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Fix for gatk-5449 #5799

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Mar 28, 2019
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5 changes: 3 additions & 2 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ final barclayVersion = System.getProperty('barclay.version','2.1.0')
final sparkVersion = System.getProperty('spark.version', '2.2.0')
final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
final disqVersion = System.getProperty('disq.version','0.3.0')
final genomicsdbVersion = System.getProperty('genomicsdb.version','1.0.0-rc2')
final genomicsdbVersion = System.getProperty('genomicsdb.version','1.0.1')
final testNGVersion = '6.11'
// Using the shaded version to avoid conflicts between its protobuf dependency
// and that of Hadoop/Spark (either the one we reference explicitly, or the one
Expand Down Expand Up @@ -227,7 +227,8 @@ dependencies {
externalSourceConfiguration 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
compile ('org.genomicsdb:genomicsdb:' + genomicsdbVersion) {
exclude module: 'log4j'
exclude module: 'spark-core_2.10'
exclude module: 'spark-core_2.11'
exclude module: 'spark-sql_2.11'
exclude module: 'htsjdk'
exclude module: 'protobuf-java'
}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -338,6 +338,14 @@ public void testGenomicsDBAlleleSpecificAnnotations() throws IOException {
new String[]{"-G", "StandardAnnotation", "-G", "AS_StandardAnnotation"});
}

@Test (enabled = true)
public void testGenomicsDBAlleleSpecificAnnotationsInTheMiddleOfSpanningDeletion() throws IOException {
testGenomicsDBAgainstCombineGVCFs(Arrays.asList(COMBINEGVCFS_TEST_DIR+"NA12878.AS.chr20snippet.g.vcf", COMBINEGVCFS_TEST_DIR+"NA12892.AS.chr20snippet.g.vcf"),
new ArrayList<SimpleInterval>(Arrays.asList(new SimpleInterval("20", 10433313, 10700000))),
b37_reference_20_21,
new String[]{"-G", "StandardAnnotation", "-G", "AS_StandardAnnotation"});
}

/**
* Converts a list of large file paths into equivalent cloud paths
* This must be done non-statically because any failure during static initialization results in hard to understand
Expand Down