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Merge pull request #251 from broadinstitute/md_mapq_reassign 

Command-line read filters are now applied before Walker default filters
This commit is contained in:
droazen 2013-05-31 09:05:24 -07:00
parent ed4f19d79b b16de45ce4
commit a665d759cd
2 changed files with 56 additions and 1 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -344,11 +344,18 @@ public class GenomeAnalysisEngine {
* @return A collection of available filters.
*/
public Collection<ReadFilter> createFilters() {
final List<ReadFilter> filters = WalkerManager.getReadFilters(walker,this.getFilterManager());
final List<ReadFilter> filters = new LinkedList<>();
// First add the user requested filters
if (this.getArguments().readGroupBlackList != null && this.getArguments().readGroupBlackList.size() > 0)
filters.add(new ReadGroupBlackListFilter(this.getArguments().readGroupBlackList));
for(final String filterName: this.getArguments().readFilters)
filters.add(this.getFilterManager().createByName(filterName));
// now add the walker default filters. This ordering is critical important if
// users need to apply filters that fix up reads that would be removed by default walker filters
filters.addAll(WalkerManager.getReadFilters(walker,this.getFilterManager()));
return Collections.unmodifiableList(filters);
}

48
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
View File

@ -26,12 +26,20 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.qc.ErrorThrowing;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.PrintStream;
import java.util.Arrays;
/**
@ -126,4 +134,44 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
executeTest(cfg.toString(), spec);
}
}
// --------------------------------------------------------------------------------
//
// Test that read filters are being applied in the order we expect
//
// --------------------------------------------------------------------------------
@ReadFilters({MappingQualityUnavailableFilter.class})
public static class DummyReadWalkerWithMapqUnavailableFilter extends ReadWalker<Integer, Integer> {
@Output
PrintStream out;
@Override
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
return 1;
}
@Override
public Integer reduceInit() {
return 0;
}
@Override
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
@Override
public void onTraversalDone(Integer result) {
out.println(result);
}
}
@Test(enabled = true)
public void testUserReadFilterAppliedBeforeWalker() {
WalkerTestSpec spec = new WalkerTestSpec("-R " + b37KGReference + " -I " + privateTestDir + "allMAPQ255.bam"
+ " -T DummyReadWalkerWithMapqUnavailableFilter -o %s -L MT -rf ReassignMappingQuality",
1, Arrays.asList("ecf27a776cdfc771defab1c5d19de9ab"));
executeTest("testUserReadFilterAppliedBeforeWalker", spec);
}
}