Commit a65a6809 authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 5.0-190703+dfsg

parent 984ed8b0

beagleutil/ChromIds.java

+5 −6
Original line number Diff line number Diff line
@@ -18,10 +18,11 @@ 
 */

package beagleutil;



import java.util.ArrayList;

import java.util.Arrays;

import java.util.List;

import java.util.concurrent.ConcurrentHashMap;

import java.util.concurrent.ConcurrentMap;

import java.util.concurrent.CopyOnWriteArrayList;



/**

 * <p>Class {@code ChromIds} is a singleton class that represents a
@@ -38,7 +39,7 @@ public final class ChromIds { 
    private final ThreadSafeIndexer<String> indexer;



    private final ConcurrentMap<String, Integer> map;

    private volatile CopyOnWriteArrayList<String> ids;

    private volatile List<String> ids;



    private ChromIds() {

        // private constructor to restrict instantiation.
@@ -46,7 +47,7 @@ public final class ChromIds { 
        this.indexer = new ThreadSafeIndexer<>(initCapacity);



        this.map = new ConcurrentHashMap<>(initCapacity);

        this.ids = new CopyOnWriteArrayList<>(new String[0]);

        this.ids = new ArrayList<>();

    }



    /**
@@ -149,9 +150,7 @@ public final class ChromIds { 
     */

    public String id(int index) {

        if (index >= ids.size()) {

            for (int j=ids.size(), n=indexer.size(); j<n; ++j) {

                ids.add(indexer.item(j));

            }

            ids = indexer.items();

        }

        return ids.get(index);

    }

main/Main.java

+3 −3
Original line number Diff line number Diff line
@@ -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.28Sep18.793.jar";

    public static final String COMMAND = "java -jar beagle.28Sep18.793.jar";

    public static final String PROGRAM = "beagle.03Jul19.b33.jar";

    public static final String COMMAND = "java -jar beagle.03Jul19.b33.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.28Sep18.793.jar\" to "

            + Const.nl + "Enter \"java -jar beagle.03Jul19.b33.jar\" to "

            + "list command line argument";



    private final Par par;

vcf/AllData.java

+2 −4
Original line number Diff line number Diff line
@@ -130,8 +130,7 @@ public class AllData implements Data { 


    private static GT targGTWindow(Samples samples, GTRec[] targData,

            Pedigree ped) {

        GT gt = new BasicGT(samples, targData);

        return gt.isGTData() ? new XBasicGT(gt, ped) : gt;

        return new BasicGT(samples, targData);

    }



    @Override
@@ -214,8 +213,7 @@ public class AllData implements Data { 
        for (int j=0; j<refMarkerIndex.length; ++j) {

            restricted[j] = vma[refMarkerIndex[j]];

        }

        GT gt = new BasicGT(samples, restricted);

        return gt.isGTData() ? new XBasicGT(gt, ped) : gt;

        return new BasicGT(samples, restricted);

    }



    private void setRefHaplotypes(RefGT refGT) {

vcf/RestrictedVcfWindow.java

+4 −2
Original line number Diff line number Diff line
@@ -98,10 +98,12 @@ public class RestrictedVcfWindow implements Closeable { 
        for (int j = fullOverlap, n=nextMarkers.nMarkers(); j<n; ++j) {

            Marker m = nextMarkers.marker(j);

            if (next!=null && next.marker().chromIndex()==m.chromIndex()) {

                while (next != null && next.marker().pos() < m.pos()) {

                while (next != null && next.marker().chromIndex()==m.chromIndex()

                        && next.marker().pos()<m.pos()) {

                    next = it.hasNext() ? it.next() : null;

                }

                while (next != null && next.marker().pos() == m.pos()

                while (next != null && next.marker().chromIndex()==m.chromIndex()

                        && next.marker().pos()==m.pos()

                        && next.marker().equals(m)==false) {

                    next = it.hasNext() ? it.next() : null;

                }

vcf/TargetData.java

+1 −2
Original line number Diff line number Diff line
@@ -88,8 +88,7 @@ public class TargetData implements Data { 


    private static GT targGT(Samples samples, GTRec[] targData,

            Pedigree ped) {

        GT gt = new BasicGT(samples, targData);

        return gt.isGTData() ? new XBasicGT(gt, ped) : gt;

        return new BasicGT(samples, targData);

    }



    @Override