From 60c3eb4b60cf377956bf5cbca5dcc8714f587d8b Mon Sep 17 00:00:00 2001 From: rpoplin Date: Fri, 11 Dec 2009 19:02:29 +0000 Subject: [PATCH] Added help.description to the recalibration walkers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/recalibration/CovariateCounterWalker.java | 2 ++ .../gatk/walkers/recalibration/TableRecalibrationWalker.java | 2 ++ 2 files changed, 4 insertions(+) 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 6869e6c93..83a997f57 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -61,6 +61,8 @@ import net.sf.samtools.SAMRecord; * * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and must be at the start of the list. * Note: This walker is designed to be used in conjunction with TableRecalibrationWalker. + * + * @help.description First pass of the recalibration. Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). */ @By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index 94ddce851..6ae72dbd5 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -55,6 +55,8 @@ import java.io.FileNotFoundException; * * Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. * Note: This walker is designed to be used in conjunction with CovariateCounterWalker. + * + * @help.description Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as mesaured by reference mismatch rate. */ @WalkerName("TableRecalibration")