From fe3cfb067cd81859babd08960edae8f71cb7ea25 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 28 Oct 2010 02:11:33 +0000
Subject: [PATCH] very minor cleanup

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4590 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/annotator/genomicannotator/GenomicAnnotator.java    | 2 +-
 java/src/org/broadinstitute/sting/utils/MathUtils.java          | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
index 94e0e4f8b..01df8d0b9 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
@@ -71,7 +71,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> implements Tre
     @Argument(fullName="select", shortName="s", doc="Optionally specifies which subset of columns from which -B inputs should be used for annotations. For example, -B:mydbsnp,AnnotatorInputTable /path/to/mydbsnp.txt -B:mytable,AnnotatorInputTable /path/mytable.txt -s mydbsnp.avHet,mydbsnp.name,mytable.column3 will cause annotations to only be generated from the 3 columns specified using -s.", required=false)
     protected String[] SELECT_COLUMNS = {};
 
-    @Argument(fullName="join", shortName="J", doc="Optionally specifies a file and column within that file that should be LEFT-JOIN'ed to a column in a previously-specified file. The file provided to -J must be tab-delimited, with the first non-comment/non-empty line containing column names. (example: -B name,AnnotatorInputTable,/path/to/file1   -J name2,/path/to/file2,name.columnName=name2.columnName2  - this will join the table in file2 to the table in file1) ", required=false)
+    @Argument(fullName="join", shortName="J", doc="Optionally specifies a file and column within that file that should be LEFT-JOIN'ed to a column in a previously-specified file. The file provided to -J must be tab-delimited, with the first non-comment/non-empty line containing column names. (example: -B:name,AnnotatorInputTable /path/to/file1   -J name2,/path/to/file2,name.columnName=name2.columnName2  - this will join the table in file2 to the table in file1) ", required=false)
     protected String[] JOIN_ARGS = {};
 
     @Argument(fullName="oneToMany", shortName="m", doc="If more than one record from the same file matches a particular locus (for example, multiple dbSNP records with the same position), create multiple entries in the ouptut VCF file - one for each match. If a particular tabular file has J matches, and another tabular file has K matches for a given locus, then J*K output VCF records will be generated - one for each pair of K, J.   If this flag is not provided, the multiple records are still generated, but they are stored in the INFO field of a single output VCF record, with their annotation keys differentiated by appending '_i' with i varying from 1 to K*J. ", required=false)
diff --git a/java/src/org/broadinstitute/sting/utils/MathUtils.java b/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 4243f55ba..ee6897de8 100755
--- a/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -31,7 +31,6 @@ import java.math.BigDecimal;
 import java.util.*;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.playground.gatk.walkers.genotyper.AlleleFrequencyCalculationModel;
 
 /**
  * MathUtils is a static class (no instantiation allowed!) with some useful math methods.