The newest release of GenomicsDB treats spanning deletions (spanning

from earlier positions) as deletions in the min PL value computation.
This behavior now matches the behavior of CombineGVCFs.

A more detailed description of the issue is provided in
#4963

* Deleted a couple of files which are no longer necessary.
* Fixed the index of newMQcalc.combined.g.vcf

build.gradle

@@ -63,7 +63,7 @@ final sparkVersion = System.getProperty('spark.version', '2.2.0')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
 final disqVersion = System.getProperty('disq.version','0.1.0')
 final tensorflowVersion = System.getProperty('tensorflow.version','1.9.0')
-final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.0-proto-3.0.0-beta-1+bdce8be25b873')
+final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.2-proto-3.0.0-beta-1+90dad1af8ce0e4d')
 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

src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java

@@ -57,6 +57,7 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String NA_12878_PHASED = largeFileTestDir + "NA12878.phasedData.Chr20.vcf"; //NOTE: this is not phased according to the vcf spec but it reflects phasing currently produced by haplotype caller
     private static final String MULTIPLOID_DATA_HG37 = largeFileTestDir + "gvcfs/HapMap5plex.ploidy10.b37.g.vcf";
     private static final String NA12878_HG37 = toolsTestDir + "GenomicsDBImport/expected.testGVCFMode.gatk4.g.vcf";
+    //This file was generated by running CombineGVCFs on the input files
     private static final String MULTIPLOID_EXPECTED_RESULT = toolsTestDir + "GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf";
     private static final String MNP_GVCF = toolsTestDir + "GenomicsDBImport/mnp.input.g.vcf";
     private static final String ARTIFICIAL_PHASED = getTestDataDir() + "/ArtificalPhasedData.1.g.vcf";
@@ -116,7 +117,7 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String ANOTHER_ATTRIBUTE_KEY = "AA";
 
     private static final List<String> GVCFS_WITH_NEW_MQ = Arrays.asList(toolsTestDir + "/GenomicsDBImport/expected.testGVCFMode.gatk4.g.vcf", getTestDataDir() + "/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf");
-    private static final String COMBINED_WITH_NEW_MQ = toolsTestDir + "/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf";
+    private static final String COMBINED_WITH_NEW_MQ = toolsTestDir + "/walkers/CombineGVCFs/newMQcalc.combined.g.vcf";
     private static final List<SimpleInterval> INTERVAL2 = Arrays.asList(new SimpleInterval("20", 1, 11_000_000));
     private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList("RAW_MQ","RAW_MQandDP");  //CombineGVCFs doesn't support the old RAW_MQ anymore