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I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.

This commit is contained in:
Eric Banks 2012-11-26 11:34:59 -05:00
parent b15b62157a
commit 4f7fa3009a
2 changed files with 17 additions and 19 deletions
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28
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -82,7 +82,7 @@ import java.util.*;
@Allows(value={DataSource.READS, DataSource.REFERENCE}) @Allows(value={DataSource.READS, DataSource.REFERENCE})
@Reference(window=@Window(start=-50,stop=50)) @Reference(window=@Window(start=-50,stop=50))
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible { public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible, TreeReducible<Integer> {
@ArgumentCollection @ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@ -275,14 +275,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
return true; return true;
} }
/**
* Initialize the number of loci processed to zero.
*
* @return 0
*/
public Integer reduceInit() { return 0; }
/** /**
* We want reads that span deletions * We want reads that span deletions
* *
@ -323,15 +315,15 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
return 1; return 1;
} }
/** @Override
* Increment the number of loci processed. public Integer reduceInit() { return 0; }
*
* @param value result of the map. @Override
* @param sum accumulator for the reduce. public Integer reduce(Integer value, Integer sum) { return value + sum; }
* @return the new number of loci processed.
*/ @Override
public Integer reduce(Integer value, Integer sum) { public Integer treeReduce(Integer lhs, Integer rhs) {
return sum + value; return lhs + rhs;
} }
/** /**

8
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -151,7 +151,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
} }
@Test @Test
public void testTabixAnnotations() { public void testTabixAnnotationsAndParallelism() {
final String MD5 = "99938d1e197b8f10c408cac490a00a62"; final String MD5 = "99938d1e197b8f10c408cac490a00a62";
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) { for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
@ -159,6 +159,12 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
Arrays.asList(MD5)); Arrays.asList(MD5));
executeTest("Testing lookup vcf tabix vs. vcf tribble", spec); executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
} }
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -A HomopolymerRun -nt 2 --variant:vcf " + validationDataLocation + "CEU.exon.2010_03.sites.vcf -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
Arrays.asList(MD5));
executeTest("Testing lookup vcf tabix vs. vcf tribble plus parallelism", spec);
} }
@Test @Test