[med-svn] [Git][med-team/beagle][master] 3 commits: New upstream version 250227

[Dylan Aïssi (@daissi)]

Dylan Aïssi pushed to branch master at Debian Med / beagle


Commits:
545cfec9 by Dylan Aïssi at 2025-07-19T09:44:28+02:00
New upstream version 250227
- - - - -
508cbfff by Dylan Aïssi at 2025-07-19T09:44:29+02:00
Update upstream source from tag 'upstream/250227'

Update to upstream version '250227'
with Debian dir 0cf543dfbd5c1a1081b4adc86367c323d672fe31
- - - - -
00e17de2 by Dylan Aïssi at 2025-07-19T09:45:05+02:00
Bump debian/changelog

- - - - -


5 changed files:

- bref/Bref3.java
- bref/SeqCoder3.java
- bref/UnBref3.java
- debian/changelog
- 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.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+beagle (250227-1) UNRELEASED; urgency=medium
+
+  * New upstream version 250227
+
+ -- Dylan Aïssi <daissi at debian.org>  Sat, 19 Jul 2025 09:44:33 +0200
+
 beagle (241217-3) unstable; urgency=medium
 
   * Don't run at all autopkgtest on unsupported architectures.


=====================================
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/-/compare/0e360e20031e8c1e4b62063dbd6a6b52a593fa07...00e17de2387030bdd5889f1140501c52d86c0db0

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/compare/0e360e20031e8c1e4b62063dbd6a6b52a593fa07...00e17de2387030bdd5889f1140501c52d86c0db0
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250719/e73d853d/attachment-0001.htm>