[med-svn] [Git][med-team/beagle][upstream] New upstream version 250227

[Dylan Aïssi (@daissi)]

Dylan Aïssi pushed to branch upstream at Debian Med / beagle


Commits:
545cfec9 by Dylan Aïssi at 2025-07-19T09:44:28+02:00
New upstream version 250227
- - - - -


4 changed files:

- bref/Bref3.java
- bref/SeqCoder3.java
- bref/UnBref3.java
- main/Main.java


Changes:

=====================================
bref/Bref3.java
=====================================
@@ -37,7 +37,7 @@ import vcf.Samples;
  */
 public class Bref3 {
 
-    private static final String PROGRAM = "bref3.17Dec24.224.jar";
+    private static final String PROGRAM = "bref3.27Feb25.75f.jar";
 
     /**
      * The {@code main()} method is the entry point to the bref program.


=====================================
bref/SeqCoder3.java
=====================================
@@ -240,7 +240,7 @@ public class SeqCoder3 {
             }
         }
         addMajorAllele(seq2NonMajorCnt, majorAllele);
-        if (seq2AlleleSeqMap.size() >= maxNSeq) {
+        if (seq2AlleleSeqMap.size() > maxNSeq) {
             seq2AlleleSeqMap.subList(nStartSeq, seq2AlleleSeqMap.size()).clear();
             return false;
         }


=====================================
bref/UnBref3.java
=====================================
@@ -37,7 +37,7 @@ import vcf.VcfWriter;
  */
 public class UnBref3 {
 
-    private static final String program = "unbref3.17Dec24.224.jar";
+    private static final String program = "unbref3.27Feb25.75f.jar";
 
     /**
      * The {@code main()} method is the entry point to the bref program.


=====================================
main/Main.java
=====================================
@@ -58,12 +58,12 @@ public class Main {
     /**
      * The program name and commit version.
      */
-    public static final String PROGRAM = "beagle.17Dec24.224.jar";
+    public static final String PROGRAM = "beagle.27Feb25.75f.jar";
 
     /**
      * The command to invoke the program.
      */
-    public static final String COMMAND = "java -jar beagle.17Dec24.224.jar";
+    public static final String COMMAND = "java -jar beagle.27Feb25.75f.jar";
 
     /**
      * The copyright string.



View it on GitLab: https://salsa.debian.org/med-team/beagle/-/commit/545cfec90c7e1e0b3d5468803e04000566f7cba5

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/commit/545cfec90c7e1e0b3d5468803e04000566f7cba5
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