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require reference as asserted in documentation #8067

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merged 3 commits into from
Oct 21, 2022
Merged

require reference as asserted in documentation #8067

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bbc7b9a
require reference as asserted in documentation
tmelman Oct 21, 2022
b5c1427
Subbed File.createTempFile for BaseTest.createTempFile
tmelman Oct 21, 2022
ddb58a5
Changed args from list to ArgumentBuilder
tmelman Oct 21, 2022
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5 changes: 5 additions & 0 deletions ...main/java/org/broadinstitute/hellbender/tools/copynumber/utils/MergeAnnotatedRegions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,11 @@ public class MergeAnnotatedRegions extends GATKTool {

final static String DEFAULT_SEPARATOR = "__";

@Override
public boolean requiresReference() {
return true;
}

@Override
public void traverse() {

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27 changes: 19 additions & 8 deletions ...roadinstitute/hellbender/tools/copynumber/utils/MergeAnnotatedRegionsIntegrationTest.java
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@@ -1,12 +1,15 @@
package org.broadinstitute.hellbender.tools.copynumber.utils;

import com.google.common.collect.ImmutableSortedMap;
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.testutils.BaseTest;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.testng.Assert;
import org.testng.annotations.Test;

Expand All @@ -23,14 +26,11 @@ public class MergeAnnotatedRegionsIntegrationTest extends CommandLineProgramTest
@Test
public void basicTest() throws IOException {
// This test is a bit more like the real world
final File outputFile = File.createTempFile("mergeannotatedregions", ".seg");
final List<String> arguments = new ArrayList<>();
arguments.add("--" + CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME);
arguments.add(SIMPLE_TEST_FILE);
arguments.add("--" + StandardArgumentDefinitions.REFERENCE_LONG_NAME);
arguments.add(REF);
arguments.add("-" + StandardArgumentDefinitions.OUTPUT_SHORT_NAME);
arguments.add(outputFile.getAbsolutePath());
final File outputFile = BaseTest.createTempFile("mergeannotatedregions", ".seg");
final ArgumentsBuilder arguments = new ArgumentsBuilder();
arguments.add(CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME, SIMPLE_TEST_FILE);
arguments.add(StandardArgumentDefinitions.REFERENCE_LONG_NAME, REF);
arguments.add(StandardArgumentDefinitions.OUTPUT_SHORT_NAME, outputFile.getAbsolutePath());
runCommandLine(arguments);

final AnnotatedIntervalCollection collection =
Expand All @@ -50,4 +50,15 @@ public void basicTest() throws IOException {
Assert.assertEquals(collection.getRecords().get(4), new AnnotatedInterval(new SimpleInterval("2", 1098, 2305),
ImmutableSortedMap.of("Num_Probes", "200", "Segment_Mean", "-0.10", "Segment_Call", "0")));
}

@Test(expectedExceptions = CommandLineException.class)
public void requiresReferenceTest() throws IOException {
// This test is a bit more like the real world
final File outputFile = BaseTest.createTempFile("mergeannotatedregions", ".seg");
final ArgumentsBuilder arguments = new ArgumentsBuilder();
arguments.add(CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME, SIMPLE_TEST_FILE);
arguments.add(StandardArgumentDefinitions.OUTPUT_SHORT_NAME, outputFile.getAbsolutePath());
runCommandLine(arguments);
}

}