ca48ea78df9ddcd7cbebd1487bf0a3d3ed5c9211,java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java,SAMFileWriterArgumentTypeDescriptor,parse,#ParsingEngine#ArgumentSource#Class#ArgumentMatches#,104

Before Change


            stub.setCompressionLevel(compressionLevel);

        stub.setIndexOnTheFly(!argumentIsPresent(disableWriteIndexArgumentDefinition(source),matches));
        stub.setSimplifyBAM(argumentIsPresent(createSimplifyBAMArgumentDefinition(source),matches));

        // WARNING: Side effects required by engine!
        parsingEngine.addTags(stub,getArgumentTags(matches));

After Change



        Boolean indexOnTheFly = !argumentIsPresent(disableWriteIndexArgumentDefinition(source),matches) ? true : null;
        Boolean generateMD5 = argumentIsPresent(this.enableMD5GenerationArgumentDefinition(source),matches) ? true : null;
        Boolean simplifyBAM = argumentIsPresent(createSimplifyBAMArgumentDefinition(source),matches);

        // Validate the combination of parameters passed in.