From dabdd0a0fd765c47cb191264ad3c60c1d8151a61 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 17 Mar 2014 12:28:27 -0400 Subject: [PATCH] Remove unused and unnecessary argument --- .../sting/gatk/arguments/GATKArgumentCollection.java | 9 --------- 1 file changed, 9 deletions(-) diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index e86780eb4..bb4c2ee82 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -337,15 +337,6 @@ public class GATKArgumentCollection { @Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "Global Qscore Bayesian prior to use for BQSR", required = false) public double globalQScorePrior = -1.0; - /** - * It is absolutely not recommended practice to run base quality score recalibration on BAM files that have been - * processed with ReduceReads. By default, the GATK will error out if it detects that you are trying to recalibrate - * a reduced BAM file. However, this flag allows you to disable the warning and proceed anyway. For the sake of your - * data, please only use this option if you really know what you are doing. - */ - @Advanced - @Argument(fullName = "allow_bqsr_on_reduced_bams_despite_repeated_warnings", shortName="allowBqsrOnReducedBams", doc="Ignore all warnings about how it's a really bad idea to run BQSR on a reduced BAM file (AT YOUR OWN RISK!)", required = false) - public boolean ALLOW_BQSR_ON_REDUCED_BAMS = false; // -------------------------------------------------------------------------------------------------------------- //