Move bqsr utils to protected

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Eric Banks 2013-01-07 15:41:21 -05:00

parent 5371613ad1

commit 35699a8376

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public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java

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public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java → protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java

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