debian/changelog

-beagle (5.1-191108+dfsg-1) UNRELEASED; urgency=medium
+beagle (5.1-191120+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream release.
   * Replace ADTTMP with AUTOPKGTEST_TMP.

main/Main.java

@@ -65,8 +65,8 @@ public class Main {
      * The program name and version.
      */
     public static final String VERSION = "(version 5.1)";
-    public static final String PROGRAM = "beagle.08Nov19.3ec.jar";
-    public static final String COMMAND = "java -jar beagle.08Nov19.3ec.jar";
+    public static final String PROGRAM = "beagle.20Nov19.573.jar";
+    public static final String COMMAND = "java -jar beagle.20Nov19.573.jar";
 
     /**
      * The copyright string.
@@ -78,7 +78,7 @@ public class Main {
      */
     public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION
             + Const.nl + Main.COPYRIGHT
-            + Const.nl + "Enter \"java -jar beagle.08Nov19.3ec.jar\" to "
+            + Const.nl + "Enter \"java -jar beagle.20Nov19.573.jar\" to "
             + "list command line argument";
 
     private final Par par;

vcf/RefIt.java

@@ -69,6 +69,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {
     private final List<RefGTRec> midBuffer;
     private final Deque<RefGTRec> recBuffer;
     private final SeqCoder3 seqCoder;
+    private final int maxSeqCodedAlleles;
+    private final int maxSeqCodingMajorCnt;
 
     private final ExecutorService es;
 
@@ -141,6 +143,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {
         } ;
         this.markerFilter = markerFilter;
         this.seqCoder = new SeqCoder3(vcfHeader.samples());
+        this.maxSeqCodedAlleles = Math.min(seqCoder.maxNSeq(), SeqCoder3.MAX_NALLELES);
+        this.maxSeqCodingMajorCnt = maxSeqCodingMajorCnt(vcfHeader.samples());
 
         this.lastChrom = -1;
         this.stringBuffer = new ArrayBlockingQueue<>(1);
@@ -152,6 +156,11 @@ public class RefIt implements SampleFileIt<RefGTRec> {
         fillEmissionBuffer();
     }
 
+    private int maxSeqCodingMajorCnt(Samples samples) {
+        int nHaps = samples.nSamples() << 1;
+        return (int) Math.floor(nHaps*SeqCoder3.COMPRESS_FREQ_THRESHOLD - 1);
+    }
+
     private static void startFileReadingThread(ExecutorService es,
             ArrayBlockingQueue<String[]> q, String firstRec, FileIt<String> it,
             int bufferSize) {
@@ -308,9 +317,9 @@ public class RefIt implements SampleFileIt<RefGTRec> {
         return sb.toString();
     }
 
-    private static boolean applySeqCoding(RefGTRec rec) {
+    private boolean applySeqCoding(RefGTRec rec) {
         assert rec.isAlleleCoded();
-        if (rec.marker().nAlleles() > SeqCoder3.MAX_NALLELES) {
+        if (rec.marker().nAlleles() >= maxSeqCodedAlleles) {
             return false;
         }
         int nHaps = rec.size();
@@ -321,6 +330,6 @@ public class RefIt implements SampleFileIt<RefGTRec> {
                 majCnt -= rec.alleleCount(a);
             }
         }
-        return (SeqCoder3.COMPRESS_FREQ_THRESHOLD >=(1.0f + majCnt)/nHaps);
+        return majCnt<=maxSeqCodingMajorCnt;
     }
 }