[med-svn] [Git][med-team/beagle][upstream] New upstream version 5.0-190712+dfsg

[Dylan Aïssi]

Dylan Aïssi pushed to branch upstream at Debian Med / beagle


Commits:
7f4a872f by Dylan Aïssi at 2019-07-13T15:09:38Z
New upstream version 5.0-190712+dfsg
- - - - -


2 changed files:

- beagleutil/Samples.java
- main/Main.java


Changes:

=====================================
beagleutil/Samples.java
=====================================
@@ -57,8 +57,8 @@ public final class Samples {
         for (int j=0; j<idIndices.length; ++j) {
             int idIndex = idIndices[j];
             if (idIndexToIndex[idIndex] != -1) {
-                String s = "duplicate sample: " + sampleIds.id(idIndex) +
-                        " (ID index: " + idIndex + ")";
+                String s = "ERROR: Duplicate sample (" + sampleIds.id(idIndex) +
+                        ") in target and/or reference file";
                 throw new IllegalArgumentException(s);
             }
             else {


=====================================
main/Main.java
=====================================
@@ -68,8 +68,8 @@ public class Main {
      * The program name and version.
      */
     public static final String VERSION = "(version 5.0)";
-    public static final String PROGRAM = "beagle.03Jul19.b33.jar";
-    public static final String COMMAND = "java -jar beagle.03Jul19.b33.jar";
+    public static final String PROGRAM = "beagle.12Jul19.0df.jar";
+    public static final String COMMAND = "java -jar beagle.12Jul19.0df.jar";
 
     /**
      * The copyright string.
@@ -81,7 +81,7 @@ public class Main {
      */
     public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
             + Const.nl + Main.COPYRIGHT
-            + Const.nl + "Enter \"java -jar beagle.03Jul19.b33.jar\" to "
+            + Const.nl + "Enter \"java -jar beagle.12Jul19.0df.jar\" to "
             + "list command line argument";
 
     private final Par par;
@@ -193,14 +193,16 @@ public class Main {
 
     private void printOutput(CurrentData cd, GT phasedTarg) {
         assert par.gt()!=null;
-        int refStart = cd.prevSpliceStart();
-        int refEnd = cd.nextSpliceStart();
         int nThreads = par.nthreads();
         if (cd.nMarkers()==cd.nTargMarkers() || par.impute() == false) {
-            windowWriter.print(phasedTarg, refStart, refEnd, nThreads);
+            int targStart = cd.prevTargetSpliceStart();
+            int targEnd = cd.nextTargetSpliceStart();
+            windowWriter.print(phasedTarg, targStart, targEnd, nThreads);
         }
         else {
             long t0 = System.nanoTime();
+            int refStart = cd.prevSpliceStart();
+            int refEnd = cd.nextSpliceStart();
             ImpData impData = new ImpData(par, cd, phasedTarg, genMap);
             AtomicReferenceArray<StateProbs> stateProbs = ImpLS.stateProbs(impData);
             windowWriter.print(impData, stateProbs, refStart, refEnd);



View it on GitLab: https://salsa.debian.org/med-team/beagle/commit/7f4a872f68e23e1730dd3f4accf6854c79db3191

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/commit/7f4a872f68e23e1730dd3f4accf6854c79db3191
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/20190713/213ba34d/attachment-0001.html>