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Merge pull request #153 from broadinstitute/md_hc_ld_merge_off 

Turn off the LD merging code by default
This commit is contained in:
Ryan Poplin 2013-04-09 07:12:16 -07:00
parent ae0612b6e8 33ecec535d
commit b8bd10469d
3 changed files with 5 additions and 7 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -282,8 +282,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
protected List<String> annotationsToExclude = new ArrayList<String>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator"}));
@Advanced
@Argument(fullName="dontMergeVariantsViaLD", shortName="dontMergeVariantsViaLD", doc="If specified, we will include low quality bases when doing the assembly", required = false)
protected boolean dontMergeVariantsViaLD = false;
@Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="If specified, we will merge variants together into block substitutions that are in strong local LD", required = false)
protected boolean mergeVariantsViaLD = false;
/**
* Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
@ -433,9 +433,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
final MergeVariantsAcrossHaplotypes variantMerger = dontMergeVariantsViaLD
? new MergeVariantsAcrossHaplotypes()
: new LDMerger(DEBUG, 10, 1);
final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS, variantMerger );

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "80b9280b1e65952f60ba2fd738d4840f");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6b673efb6f12b5deebb3e63fe94c48ed");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("e30b974b038293841e6be23c93ce76e1"));
Arrays.asList("020b1a4feb82f050894f6066dc07cc4a"));
executeTest("HC calling on a ReducedRead BAM", spec);
}