Commit 7f4a872f authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 5.0-190712+dfsg

parent a65a6809

beagleutil/Samples.java

+2 −2
Original line number Diff line number Diff line
@@ -57,8 +57,8 @@ public final class Samples { 
        for (int j=0; j<idIndices.length; ++j) {

            int idIndex = idIndices[j];

            if (idIndexToIndex[idIndex] != -1) {

                String s = "duplicate sample: " + sampleIds.id(idIndex) +

                        " (ID index: " + idIndex + ")";

                String s = "ERROR: Duplicate sample (" + sampleIds.id(idIndex) +

                        ") in target and/or reference file";

                throw new IllegalArgumentException(s);

            }

            else {

main/Main.java

+8 −6
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.03Jul19.b33.jar";

    public static final String COMMAND = "java -jar beagle.03Jul19.b33.jar";

    public static final String PROGRAM = "beagle.12Jul19.0df.jar";

    public static final String COMMAND = "java -jar beagle.12Jul19.0df.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.03Jul19.b33.jar\" to "

            + Const.nl + "Enter \"java -jar beagle.12Jul19.0df.jar\" to "

            + "list command line argument";



    private final Par par;
@@ -193,14 +193,16 @@ public class Main { 


    private void printOutput(CurrentData cd, GT phasedTarg) {

        assert par.gt()!=null;

        int refStart = cd.prevSpliceStart();

        int refEnd = cd.nextSpliceStart();

        int nThreads = par.nthreads();

        if (cd.nMarkers()==cd.nTargMarkers() || par.impute() == false) {

            windowWriter.print(phasedTarg, refStart, refEnd, nThreads);

            int targStart = cd.prevTargetSpliceStart();

            int targEnd = cd.nextTargetSpliceStart();

            windowWriter.print(phasedTarg, targStart, targEnd, nThreads);

        }

        else {

            long t0 = System.nanoTime();

            int refStart = cd.prevSpliceStart();

            int refEnd = cd.nextSpliceStart();

            ImpData impData = new ImpData(par, cd, phasedTarg, genMap);

            AtomicReferenceArray<StateProbs> stateProbs = ImpLS.stateProbs(impData);

            windowWriter.print(impData, stateProbs, refStart, refEnd);