[med-svn] [beagle] 02/03: New upstream version 4.1~180127+dfsg

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository beagle.

commit baf37dc83b01750f4d0e1ee9951db521b6f181e6
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Tue Jan 30 23:31:07 2018 +0100

    New upstream version 4.1~180127+dfsg
---
 main/LowMemHapAlleleProbs.java | 6 +++++-
 main/Main.java                 | 6 +++---
 vcf/R2Estimator.java           | 2 +-
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/main/LowMemHapAlleleProbs.java b/main/LowMemHapAlleleProbs.java
index 2001db7..f55bc20 100644
--- a/main/LowMemHapAlleleProbs.java
+++ b/main/LowMemHapAlleleProbs.java
@@ -98,7 +98,11 @@ public class LowMemHapAlleleProbs implements HapAlleleProbs {
     }
 
     private static float convertToFloat(byte b) {
-        return (b + 128.5f)*INCREMENT;
+        switch(b) {
+            case Byte.MIN_VALUE: return 0f;
+            case Byte.MAX_VALUE: return 1f;
+            default: return (b + 128.5f)*INCREMENT;
+        }
     }
 
     @Override
diff --git a/main/Main.java b/main/Main.java
index 397b0c6..6a73a14 100644
--- a/main/Main.java
+++ b/main/Main.java
@@ -65,8 +65,8 @@ public class Main {
     /**
      * The program name and version.
      */
-    public static final String program = "beagle.08Jun17.d8b.jar (version 4.1)";
-    public static final String command = "java -jar beagle.08Jun17.d8b.jar";
+    public static final String program = "beagle.27Jan18.7e1.jar (version 4.1)";
+    public static final String command = "java -jar beagle.27Jan18.7e1.jar";
 
     /**
      * The copyright string.
@@ -78,7 +78,7 @@ public class Main {
      */
     public static final String shortHelp = Main.program
             + Const.nl + Main.copyright
-            + Const.nl + "Enter \"java -jar beagle.08Jun17.d8b.jar\" for a "
+            + Const.nl + "Enter \"java -jar beagle.27Jan18.7e1.jar\" for a "
             + "summary of command line " + "arguments.";
 
     private final Par par;
diff --git a/vcf/R2Estimator.java b/vcf/R2Estimator.java
index e52459c..10ab8ce 100644
--- a/vcf/R2Estimator.java
+++ b/vcf/R2Estimator.java
@@ -36,7 +36,7 @@ public final class R2Estimator {
     private double sumSquareCall = 0;
     private double sumExpected = 0;
     private double sumExpectedSquare = 0;
-    private double sumSquareExpected= 0;
+    private double sumSquareExpected = 0;
     private double sumCallExpected = 0;
 
     /**

-- 
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