From 88fd762436ee049b25997ecf4f578358cccd023a Mon Sep 17 00:00:00 2001 From: rpoplin Date: Sat, 14 Nov 2009 19:37:46 +0000 Subject: [PATCH] The -rf argument is now being used for read filter and is colliding with my walkers. Changed mine to -recalFile git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2048 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/Recalibration/CovariateCounterWalker.java | 2 +- .../gatk/walkers/Recalibration/TableRecalibrationWalker.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java index 2969888b2..f24136cd3 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java @@ -72,7 +72,7 @@ public class CovariateCounterWalker extends LocusWalker { private String PLATFORM = "SLX"; @Argument(fullName = "windowSizeNQS", shortName="nqs", doc="How big of a window should the MinimumNQSCovariate use for its calculation", required=false) private int WINDOW_SIZE = 3; - @Argument(fullName="recal_file", shortName="rf", required=false, doc="Filename for the outputted covariates table recalibration file") + @Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the outputted covariates table recalibration file") private String RECAL_FILE = "output.recal_data.csv"; @Argument(fullName="noPrintHeader", shortName="noHeader", required=false, doc="Don't print the usual header on the table recalibration file") private boolean NO_PRINT_HEADER = false; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java index 1190430b9..9f519cb2e 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/TableRecalibrationWalker.java @@ -56,7 +56,7 @@ import java.io.FileNotFoundException; @WalkerName("TableRecalibrationRefactored") public class TableRecalibrationWalker extends ReadWalker { - @Argument(fullName="recal_file", shortName="rf", doc="Input recalibration table file generated by CountCovariates", required=true) + @Argument(fullName="recal_file", shortName="recalFile", doc="Input recalibration table file generated by CountCovariates", required=true) public String RECAL_FILE; @Argument(fullName="outputBam", shortName="outputBam", doc="output BAM file", required=false) public SAMFileWriter OUTPUT_BAM = null;