Commit 169b5c18 authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 5.0-180915+dfsg

parent 383b5902

imp/ImputedRecBuilder.java

+22 −14
Original line number Diff line number Diff line
@@ -261,6 +261,12 @@ public final class ImputedRecBuilder { 
    }



    private void printInfoField(PrintWriter out, boolean isImputed) {

        if (nAlleles==1) {

            if (isImputed) {

                out.print("IMP");

            }

        }

        else {

            for (int a=1; a<nAlleles; ++a) {

                out.print( (a==1) ? "DR2=" : Const.comma);

                out.print(R2_VALS[(int) Math.rint(100*r2(a))]);
@@ -277,6 +283,7 @@ public final class ImputedRecBuilder { 
                out.print(";IMP");

            }

        }

    }



    private float r2(int allele) {

        float sum = sumAlProbs[allele];
@@ -294,6 +301,7 @@ public final class ImputedRecBuilder { 


    private static String[] defaultHomRefFields() {

        String[] sa = new String[5];

        sa[1] = Const.tab + "0|0";

        sa[2] = Const.tab + "0|0:0";

        for (int j=3; j<sa.length; ++j) {

            sa[j] = sa[j-1] + ",0";
@@ -303,7 +311,7 @@ public final class ImputedRecBuilder { 


    private static String[] homRefFields(boolean ap, boolean gp) {

        String[] homRefField = new String[DEFAULT_HOM_REF_FIELDS.length];

        for (int nAl=2; nAl<homRefField.length; ++nAl) {

        for (int nAl=1; nAl<homRefField.length; ++nAl) {

            StringBuilder sb = new StringBuilder(DEFAULT_HOM_REF_FIELDS[nAl]);

            if (ap) {

                for (int a=1; a<nAl; ++a) {

imp/ImputedVcfWriter.java

+6 −6
Original line number Diff line number Diff line
@@ -61,7 +61,9 @@ public class ImputedVcfWriter { 
     * @param refEnd an upper bound (exclusive) on the reference markers

     * that will be printed

     * @throws IndexOutOfBoundsException if

     * {@code (minRefStart < 0 || maxRefEnd > impData.refGT().nMarkers())}

     * {@code (refStart < 0 || refEnd > impData.refGT().nMarkers())}

     * @throws IndexOutOfBoundsException if

     * {@code targCluster < 0 || targCluster >= impData.nClusters()}

     * @throws NullPointerException if {@code impData == null}

     */

    public ImputedVcfWriter(ImpData impData, int targCluster, int refStart,
@@ -76,18 +78,16 @@ public class ImputedVcfWriter { 
        this.targCluster = targCluster;

        if (targCluster==0) {

            this.refStart = refStart;

            int tmpClustEnd = Math.max(refStart, impData.refClusterEnd(targCluster));

            this.clustEnd = Math.min(tmpClustEnd, refEnd);

            this.refEnd = Math.min(impData.refClusterStart(targCluster + 1), refEnd);

        }

        else if (targCluster < impData.nClusters()-1) {

        else {

            this.refStart = Math.max(refStart, impData.refClusterStart(targCluster));

        }

        if (targCluster < impData.nClusters()-1) {

            int tmpClustEnd = Math.max(refStart, impData.refClusterEnd(targCluster));

            this.clustEnd = Math.min(tmpClustEnd, refEnd);

            this.refEnd = Math.min(impData.refClusterStart(targCluster + 1), refEnd);

        }

        else {

            this.refStart = Math.max(refStart, impData.refClusterStart(targCluster));

            this.clustEnd = refEnd;

            this.refEnd = refEnd;

        }

main/Main.java

+3 −3
Original line number Diff line number Diff line
@@ -70,8 +70,8 @@ public class Main { 
     * The program name and version.

     */

    public static final String VERSION = "(version 5.0)";

    public static final String PROGRAM = "beagle.03Jul18.40b.jar";

    public static final String COMMAND = "java -jar beagle.03Jul18.40b.jar";

    public static final String PROGRAM = "beagle.15Sep18.8a0.jar";

    public static final String COMMAND = "java -jar beagle.15Sep18.8a0.jar";



    /**

     * The copyright string.
@@ -83,7 +83,7 @@ public class Main { 
     */

    public static final String SHORT_HELP = Main.PROGRAM + " " + VERSION

            + Const.nl + Main.COPYRIGHT

            + Const.nl + "Enter \"java -jar beagle.03Jul18.40b.jar\" to "

            + Const.nl + "Enter \"java -jar beagle.15Sep18.8a0.jar\" to "

            + "list command line argument";



    private final Par par;

main/MainHelper.java

+1 −1
Original line number Diff line number Diff line
@@ -101,7 +101,7 @@ public class MainHelper { 
                    rand.nextLong());

            long t1 = System.nanoTime();

            PhaseLS.run(phaseData, estPhase, recombRegress);

            if (recombRegress!=null) {

            if (recombRegress!=null && recombRegress.cnt()>=100) {

                recombFactor = recombFactor(cd, recombRegress);

            }

            long elapsedNanos = System.nanoTime() - t0;