[med-svn] [Git][med-team/beagle][upstream] New upstream version 5.1-200518+dfsg

[Dylan Aïssi]

Dylan Aïssi pushed to branch upstream at Debian Med / beagle


Commits:
699eed29 by Dylan Aïssi at 2020-05-31T15:59:56+02:00
New upstream version 5.1-200518+dfsg
- - - - -


2 changed files:

- main/Main.java
- vcf/BasicMarker.java


Changes:

=====================================
main/Main.java
=====================================
@@ -65,8 +65,8 @@ public class Main {
      * The program name and version.
      */
     public static final String VERSION = "(version 5.1)";
-    public static final String PROGRAM = "beagle.27Apr20.b81.jar";
-    public static final String COMMAND = "java -jar beagle.27Apr20.b81.jar";
+    public static final String PROGRAM = "beagle.18May20.d20.jar";
+    public static final String COMMAND = "java -jar beagle.18May20.d20.jar";
 
     /**
      * The copyright string.
@@ -78,7 +78,7 @@ public class Main {
      */
     public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
             + Const.nl + Main.COPYRIGHT
-            + Const.nl + "Enter \"java -jar beagle.27Apr20.b81.jar\" to "
+            + Const.nl + "Enter \"java -jar beagle.18May20.d20.jar\" to "
             + "list command line argument";
 
     private final Par par;


=====================================
vcf/BasicMarker.java
=====================================
@@ -23,10 +23,9 @@ import blbutil.Const;
 import blbutil.StringUtil;
 import blbutil.Utilities;
 import java.util.Arrays;
-import java.util.HashMap;
 import java.util.HashSet;
-import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * <p>Class {@code BasicMarker} represents a genetic marker.
@@ -39,8 +38,8 @@ import java.util.Set;
 public class BasicMarker implements Marker {
 
     private static final String[] EMPTY_ID_ARRAY = new String[0];
-    private static final Map<String, String[]> ALLELES_MAP
-            = new HashMap<>(24);
+    private static final ConcurrentHashMap<String, String[]> ALLELES_MAP
+            = new ConcurrentHashMap<>(24); // allows re-use of String[] arrays
 
     private final int chromIndex;
     private final int pos;
@@ -189,7 +188,7 @@ public class BasicMarker implements Marker {
         }
     }
 
-    /* Return specified String[] alleles if not a SNV */
+    /* Returns specified String[] alleles if not a SNV */
     private static String[] canonicalAlleles(String[] alleles) {
         if (isSNV(alleles)) {
             String key = alleles[0];



View it on GitLab: https://salsa.debian.org/med-team/beagle/-/commit/699eed2975f501a3637ccee42d3c17f16acb3ae2

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/commit/699eed2975f501a3637ccee42d3c17f16acb3ae2
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