[med-svn] [beagle] 02/04: Imported Upstream version 4.1~170608+dfsg

[Dylan Aïssi]

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

commit d727e4ad8379c5379065b0e718bf80e8189a4f78
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Jun 23 21:46:58 2017 +0200

    Imported Upstream version 4.1~170608+dfsg
---
 main/LowMemHapAlleleProbs.java |  5 +---
 main/Main.java                 |  6 ++---
 vcf/BrefIt.java                | 55 ++++++++++++++++++++++--------------------
 3 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/main/LowMemHapAlleleProbs.java b/main/LowMemHapAlleleProbs.java
index e1403f7..2001db7 100644
--- a/main/LowMemHapAlleleProbs.java
+++ b/main/LowMemHapAlleleProbs.java
@@ -72,14 +72,11 @@ public class LowMemHapAlleleProbs implements HapAlleleProbs {
             int end = markers.sumAlleles(m+1);
             for (int j=start; j<end; ++j) {
                 float p = alleleProbs[j];
-                if (p < 0 || p > 1.01f || Float.isNaN(p)) {
+                if (p < 0 || p > 1.05f || Float.isNaN(p)) {
                     throw new IllegalArgumentException(String.valueOf(p));
                 }
                 sum += alleleProbs[j];
             }
-            if (sum > 1.01f) {
-                throw new IllegalArgumentException(String.valueOf(sum));
-            }
             for (int j=start; j<end - 1; ++j) {
                 nonRefProbs[index++] = convertToByte(alleleProbs[j] / sum);
             }
diff --git a/main/Main.java b/main/Main.java
index 64f7d71..397b0c6 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.21Jan17.6cc.jar (version 4.1)";
-    public static final String command = "java -jar beagle.21Jan17.6cc.jar";
+    public static final String program = "beagle.08Jun17.d8b.jar (version 4.1)";
+    public static final String command = "java -jar beagle.08Jun17.d8b.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.21Jan17.6cc.jar\" for a "
+            + Const.nl + "Enter \"java -jar beagle.08Jun17.d8b.jar\" for a "
             + "summary of command line " + "arguments.";
 
     private final Par par;
diff --git a/vcf/BrefIt.java b/vcf/BrefIt.java
index 9027546..74fe2a7 100644
--- a/vcf/BrefIt.java
+++ b/vcf/BrefIt.java
@@ -222,35 +222,38 @@ public final class BrefIt implements SampleFileIt<VcfEmission> {
 
     private void fillBuffer() {
         assert emBuffer.isEmpty();
+        int nRecords;
         try {
-            int nRecords = is.readInt();
-            if (nRecords>0) {
-                String chrom  = is.readUTF();
-                int chromIndex = ChromIds.instance().getIndex(chrom);
-                int nSeq = is.readByte() + SHIFT;
-                IntArray hapToSeq = readHapToSeq(nSeq);
-                for (int j=0; j<nRecords; ++j) {
-                    Marker marker = readMarker(chromIndex);
-                    byte flag = is.readByte();
-                    switch (flag) {
-                        case 0:
-                            VcfEmission em = readSeqCodedRecord(marker,
-                                    samples, hapToSeq, nSeq);
-                            if (markerFilter.accept(marker)) {
-                                emBuffer.add(em);
-                            }
-                            break;
-                        case 1:
-                            em = readLowMafRecord(marker, samples);
-                            if (markerFilter.accept(marker)) {
-                                emBuffer.add(em);
-                            }
-                            break;
-                        default:
-                            Utilities.exit("Error reading file.");
+            do {
+                nRecords = is.readInt();
+                if (nRecords>0) {
+                    String chrom  = is.readUTF();
+                    int chromIndex = ChromIds.instance().getIndex(chrom);
+                    int nSeq = is.readByte() + SHIFT;
+                    IntArray hapToSeq = readHapToSeq(nSeq);
+                    for (int j=0; j<nRecords; ++j) {
+                        Marker marker = readMarker(chromIndex);
+                        byte flag = is.readByte();
+                        switch (flag) {
+                            case 0:
+                                VcfEmission em = readSeqCodedRecord(marker,
+                                        samples, hapToSeq, nSeq);
+                                if (markerFilter.accept(marker)) {
+                                    emBuffer.add(em);
+                                }
+                                break;
+                            case 1:
+                                em = readLowMafRecord(marker, samples);
+                                if (markerFilter.accept(marker)) {
+                                    emBuffer.add(em);
+                                }
+                                break;
+                            default:
+                                Utilities.exit("Error reading file.");
+                        }
                     }
                 }
-            }
+            } while (nRecords>0 && emBuffer.isEmpty());
         } catch (IOException ex) {
             Utilities.exit("Error reading file", ex);
         }

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