From 35699a8376513783acd31084a11db03b044dd066 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 7 Jan 2013 15:41:21 -0500 Subject: [PATCH] Move bqsr utils to protected --- .../org/broadinstitute/sting/utils/recalibration/BQSRMode.java | 0 .../sting/utils/recalibration/BQSRReadTransformer.java | 0 .../sting/utils/recalibration/BaseRecalibration.java | 0 .../org/broadinstitute/sting/utils/recalibration/EventType.java | 0 .../broadinstitute/sting/utils/recalibration/QualQuantizer.java | 0 .../sting/utils/recalibration/QuantizationInfo.java | 0 .../broadinstitute/sting/utils/recalibration/ReadCovariates.java | 0 .../org/broadinstitute/sting/utils/recalibration/RecalDatum.java | 0 .../broadinstitute/sting/utils/recalibration/RecalDatumNode.java | 0 .../org/broadinstitute/sting/utils/recalibration/RecalUtils.java | 0 .../sting/utils/recalibration/RecalibrationReport.java | 0 .../sting/utils/recalibration/RecalibrationTables.java | 0 12 files changed, 0 insertions(+), 0 deletions(-) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java (100%) rename {public => protected}/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java (100%) 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