diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java