From 7d11b4d5f160185fe6521ee5821b3d2bd412cea8 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 12 Mar 2014 10:19:16 -0400 Subject: [PATCH] Balancing training classes between SNP/Indel and TP/FP. -- This results in much more consistent distribution of LOD scores for SNPs and Indels. -- Removing genotype summary stats since they are now produced by default. -- Added functionality to specify certain subsets of the training data to be used in Tranche file generation, -good:tranche=true set.vcf --- .../main/java/org/broadinstitute/sting/utils/MathUtils.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java index e73797705..b8d966011 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java @@ -1537,6 +1537,9 @@ public class MathUtils { * @param N - the number of elements to draw */ public static List randomSample(final List list, final int N) { + if (list.isEmpty() ) { + return list; + } return sliceListByIndices(sampleIndicesWithReplacement(list.size(),N),list); }