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.