Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz

Output filenames with the vcf.gz extension are gzipped, those containing the string ".bcf" result in VCF
broadgsa · Dec 6, 2016 · fbfda33 · fbfda33
2 parents ad67e36 + 15757b4
commit fbfda33
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/.../src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java b/.../src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java
@@ -149,7 +149,8 @@ private VariantContextWriter vcfWriterToFile(final VariantContextWriterStub stub
         // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
         // TODO -- remove me when argument generateShadowBCF is removed
         if ( stub.alsoWriteBCFForTest() &&
-                ! (options.contains(Options.FORCE_BCF) || file != null && file.getName().contains(".bcf")) ) {
+                ! ( options.contains(Options.FORCE_BCF) ||
+                        file != null && (file.getName().endsWith(".bcf") || file.getName().endsWith(".bcf.gz")) ) ) {
             final File bcfFile = BCF2Utils.shadowBCF(file);
             if ( bcfFile != null ) {
                 final VariantContextWriter bcfWriter = new VariantContextWriterBuilder()

diff --git a/...ngine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/...ngine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java
@@ -216,7 +216,8 @@ public EnumSet<Options> getWriterOptions(boolean indexOnTheFly) {
         if ( writeFullFormatField ) options.add(Options.WRITE_FULL_FORMAT_FIELD);
 
         final File file = getOutputFile();
-        if ( forceBCF || (file != null && options.contains(Options.FORCE_BCF) || file != null && file.getName().contains(".bcf")) )
+        if ( forceBCF || (file != null && options.contains(Options.FORCE_BCF) ||
+                file != null && (file.getName().endsWith(".bcf") || file.getName().endsWith(".bcf.gz"))) )
             options.add(Options.FORCE_BCF);
 
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);