From 02942a97ef6e7e14019efa502b0b03fea3c68c1f Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 7 Oct 2022 16:22:19 -0400
Subject: [PATCH] Remove deprecation from Allele.acceptableAlleleBases #1623
 (#1625)

* Remove deprecation from Allele.acceptableAlleleBases
* These methods were deprecated in 3.0.0, it seems like that was probably a mistake
  since there is no obvious replacement for this useful functionality.
* fixes #1623
---
 src/main/java/htsjdk/variant/variantcontext/Allele.java    | 7 ++-----
 .../java/htsjdk/variant/variantcontext/SimpleAllele.java   | 2 +-
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/main/java/htsjdk/variant/variantcontext/Allele.java b/src/main/java/htsjdk/variant/variantcontext/Allele.java
index 36da06aba0..b256d2d9dd 100644
--- a/src/main/java/htsjdk/variant/variantcontext/Allele.java
+++ b/src/main/java/htsjdk/variant/variantcontext/Allele.java
@@ -26,6 +26,7 @@
 package htsjdk.variant.variantcontext;
 
 import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Immutable representation of an allele.
@@ -285,7 +286,6 @@ static boolean wouldBeSingleBreakend(byte[] bases) {
      * @param bases  bases representing a reference allele
      * @return true if the bases represent the well formatted allele
      */
-    @Deprecated
     static boolean acceptableAlleleBases(String bases) {
         return acceptableAlleleBases(bases.getBytes(), true);
     }
@@ -295,16 +295,14 @@ static boolean acceptableAlleleBases(String bases) {
      * @param isReferenceAllele is a reference allele
      * @return true if the bases represent the well formatted allele
      */
-    @Deprecated
     static boolean acceptableAlleleBases(String bases, boolean isReferenceAllele) {
-        return acceptableAlleleBases(bases.getBytes(), isReferenceAllele);
+        return acceptableAlleleBases(bases.getBytes(StandardCharsets.UTF_8), isReferenceAllele);
     }
 
     /**
      * @param bases  bases representing a reference allele
      * @return true if the bases represent the well formatted allele
      */
-    @Deprecated
     static boolean acceptableAlleleBases(byte[] bases) {
         return acceptableAlleleBases(bases, true);
     }
@@ -315,7 +313,6 @@ static boolean acceptableAlleleBases(byte[] bases) {
      * @param isReferenceAllele true if a reference allele
      * @return true if the bases represent the well formatted allele
      */
-    @Deprecated
     static boolean acceptableAlleleBases(byte[] bases, boolean isReferenceAllele) {
         if ( wouldBeNullAllele(bases) )
             return false;
diff --git a/src/main/java/htsjdk/variant/variantcontext/SimpleAllele.java b/src/main/java/htsjdk/variant/variantcontext/SimpleAllele.java
index ba4c3d2d44..db61712410 100644
--- a/src/main/java/htsjdk/variant/variantcontext/SimpleAllele.java
+++ b/src/main/java/htsjdk/variant/variantcontext/SimpleAllele.java
@@ -76,7 +76,7 @@ protected SimpleAllele(final byte[] bases, final boolean isRef) {
         this.bases = bases;
 
         if ( ! Allele.acceptableAlleleBases(bases, isRef) )
-            throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
+            throw new IllegalArgumentException("Unexpected base in allele bases '" + new String(bases)+"'");
     }
 
     protected SimpleAllele(final String bases, final boolean isRef) {