[med-svn] [Git][med-team/beagle][upstream] New upstream version 220722

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / beagle


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


5 changed files:

- bref/Bref3.java
- bref/UnBref3.java
- 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.


=====================================
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/-/commit/fb02eb95180ae9020f54219c09c26e9428e86cc5

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/commit/fb02eb95180ae9020f54219c09c26e9428e86cc5
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