Add --genomicsdb-use-vcf-codec workaround to GenotypeGVCFs

bbimber · bbimber · commit 9563a46c8f12 · 2020-06-18T10:44:33.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java
@@ -50,10 +50,13 @@ public void execute(File referenceFasta, File outputFile, @Nullable List<String>
         else if (AbstractGenomicsDBImportHandler.TILE_DB_FILETYPE.isType(inputFile))
         {
             args.add("gendb://" + inputFile.getParentFile().getPath());
+            //See: https://github.com/broadinstitute/gatk/issues/6667
+            args.add("--genomicsdb-use-vcf-codec");
         }
         else if (inputFile.isDirectory())
         {
             args.add("gendb://" + inputFile.getPath());
+            args.add("--genomicsdb-use-vcf-codec");
         }
         else
         {

Original file line number	Diff line number	Diff line change
`@@ -50,10 +50,13 @@ public void execute(File referenceFasta, File outputFile, @Nullable List<String>`
`50`	`50`	`else if (AbstractGenomicsDBImportHandler.TILE_DB_FILETYPE.isType(inputFile))`
`51`	`51`	`{`
`52`	`52`	`args.add("gendb://" + inputFile.getParentFile().getPath());`
	`53`	`+ //See: https://github.com/broadinstitute/gatk/issues/6667`
	`54`	`+ args.add("--genomicsdb-use-vcf-codec");`
`53`	`55`	`}`
`54`	`56`	`else if (inputFile.isDirectory())`
`55`	`57`	`{`
`56`	`58`	`args.add("gendb://" + inputFile.getPath());`
	`59`	`+ args.add("--genomicsdb-use-vcf-codec");`
`57`	`60`	`}`
`58`	`61`	`else`
`59`	`62`	`{`