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Merge pull request #490 from broadinstitute/vrr_reference_model_unsorted_records_bugfix 

Fixed out of order non-variant gVCF entries when trimming is active.
This commit is contained in:
Valentin Ruano Rubio 2014-02-07 12:21:12 -05:00
parent 369fbd4439 4a3c8e68fa
commit 8e87e083ff
2 changed files with 28 additions and 10 deletions
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22
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
View File

@ -489,16 +489,20 @@ class ActiveRegionTrimmer {
final GenomeLoc idealSpan = locParser.createPaddedGenomeLoc(variantSpan, padding);
final GenomeLoc finalSpan = maximumSpan.intersect(idealSpan).union(variantSpan);
final Pair<GenomeLoc,GenomeLoc> nonVariantRegions = nonVariantTargetRegions(originalRegion, variantSpan);
// Make double sure that, if we are emitting GVCF we won't call non-variable positions beyond the target active region span.
// In regular call we don't do so so we don't care and we want to maintain behavior, so the conditional.
final GenomeLoc callableSpan = emitReferenceConfidence ? variantSpan.intersect(originalRegionRange) : variantSpan;
final Pair<GenomeLoc,GenomeLoc> nonVariantRegions = nonVariantTargetRegions(originalRegion, callableSpan);
if ( debug ) {
logger.info("events : " + withinActiveRegion);
logger.info("region : " + originalRegion);
logger.info("variantSpan : " + variantSpan);
logger.info("pad : " + padding);
logger.info("idealSpan : " + idealSpan);
logger.info("maximumSpan : " + maximumSpan);
logger.info("finalSpan : " + finalSpan);
logger.info("events : " + withinActiveRegion);
logger.info("region : " + originalRegion);
logger.info("callableSpan : " + callableSpan);
logger.info("padding : " + padding);
logger.info("idealSpan : " + idealSpan);
logger.info("maximumSpan : " + maximumSpan);
logger.info("finalSpan : " + finalSpan);
}
return new Result(emitReferenceConfidence,true,originalRegion,padding, usableExtension,withinActiveRegion,nonVariantRegions,finalSpan,idealSpan,maximumSpan,variantSpan);
@ -527,7 +531,7 @@ class ActiveRegionTrimmer {
locParser.createGenomeLoc(contig, finalStop + 1, targetStop)) :
new Pair<>(locParser.createGenomeLoc(contig, targetStart, finalStart - 1),GenomeLoc.UNMAPPED);
} else if (postTrimmingRequired)
return new Pair<>(locParser.createGenomeLoc(targetRegionRange.getContig(), finalStop + 1, targetStop),GenomeLoc.UNMAPPED);
return new Pair<>(GenomeLoc.UNMAPPED,locParser.createGenomeLoc(targetRegionRange.getContig(), finalStop + 1, targetStop));
else
return new Pair<>(GenomeLoc.UNMAPPED,GenomeLoc.UNMAPPED);
}

16
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -47,11 +47,13 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@ -84,7 +86,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
executeTest(name, spec);
final Pair<List<File>,List<String>> executionOutput = executeTest(name, spec);
}
@Test
@ -127,4 +129,16 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
private final static String WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS = privateTestDir + "gvcf_unsorted_records_bug.interval_list";
private final static String WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM = privateTestDir + "gvcf_unsorted_records_bug.bam";
@Test()
public void testWrongGVCFNonVariantRecordOrderBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("324eb46738a364cd7dc5fa0b62491a5e"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
}