From 4fa439d89e4786f645c7c3d1b28ae48cfa02d0ea Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 9 Jan 2013 11:06:10 -0500
Subject: [PATCH] Move some classes back to public because they are used in the
 engine.  Move some test classes to protected.  We should have no more
 public->protected dependancies now

---
 .../diagnostics/targets/DiagnoseTargetsIntegrationTest.java       | 0
 .../gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java | 0
 .../walkers/diagnostics/targets/SampleStatisticsUnitTest.java     | 0
 .../sting/utils/recalibration/ContextCovariateUnitTest.java       | 0
 .../sting/utils/recalibration/CycleCovariateUnitTest.java         | 0
 .../sting/utils/recalibration/QualQuantizerUnitTest.java          | 0
 .../sting/utils/recalibration/ReadCovariatesUnitTest.java         | 0
 .../sting/utils/recalibration/ReadGroupCovariateUnitTest.java     | 0
 .../sting/utils/recalibration/RecalDatumUnitTest.java             | 0
 .../sting/utils/recalibration/RecalUtilsUnitTest.java             | 0
 .../sting/utils/recalibration/RecalibrationReportUnitTest.java    | 0
 .../sting/utils/recalibration/RecalibrationTablesUnitTest.java    | 0
 .../sting/utils/recalibration/RecalibrationTestUtils.java         | 0
 .../broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java | 0
 .../broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java  | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java    | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java   | 0
 .../sting/gatk/walkers/diffengine/DiffableReader.java             | 0
 .../broadinstitute/sting/gatk/walkers/diffengine/Difference.java  | 0
 22 files changed, 0 insertions(+), 0 deletions(-)
 rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java (100%)
 rename {public => protected}/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java (100%)
 rename {protected => public}/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java (100%)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
similarity index 100%
rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java