diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java