From e7d41d8d334221c12dc89a080a3ec55bb9cc4bfb Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 17 Nov 2011 12:00:28 -0500
Subject: [PATCH] Minor cleanup

---
 .../gatk/walkers/variantutils/SelectVariants.java      | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 609593acc..b92b1cee0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -24,10 +24,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.apache.poi.hpsf.Variant;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -275,8 +273,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     private double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 0;
 
     /**
-     * Variants are kept in memory to guarantee that exactly n variants will be chosen randomly, so use it only for a reasonable
-     * number of variants.  Use --select_random_fraction for larger numbers of variants.
+     * Variants are kept in memory to guarantee that exactly n variants will be chosen randomly, so make sure you supply the program with enough memory
+     * given your input set.  This option will NOT work well for large callsets; use --select_random_fraction for sets with a large numbers of variants.
      */
     @Argument(fullName="select_random_number", shortName="number", doc="Selects a number of variants at random from the variant track", required=false)
     private int numRandom = 0;
@@ -532,7 +530,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                     }
                 }
                 if (SELECT_RANDOM_NUMBER) {
-                    randomlyAddVariant(++variantNumber, sub, ref.getBase());
+                    randomlyAddVariant(++variantNumber, sub);
                 }
                 else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
                     vcfWriter.add(sub);
@@ -705,7 +703,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         return sub;
     }
 
-    private void randomlyAddVariant(int rank, VariantContext vc, byte refBase) {
+    private void randomlyAddVariant(int rank, VariantContext vc) {
         if (nVariantsAdded < numRandom)
             variantArray[nVariantsAdded++] = new RandomVariantStructure(vc);