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Remove unused and unnecessary argument

This commit is contained in:
Eric Banks 2014-03-17 12:28:27 -04:00
parent 34c697bf12
commit dabdd0a0fd
1 changed files with 0 additions and 9 deletions
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public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -337,15 +337,6 @@ public class GATKArgumentCollection {
@Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "Global Qscore Bayesian prior to use for BQSR", required = false) @Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "Global Qscore Bayesian prior to use for BQSR", required = false)
public double globalQScorePrior = -1.0; 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;
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //