From 0509d316d921d99fd37055a4f5efa60c5cca2bec Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 23 Mar 2012 16:15:19 -0400 Subject: [PATCH] More information in the recalibration report * added empirical quality counts to allow quantization during on-the-fly recalibration to any level * added number of observations and errors to all tables to enable plotting of all covariates --- .../sting/gatk/walkers/bqsr/RecalDataManager.java | 5 ++--- .../sting/utils/recalibration/BaseRecalibration.java | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java index 742be4bbd..a2edd2806 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java @@ -63,12 +63,13 @@ public class RecalDataManager { public final static String ARGUMENT_VALUE_COLUMN_NAME = "Value"; public final static String QUANTIZED_VALUE_COLUMN_NAME = "QuantizedScore"; + public static final String QUANTIZED_COUNT_COLUMN_NAME = "Count"; public final static String READGROUP_COLUMN_NAME = "ReadGroup"; public final static String EVENT_TYPE_COLUMN_NAME = "EventType"; public final static String EMPIRICAL_QUALITY_COLUMN_NAME = "EmpiricalQuality"; public final static String ESTIMATED_Q_REPORTED_COLUMN_NAME = "EstimatedQReported"; public final static String QUALITY_SCORE_COLUMN_NAME = "QualityScore"; - public final static String COVARIATE_VALUE_SCORE_COLUMN_NAME = "CovariateValue"; + public final static String COVARIATE_VALUE_COLUMN_NAME = "CovariateValue"; public final static String COVARIATE_NAME_COLUMN_NAME = "CovariateName"; public final static String COLOR_SPACE_QUAL_ATTRIBUTE_TAG = "CQ"; // The tag that holds the color space quality scores for SOLID bams @@ -77,8 +78,6 @@ public class RecalDataManager { private static boolean warnUserNullPlatform = false; - - public enum SOLID_RECAL_MODE { /** * Treat reference inserted bases as reference matching bases. Very unsafe! diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index a000732c4..cf44e7c36 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -124,7 +124,7 @@ public class BaseRecalibration { ArrayList columnNamesOrderedList = new ArrayList(5); columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.QUALITY_SCORE_COLUMN_NAME); - columnNamesOrderedList.add(RecalDataManager.COVARIATE_VALUE_SCORE_COLUMN_NAME); + columnNamesOrderedList.add(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.COVARIATE_NAME_COLUMN_NAME); columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME); return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList);