From b3c3023c3ced88987e586918fd9c439846035995 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 14 Jun 2010 18:56:08 +0000
Subject: [PATCH] Allows callers to handle HLA reference files as input (rather
 than hard-coded paths)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../HLAcaller/CalculateBaseLikelihoodsWalker.java     | 11 -----------
 .../gatk/walkers/HLAcaller/FindClosestHLAWalker.java  | 11 ++++++++---
 .../gatk/walkers/HLAcaller/HLACallerWalker.java       | 10 ++++++----
 3 files changed, 14 insertions(+), 18 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 84205de97..e332e6c89 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
@@ -58,17 +58,6 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
     @Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
     public int MINREQUIREDMATCHES = 0;
 
-    String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_DICTIONARY.sam";
-    String CaucasianAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_Caucasians.freq";
-    String BlackAlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_BlackUSA.freq";
-    String AlleleFrequencyFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_CaucasiansUSA.freq";
-    String UniqueAllelesFile               = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/UniqueAlleles";
-    SAMFileReader HLADictionaryReader = new SAMFileReader();
-    String[] HLAreads, HLAnames;
-    Integer[] HLAstartpos, HLAstoppos;
-
-    Hashtable AlleleFrequencies,UniqueAlleles;
-
     int[][] LOD, LikelihoodScores;
     ArrayList<String> ReadsToDiscard = new ArrayList<String>();
 
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 199fc6ef9..2095d2c99 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
@@ -60,10 +60,15 @@ 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;
     
-    String HLAdatabaseFile              = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_DICTIONARY.txt";
-    String PolymorphicSitesFile         = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_POLYMORPHIC_SITES.txt";
-    String AlleleFrequencyFile          = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_FREQUENCIES.txt";
+    @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";
+
+    @Argument(fullName = "PolymorphicSites", shortName = "PolymorphicSites", doc = "file containing polymorphic sites within the HLA", required = true)
+    public String PolymorphicSitesFile = "HLA_POLYMORPHIC_SITES.txt";
+    
     HLAFileReader HLADictionaryReader = new HLAFileReader();    
 
     boolean DatabaseLoaded = false;
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 8a98f6e17..6be125e98 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
@@ -69,12 +69,14 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
     @Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
     public int MINREQUIREDMATCHES = 5;
 
+    @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";
+
     GATKArgumentCollection args = this.getToolkit().getArguments();
     
-    String AlleleFrequencyFile          = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_FREQUENCIES.txt";
-    String PolymorphicSitesfile         = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_POLYMORPHIC_SITES.txt";
-    String HLAdatabaseFile              = "/humgen/gsa-scr1/GSA/sjia/HLA_CALLER/HLA_DICTIONARY.txt";
-
     // Initializing variables
     
     HLAFileReader HLADictionaryReader = new HLAFileReader();