From 7078219b89c7eed741b649c08bb3064034e50cdb Mon Sep 17 00:00:00 2001 From: rpoplin Date: Fri, 15 Jan 2010 19:17:52 +0000 Subject: [PATCH] Updating outdated comments. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2595 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/recalibration/CovariateCounterWalker.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java index cbb542b1a..96bb096e4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -52,9 +52,9 @@ import net.sf.samtools.SAMRecord; * Since there is a large amount of data one can then calculate an empirical probability of error * given the particular covariates seen at this site, where p(error) = num mismatches / num observations * The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score) - * The first lines of the output file give the name of the covariate classes that were used for this calculation. + * The first non-comment line of the output file gives the name of the covariates that were used for this calculation. * - * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and must be at the start of the list. + * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified * Note: This walker is designed to be used in conjunction with TableRecalibrationWalker. * * @author rpoplin @@ -472,7 +472,7 @@ public class CovariateCounterWalker extends LocusWalker { // Output the RecalDatum entry recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() ); } else { // Another layer in the nested hash map - printMappingsSorted( recalTableStream, curPos + 1, key, (Map) val); + printMappingsSorted( recalTableStream, curPos + 1, key, (Map) val ); } } } @@ -490,7 +490,7 @@ public class CovariateCounterWalker extends LocusWalker { // Output the RecalDatum entry recalTableStream.println( ((RecalDatumOptimized)val).outputToCSV() ); } else { // Another layer in the nested hash map - printMappings( recalTableStream, curPos + 1, key, (Map) val); + printMappings( recalTableStream, curPos + 1, key, (Map) val ); } } }