Commit 51693017 authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 5.1-191120+dfsg

parent 0d3b277c

main/Main.java

+3 −3
Original line number Diff line number Diff line
@@ -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

+12 −3
Original line number Diff line number Diff line
@@ -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;

    }

}