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Merge pull request #484 from broadinstitute/jt_select_variants_nt_maven 

Fix for the SelectVariants -nt race condition corruption of the AD and PL fields
This commit is contained in:
droazen 2014-02-05 08:15:02 -05:00
parent 1de7a27471 7923e786e9
commit 22bcd10372
11 changed files with 127 additions and 4 deletions
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1
.gitignore vendored
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@ -24,3 +24,4 @@ dump/
lib/
out/
/atlassian-ide-plugin.xml
maven-metadata-local.xml

5
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
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@ -92,6 +92,11 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
final String args = "-select 'DP > 30' -V " + testfile;
new ParallelSelectTestProvider(b37KGReference, args, "c64b45a14d41b1e5cddbe036b47e7519", nt);
}
{ // AD and PL decoding race condition
final String testfile = privateTestDir + "race_condition.vcf";
final String args = "-env -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
new ParallelSelectTestProvider(b37KGReference, args, "62e6156387d6e91bd2b08ef649cb1129", nt);
}
}
return ParallelSelectTestProvider.getTests(ParallelSelectTestProvider.class);

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public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.jar 100644
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44
public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom 100644
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@ -0,0 +1,44 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>net.sf</groupId>
<artifactId>picard</artifactId>
<version>1.107.1676</version>
<name>picard</name>
<dependencies>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>variant</artifactId>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1676</version>
</dependency>
<!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 -->
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.8.2</version>
<exclusions>
<exclusion>
<groupId>org.apache.ant</groupId>
<artifactId>ant-launcher</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.sun</groupId>
<artifactId>tools.jar</artifactId>
<version>1.5</version>
<classifier>system</classifier>
<systemPath>${java.home}../lib/tools.jar</systemPath>
</dependency>
</dependencies>
</project>

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public/repo/net/sf/sam/1.107.1676/sam-1.107.1676.jar 100644
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21
public/repo/net/sf/sam/1.107.1676/sam-1.107.1676.pom 100644
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@ -0,0 +1,21 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1676</version>
<name>sam-jdk</name>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>5.5</version>
<classifier>jdk15</classifier>
</dependency>
<dependency>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
<version>1.0.3-rc3</version>
</dependency>
</dependencies>
</project>

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public/repo/org/broad/tribble/1.107.1676/tribble-1.107.1676.jar 100644
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15
public/repo/org/broad/tribble/1.107.1676/tribble-1.107.1676.pom 100644
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@ -0,0 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1676</version>
<name>tribble</name>
<dependencies>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1676</version>
</dependency>
</dependencies>
</project>

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public/repo/org/broadinstitute/variant/1.107.1676/variant-1.107.1676.jar 100644
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31
public/repo/org/broadinstitute/variant/1.107.1676/variant-1.107.1676.pom 100644
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@ -0,0 +1,31 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.broadinstitute</groupId>
<artifactId>variant</artifactId>
<version>1.107.1676</version>
<name>variant</name>
<dependencies>
<dependency>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jexl</artifactId>
<version>2.1.1</version>
</dependency>
<!-- TODO: This artifact is only in the Sting local repo, not in central, yet. -->
<dependency>
<groupId>com.google.code.cofoja</groupId>
<artifactId>cofoja</artifactId>
<version>1.0-r139</version>
</dependency>
</dependencies>
</project>

14
public/sting-root/pom.xml
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@ -59,12 +59,18 @@
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.104.1628</version>
<version>1.107.1676</version>
<exclusions>
<exclusion>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf</groupId>
<artifactId>picard</artifactId>
<version>1.104.1628</version>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>edu.mit.broad</groupId>
@ -74,12 +80,12 @@
<dependency>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.104.1628</version>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>variant</artifactId>
<version>1.105.1642</version>
<version>1.107.1676</version>
</dependency>
<dependency>
<groupId>log4j</groupId>