From 8defb30796354025c54f838cc09496f347ed15f5 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 14 Jun 2010 21:31:01 +0000
Subject: [PATCH] Documentation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java | 3 ---
 .../gatk/walkers/HLAcaller/FindClosestHLAWalker.java      | 3 ---
 .../gatk/walkers/HLAcaller/HLACallerWalker.java           | 8 ++++----
 3 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
index e332e6c89..dd82a8fd7 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
@@ -48,13 +48,10 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
     public boolean DEBUG = false;
     @Argument(fullName = "debugAlleles", shortName = "debugAlleles", doc = "Print likelihood scores for these alleles", required = false)
     public String inputAlleles = "";
-    @Argument(fullName = "ethnicity", shortName = "ethnicity", doc = "Use allele frequencies for this ethnic group", required = false)
-    public String ethnicity = "CaucasianUSA";
     @Argument(fullName = "filter", shortName = "filter", doc = "file containing reads to exclude", required = false)
     public String filterFile = "";
     @Argument(fullName = "maxAllowedMismatches", shortName = "maxAllowedMismatches", doc = "Max number of mismatches tolerated per read (default 7)", required = false)
     public int MAXALLOWEDMISMATCHES = 6;
-
     @Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
     public int MINREQUIREDMATCHES = 0;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java
index 2095d2c99..369778b80 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java
@@ -60,9 +60,6 @@ public class FindClosestHLAWalker extends ReadWalker<Integer, Integer> {
     @Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false)
     public boolean ONLYFREQUENT = false;
     
-    @Argument(fullName = "HLAfrequencies", shortName = "HLAfrequencies", doc = "HLA allele frequencies file", required = true)
-    public String AlleleFrequencyFile = "HLA_FREQUENCIES.txt";
-
     @Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true)
     public String HLAdatabaseFile = "HLA_DICTIONARY.txt";
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
index 6be125e98..0e8bc99e5 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
@@ -57,8 +57,8 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
     @Argument(fullName = "debugAlleles", shortName = "debugAlleles", doc = "Print likelihood scores for these alleles", required = false)
     public String debugAlleles = "";
 
-    @Argument(fullName = "phaseInterval", shortName = "phaseInterval", doc = "Use only these intervals in phase calculation", required = false)
-    public String phaseIntervalFile = "";
+    @Argument(fullName = "useInterval", shortName = "useInterval", doc = "Use only these intervals in phase calculation", required = false)
+    public String IntervalsFile = "";
 
     @Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false)
     public boolean ONLYFREQUENT = false;
@@ -174,9 +174,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
 
             //Load genomic intervals for bam file
             
-            if (!phaseIntervalFile.equals("")){
+            if (!IntervalsFile.equals("")){
                 TextFileReader fileReader = new TextFileReader();
-                fileReader.ReadFile(phaseIntervalFile);
+                fileReader.ReadFile(IntervalsFile);
                 String[] lines = fileReader.GetLines();
                 intervals = new int[lines.length][2];
                 for (int i = 0; i < lines.length; i++) {