[med-svn] [Git][med-team/beagle][master] 4 commits: New upstream version 220722

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / beagle


Commits:
fb02eb95 by Andreas Tille at 2022-07-28T10:51:55+02:00
New upstream version 220722
- - - - -
2bf17155 by Andreas Tille at 2022-07-28T10:51:55+02:00
routine-update: New upstream version

- - - - -
cedf730b by Andreas Tille at 2022-07-28T10:51:55+02:00
Update upstream source from tag 'upstream/220722'

Update to upstream version '220722'
with Debian dir ca47b287e0156f8e8e8af6cdc26b34e1dbb2cc54
- - - - -
c9568fa9 by Andreas Tille at 2022-07-28T10:53:26+02:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- bref/Bref3.java
- bref/UnBref3.java
- debian/changelog
- main/Main.java
- vcf/RefTargSlidingWindow.java
- vcf/TargSlidingWindow.java


Changes:

=====================================
bref/Bref3.java
=====================================
@@ -38,7 +38,7 @@ import vcf.Samples;
  */
 public class Bref3 {
 
-    private static final String program = "bref3.05May22.33a.jar";
+    private static final String program = "bref3.22Jul22.46e.jar";
 
     /**
      * The {@code main()} method is the entry point to the bref program.


=====================================
bref/UnBref3.java
=====================================
@@ -37,7 +37,7 @@ import vcf.VcfWriter;
  */
 public class UnBref3 {
 
-    private static final String program = "unbref3.05May22.33a.jar";
+    private static final String program = "unbref3.22Jul22.46e.jar";
 
     /**
      * The {@code main()} method is the entry point to the bref program.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+beagle (220722-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Thu, 28 Jul 2022 10:52:20 +0200
+
 beagle (220505-1) unstable; urgency=medium
 
   * Team upload.


=====================================
main/Main.java
=====================================
@@ -58,12 +58,12 @@ public class Main {
     /**
      * The program name and commit version.
      */
-    public static final String PROGRAM = "beagle.05May22.33a.jar";
+    public static final String PROGRAM = "beagle.22Jul22.46e.jar";
 
     /**
      * The command to invoke the program.
      */
-    public static final String COMMAND = "java -jar beagle.05May22.33a.jar";
+    public static final String COMMAND = "java -jar beagle.22Jul22.46e.jar";
 
     /**
      * The copyright string.


=====================================
vcf/RefTargSlidingWindow.java
=====================================
@@ -161,8 +161,9 @@ public class RefTargSlidingWindow implements SlidingWindow {
             if (window.lastWindow()) {
                 noMoreWindows = true;
             }
-            cumTargMarkers += window.targGT().nMarkers();
-            cumRefMarkers += window.refGT().get().nMarkers();
+            MarkerIndices indices = window.indices();
+            cumTargMarkers += (indices.nTargMarkers() - indices.targOverlapEnd());
+            cumRefMarkers += (indices.nMarkers() - indices.overlapEnd());
             return Optional.of(window);
         }
     }


=====================================
vcf/TargSlidingWindow.java
=====================================
@@ -131,7 +131,8 @@ public class TargSlidingWindow implements SlidingWindow {
             if (window.lastWindow()) {
                 noMoreWindows = true;
             }
-            cumTargMarkers += window.targGT().nMarkers();
+            MarkerIndices indices = window.indices();
+            cumTargMarkers += (indices.nTargMarkers() - indices.targOverlapEnd());
             return Optional.of(window);
         }
     }



View it on GitLab: https://salsa.debian.org/med-team/beagle/-/compare/38bf3dea61aa45e6d9d0689ddd8503cb053e85fa...c9568fa92ceda801780b470be0bbdc4126e7e245

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/compare/38bf3dea61aa45e6d9d0689ddd8503cb053e85fa...c9568fa92ceda801780b470be0bbdc4126e7e245
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