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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
This commit is contained in:
Mauricio Carneiro 2012-03-23 16:15:19 -04:00
parent 9f74969e3a
commit 0509d316d9
2 changed files with 3 additions and 4 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
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@ -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!

2
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -124,7 +124,7 @@ public class BaseRecalibration {
ArrayList<String> columnNamesOrderedList = new ArrayList<String>(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);