From 765ec5e207e0e007cba200cc6a790c0a16a45f8f Mon Sep 17 00:00:00 2001 From: zhouzhongyuan Date: Thu, 12 Nov 2020 09:21:22 +0800 Subject: [PATCH] Support BCF files in Spark. #4303 --- .../broadinstitute/hellbender/tools/HaplotypeCallerSpark.java | 4 ---- 1 file changed, 4 deletions(-) mode change 100644 => 100755 src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java diff --git a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java old mode 100644 new mode 100755 index 6df7b99b592..1e82833f277 --- a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java @@ -99,10 +99,6 @@ public Collection makeVariantAnnotations() { @Override protected void runTool(JavaSparkContext ctx) { - //TODO remove me when https://github.com/broadinstitute/gatk/issues/4303 are fixed - if (output.endsWith(FileExtensions.BCF) || output.endsWith(FileExtensions.BCF + ".gz")) { - throw new UserException.UnimplementedFeature("It is currently not possible to write a BCF file on spark. See https://github.com/broadinstitute/gatk/issues/4303 for more details ."); - } Utils.validateArg(hcArgs.dbsnp.dbsnp == null, "HaplotypeCallerSpark does not yet support -D or --dbsnp arguments" ); Utils.validateArg(hcArgs.comps.isEmpty(), "HaplotypeCallerSpark does not yet support -comp or --comp arguments" ); Utils.validateArg(hcArgs.bamOutputPath == null, "HaplotypeCallerSpark does not yet support -bamout or --bamOutput");