Examples of org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder

            Object targetValue = io.getValue();


            // Ghastly hack: reaches in and finishes building out the SAMFileReader.
            // TODO: Generalize this, and move it to its own initialization step.
            if( targetValue instanceof SAMFileReaderBuilder) {
                SAMFileReaderBuilder builder = (SAMFileReaderBuilder)targetValue;
                builder.setValidationStringency(strictnessLevel);
                targetValue = builder.build();
            }


            JVMUtils.setFieldValue( targetField.field, walker, targetValue );
        }
    }

        return SAMFileReader.class.isAssignableFrom(type);
    }


    @Override
    public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
        SAMFileReaderBuilder builder = new SAMFileReaderBuilder();


        ArgumentMatchValue readerFileName = getArgumentValue( createDefaultArgumentDefinition(source), matches );


        if( readerFileName == null )
            throw new UserException.CommandLineException("SAM file compression was supplied, but no associated writer was supplied with it.");


        builder.setSAMFile(readerFileName.asFile());


        // WARNING: Skipping required side-effect because stub is impossible to generate.
        engine.addInput(source, builder);


        // MASSIVE KLUDGE!  SAMFileReader is tricky to implement and we don't yet have a stub.  Return null, then

Related Classes of org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder

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