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Revved Picard/htsjdk 

Removed inefficient array->List conversion in AlleleCountBySample
This commit is contained in:
Phillip Dexheimer 2014-10-29 20:32:05 -04:00
parent b3b569f43a
commit fc67e50faa
6 changed files with 7 additions and 8 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java
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@ -67,7 +67,6 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator; import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators; import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators;
import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import java.util.Arrays; import java.util.Arrays;
@ -121,8 +120,8 @@ public final class AlleleCountBySample extends GenotypeAnnotation {
AC[alleleIndex - 1] = alleleCount; AC[alleleIndex - 1] = alleleCount;
AF[alleleIndex - 1] = ((double) alleleCount) / (double) ploidy; AF[alleleIndex - 1] = ((double) alleleCount) / (double) ploidy;
} }
gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, Utils.asList(AC)); gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, AC);
gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, Utils.asList(AF)); gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, AF);
} }
@Override @Override

4
public/gatk-root/pom.xml
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@ -44,8 +44,8 @@
<test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners> <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
<!-- Version numbers for picard and htsjdk --> <!-- Version numbers for picard and htsjdk -->
<htsjdk.version>1.123.1654</htsjdk.version> <htsjdk.version>1.123.1658</htsjdk.version>
<picard.version>1.123.1612</picard.version> <picard.version>1.123.1620</picard.version>
</properties> </properties>
<!-- Dependency configuration (versions, etc.) --> <!-- Dependency configuration (versions, etc.) -->

BIN
public/repo/picard/picard/1.123.1612/picard-1.123.1612.jar → public/repo/picard/picard/1.123.1620/picard-1.123.1620.jar
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4
public/repo/picard/picard/1.123.1612/picard-1.123.1612.pom → public/repo/picard/picard/1.123.1620/picard-1.123.1620.pom
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@ -3,13 +3,13 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>picard</groupId> <groupId>picard</groupId>
<artifactId>picard</artifactId> <artifactId>picard</artifactId>
<version>1.123.1612</version> <version>1.123.1620</version>
<name>picard</name> <name>picard</name>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>samtools</groupId> <groupId>samtools</groupId>
<artifactId>htsjdk</artifactId> <artifactId>htsjdk</artifactId>
<version>1.123.1654</version> <version>1.123.1658</version>
</dependency> </dependency>
<!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 --> <!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 -->
<dependency> <dependency>

BIN
public/repo/samtools/htsjdk/1.123.1654/htsjdk-1.123.1654.jar → public/repo/samtools/htsjdk/1.123.1658/htsjdk-1.123.1658.jar
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public/repo/samtools/htsjdk/1.123.1654/htsjdk-1.123.1654.pom → public/repo/samtools/htsjdk/1.123.1658/htsjdk-1.123.1658.pom
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@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>samtools</groupId> <groupId>samtools</groupId>
<artifactId>htsjdk</artifactId> <artifactId>htsjdk</artifactId>
<version>1.123.1654</version> <version>1.123.1658</version>
<name>htsjdk</name> <name>htsjdk</name>
<dependencies> <dependencies>
<dependency> <dependency>