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Changed ReadNameReadFilter to support mulitple readname inputs #8405

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merged 4 commits into from
Jul 10, 2023
Merged

Changed ReadNameReadFilter to support mulitple readname inputs #8405

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168b631
changedReadNameReadFilter to support multipleReadnames inputs (and co…
jamesemery Jul 7, 2023
47be31f
fixing a broken test and name
jamesemery Jul 7, 2023
4a8c604
fixing another edge case
jamesemery Jul 7, 2023
29f04d5
updating a test to enforce the new readname filtering behavior
jamesemery Jul 7, 2023
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11 changes: 8 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/engine/filters/ReadNameReadFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,14 @@
import org.broadinstitute.hellbender.utils.read.GATKRead;

import java.io.Serializable;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.Set;

/**
* Keep only reads with this read name.
* Keep only reads with one of these readnames.
*
* Should you need to provide many readnames to keep, you can provide a newline separated .list file of readnames to keep.
*
* <p>Matching is done by case-sensitive exact match.</p>
*/
Expand All @@ -18,11 +23,11 @@ public final class ReadNameReadFilter extends ReadFilter implements Serializable
private static final long serialVersionUID = 1L;

@Argument(fullName = ReadFilterArgumentDefinitions.READ_NAME_LONG_NAME, doc="Keep only reads with this read name", optional=false)
public String readName = null;
public Set<String> readNames = new LinkedHashSet<>(0);

@Override
public boolean test( final GATKRead read ) {
return read.getName() != null && read.getName().equals(readName);
return read.getName() != null && readNames.contains(read.getName());
}

}
13 changes: 9 additions & 4 deletions src/test/java/org/broadinstitute/hellbender/engine/ReadsContextUnitTest.java
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Expand Up @@ -11,9 +11,7 @@
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;

public final class ReadsContextUnitTest extends GATKBaseTest {
Expand Down Expand Up @@ -42,7 +40,9 @@ public Object[][] getValidReadsContextData() {
// Default-constructed ReadsContexts and ReadsContexts constructed from null ReadsDataSources/intervals
// should behave as empty context objects.
ReadNameReadFilter readNameFilter = new ReadNameReadFilter();
readNameFilter.readName = "d";
readNameFilter.readNames = Collections.singleton("d");
ReadNameReadFilter twoReadNamesReadFilter = new ReadNameReadFilter();
twoReadNamesReadFilter.readNames = Set.of("d", "b");
return new Object[][]{
{new ReadsContext(
new ReadsPathDataSource(IOUtils.getPath(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam")),
Expand All @@ -53,6 +53,11 @@ public Object[][] getValidReadsContextData() {
new ReadsPathDataSource(IOUtils.getPath(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam")),
new SimpleInterval("1", 200, 1000), // query over larger interval with readNameFilter on "d"
readNameFilter), new String[] { "d" }
},
{new ReadsContext(
new ReadsPathDataSource(IOUtils.getPath(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam")),
new SimpleInterval("1", 200, 1000), // query over larger interval with readNameFilter on "d", "b"
twoReadNamesReadFilter), new String[] { "b", "d" }
}
};
}
Expand Down
2 changes: 1 addition & 1 deletion src/test/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibraryUnitTest.java
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Expand Up @@ -614,7 +614,7 @@ public void testReadNameFilter() {
ReadNameReadFilter f = new ReadNameReadFilter();

final String fred= "fred";
f.readName = fred;
f.readNames = Collections.singleton(fred);
read.setName(fred);
Assert.assertTrue(f.test(read), read.toString());//pass

Expand Down