization() {
|
||||
public void testParallelization2() {
|
||||
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
|
||||
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
|
||||
WalkerTestSpec spec;
|
||||
|
|
@ -168,15 +168,21 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"),
|
||||
1,
|
||||
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
|
||||
Arrays.asList("b3df647811b5f13aa8eac080705c1be9")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testParallelization (2 threads)--" + testfile, spec);
|
||||
}
|
||||
|
||||
spec = new WalkerTestSpec(
|
||||
@Test
|
||||
public void testParallelization4() {
|
||||
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
|
||||
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
|
||||
WalkerTestSpec spec;
|
||||
spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"),
|
||||
1,
|
||||
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
|
||||
Arrays.asList("b3df647811b5f13aa8eac080705c1be9")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -190,7 +196,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
|
||||
1,
|
||||
Arrays.asList("3fb50cc1c955491048108956d7087c35")
|
||||
Arrays.asList("828b4c1ef6ea7e57aad626264cc2c8f6")
|
||||
);
|
||||
executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -57,10 +57,10 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
"-T SelectVariants" +
|
||||
" -R " + b36KGReference +
|
||||
" --variant:vcf3,storage=STREAM " + tmpFifo.getAbsolutePath() +
|
||||
" ---no_cmdline_in_header" +
|
||||
" --no_cmdline_in_header " +
|
||||
" -o %s",
|
||||
1,
|
||||
Arrays.asList("658f580f7a294fd334bd897102616fed")
|
||||
Arrays.asList("c145288a9f2dbe3684cace4968f8ca04")
|
||||
);
|
||||
|
||||
executeTest("testSimpleVCFStreaming", spec);
|
||||
|
|
@ -81,7 +81,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
"-T SelectVariants" +
|
||||
" -R " + b36KGReference +
|
||||
" --variant:vcf3,storage=STREAM " + testFile +
|
||||
" ---no_cmdline_in_header" +
|
||||
" --no_cmdline_in_header" +
|
||||
" -select 'QD > 2.0'" +
|
||||
" -o " + tmpFifo.getAbsolutePath(),
|
||||
0,
|
||||
|
|
|
|||
|
|
@ -23,15 +23,14 @@
|
|||
*/
|
||||
|
||||
// our package
|
||||
package org.broadinstitute.sting;
|
||||
package org.broadinstitute.sting.utils;
|
||||
|
||||
|
||||
// the imports for unit testing.
|
||||
|
||||
|
||||
import org.broadinstitute.sting.utils.Median;
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.BeforeSuite;
|
||||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
|
|
@ -35,7 +35,7 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
|
||||
|
||||
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("acee3b6bdb4b759992f54065c675a249"));
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0cb81b9332fc21d03e74caff770b8a4a"));
|
||||
executeTest("Test reading and writing breakpoint VCF", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -46,7 +46,7 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
|
||||
|
||||
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("87d5b180ef5f9dc5aaee4b02601b43a2"));
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("109bf9347965eb47706b4916bdd48a7a"));
|
||||
executeTest("Test reading and writing samtools vcf", spec1);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue