From bafa61c1fe3d83f65c50c14b53724ddca512e255 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 2 Mar 2011 17:14:36 +0000 Subject: [PATCH] LINEAR_EXACT now the default model. Passes all integration tests. 2-3x faster in low-pass data. Tests on exome data ongoing, but potentially vastly faster there. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5357 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 827288b06..9e6cc24e6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -105,7 +105,7 @@ public class UnifiedArgumentCollection { public double ALPHA_DELETION_PROBABILITY = 1e-3; @Argument(fullName = "exactCalculation", shortName = "exactCalculation", doc = "expt", required = false) - public ExactAFCalculationModel.ExactCalculation EXACT_CALCULATION_TYPE = ExactAFCalculationModel.ExactCalculation.N2_GOLD_STANDARD; + public ExactAFCalculationModel.ExactCalculation EXACT_CALCULATION_TYPE = ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL; @Deprecated @Argument(fullName="output_all_callable_bases", shortName="all_bases", doc="Please use --output_mode EMIT_ALL_SITES instead" ,required=false)