From 47d030a52d5f93108738590572ad49c90c7e7a5b Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 7 Jan 2013 15:47:25 -0500
Subject: [PATCH] Oops, move the covariates over too

---
 .../sting/utils/recalibration/covariates/ContextCovariate.java    | 0
 .../sting/utils/recalibration/covariates/Covariate.java           | 0
 .../sting/utils/recalibration/covariates/CycleCovariate.java      | 0
 .../utils/recalibration/covariates/ExperimentalCovariate.java     | 0
 .../utils/recalibration/covariates/QualityScoreCovariate.java     | 0
 .../sting/utils/recalibration/covariates/ReadGroupCovariate.java  | 0
 .../utils/recalibration/covariates/RepeatLengthCovariate.java     | 0
 .../sting/utils/recalibration/covariates/RequiredCovariate.java   | 0
 .../sting/utils/recalibration/covariates/StandardCovariate.java   | 0
 9 files changed, 0 insertions(+), 0 deletions(-)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java (100%)
 rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java (100%)

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