Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder.build()


            // 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 );
        }
    }
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