From e5df91aa23c9a9cf92fc8a573f914fdd3439c979 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 22 Aug 2012 20:17:39 -0400
Subject: [PATCH] Looks like the @WalkerName annotation doesn't work with the
 GATK docs, so I'm renaming the walkers.

---
 ...rnateReference.java => FastaAlternateReferenceMaker.java} | 3 +--
 .../fasta/{FastaReference.java => FastaReferenceMaker.java}  | 5 ++---
 2 files changed, 3 insertions(+), 5 deletions(-)
 rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaAlternateReference.java => FastaAlternateReferenceMaker.java} (98%)
 rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaReference.java => FastaReferenceMaker.java} (96%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
index 8fbd37e30..2b9744b89 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
@@ -76,10 +76,9 @@ import java.util.List;
  *
  */
 @DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
-@WalkerName("FastaAlternateReferenceMaker")
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
-public class FastaAlternateReference extends FastaReference {
+public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
 
     /**
      * Variants from these input files are used by this tool to construct an alternate reference.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
index a835560d4..362867318 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
@@ -62,15 +62,14 @@ import java.io.PrintStream;
  * <pre>
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -R ref.fasta \
- *   -T FastaReference \
+ *   -T FastaReferenceMaker \
  *   -o output.fasta \
  *   -L input.intervals
  * </pre>
  *
  */
 @DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
-@WalkerName("FastaReferenceMaker")
-public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
+public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
 
     @Output PrintStream out;