debian/beagle-doc.doc-base

 Document: beagle
-Title: Beagle 4.1
+Title: Beagle
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/beagle/beagle_4.1.pdf.gz
+Files: /usr/share/doc/beagle/beagle_5.0.pdf.gz
 
 Format: HTML
 Index: /usr/share/doc/beagle/api/index.html

debian/beagle-doc.install

 debian/tests/run-sample-analysis /usr/share/doc/beagle/examples/
 debian/upstream.docs/run.beagle.example /usr/share/doc/beagle/examples/
 debian/upstream.docs/test.vcf /usr/share/doc/beagle/examples/
-debian/upstream.docs/beagle_4.1.pdf /usr/share/doc/beagle/
+debian/upstream.docs/beagle_5.0.pdf /usr/share/doc/beagle/
 debian/_jh_build.javadoc/api /usr/share/doc/beagle

debian/beagle-doc.lintian-overrides

+# jQuery from libjs-jquery is not compatible
+beagle-doc: embedded-javascript-library * please use libjs-jquery
+beagle-doc: embedded-javascript-library * please use libjs-jquery-ui

debian/beagle.install

 beagle.jar /usr/share/beagle/
-bref.jar /usr/share/beagle/
\ No newline at end of file
+bref3.jar /usr/share/beagle/
\ No newline at end of file

debian/beagle.links

 /usr/share/beagle/beagle.jar usr/bin/beagle
-/usr/share/beagle/bref.jar usr/bin/bref
\ No newline at end of file
+/usr/share/beagle/bref3.jar usr/bin/bref3
\ No newline at end of file

debian/beagle.manpages

 debian/beagle.1
-debian/bref.1
+debian/bref3.1

debian/changelog

-beagle (5.0-180703+dfsg-1) UNRELEASED; urgency=medium
+beagle (5.0-180915+dfsg-1) unstable; urgency=medium
 
   * New upstream release.
   * During build copy *.java files in SRC/ to avoid problem with jh_build.
   * Update VCS to salsa.
   * Standards-Version: 4.2.1 (no changes needed).
+  * Rename bref.jar to bref3.jar according to upstream changes.
 
- -- Dylan Aïssi <bob.dybian@gmail.com>  Sun, 09 Sep 2018 14:22:44 +0200
+ -- Dylan Aïssi <bob.dybian@gmail.com>  Sun, 16 Sep 2018 14:02:32 +0200
 
 beagle (4.1~180127+dfsg-1) unstable; urgency=medium
 

debian/rules

@@ -10,7 +10,7 @@ override_jh_build:
 	mkdir SRC/
 	cp -t SRC/ -r beagleutil blbutil bref haplotype imp main math phase sample vcf
 	jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="main.Main" beagle.jar SRC/
-	jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="bref.Bref3" bref.jar SRC/
+	jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="bref.Bref3" bref3.jar SRC/
 
 override_dh_installchangelogs:
 	dh_installchangelogs debian/upstream.docs/release_notes

debian/source/include-binaries

 debian/upstream.docs/beagle_4.1_09Feb16.docx
 debian/upstream.docs/beagle_4.1.pdf
+debian/upstream.docs/beagle_5.0.pdf

debian/tests/run-sample-analysis

@@ -2,7 +2,7 @@
 # http://dep.debian.net/deps/dep8/
 # Autopkgtest: Test if beagle run analysis correctly
 # Author: Dylan Aïssi <bob.dybian@gmail.com>
-# Last-Update: 2016-06-17
+# Last-Update: 2018-09-16
 
 pkg=beagle
 if [ "$ADTTMP" = "" ] ; then
@@ -16,18 +16,15 @@ BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar'
 # Generate necessary files
 zcat test.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.vcf.gz
 zcat test.vcf.gz | cut -f1-9,191-200 | gzip > target.vcf.gz
-java -jar /usr/share/beagle/bref.jar ref.vcf.gz
+java -jar /usr/share/beagle/bref3.jar ref.vcf.gz > ref.bref3
 
 # Beagle with gt argument
 $BEAGLE_TEST gt=test.vcf.gz out=out.gt
 
-# Beagle with gl argument
-$BEAGLE_TEST gl=test.vcf.gz out=out.gl
-
-# Beagle with ref argument
+# Beagle with ref and gt argument
 $BEAGLE_TEST ref=ref.vcf.gz gt=target.vcf.gz out=out.ref
 
-# Beagle with bref argument
-$BEAGLE_TEST ref=ref.bref gt=target.vcf.gz out=out.bref
+# Beagle with bref3 file
+$BEAGLE_TEST ref=ref.bref3 gt=target.vcf.gz out=out.bref3
 
 rm -f $ADTTMP/*

debian/upstream.docs/README

 # Author: Dylan Assi <bob.dybian@gmail.com>
-# Last-Update: 2016-06-17
+# Last-Update: 2018-09-16
 # These files were downloaded from https://faculty.washington.edu/browning/beagle/
 # They should be updated when upstream update them.
 
-	wget https://faculty.washington.edu/browning/beagle/release_notes
-	wget https://faculty.washington.edu/browning/beagle/beagle_4.1_21Jan17.pdf -O beagle_4.1.pdf
-	wget https://faculty.washington.edu/browning/beagle/run.beagle.08Jun17.d8b.example -O run.beagle.example
-	wget https://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz -O test.vcf.gz && \
+	wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
+	wget https://faculty.washington.edu/browning/beagle/beagle_5.0_07Sep18.pdf -O beagle_5.0.pdf
+	wget https://faculty.washington.edu/browning/beagle/run.beagle.15Sep18.8a0.example -O run.beagle.example
+	wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz -O test.vcf.gz && \
 		gunzip test.vcf.gz

debian/upstream.docs/release_notes

@@ -38,3 +38,11 @@ Beagle 5.0 (10Jun18.811) release notes
 Beagle 5.0 (03Jul18.40b) release notes
 =============================================
 * Fixed a bug appearing when reference panel ALT field is '.'
+
+Beagle 5.0 (10Sep18.879) release notes
+=============================================
+* Fixed a bug in imputation output when reference panel ALT field is '.'
+
+Beagle 5.0 (15Sep18.8a0) release notes
+=============================================
+* Fixed a bug appearing when analysis window has only one target marker

debian/upstream.docs/run.beagle.example

 #!/bin/bash
-if [ ! -f beagle.08Jun17.d8b.jar ]; then
+if [ ! -f beagle.15Sep18.8a0.jar ]; then
   echo
-  echo "Downloading beagle.08Jun17.d8b.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.08Jun17.d8b.jar
+  echo "Downloading beagle.15Sep18.8a0.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.15Sep18.8a0.jar
 fi
 
-if [ ! -f bref.08Jun17.d8b.jar ]; then
+if [ ! -f bref3.15Sep18.8a0.jar ]; then
   echo
-  echo "Downloading bref.08Jun17.d8b.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref.08Jun17.d8b.jar
+  echo "Downloading bref3.15Sep18.8a0.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref3.15Sep18.8a0.jar
 fi
 
 echo
 
-if [ ! -f test.08Jun17.d8b.vcf.gz ]; then
+if [ ! -f test.15Sep18.8a0.vcf.gz ]; then
     echo
-    echo "*** Downloading some 1000 Genomes Project data to file: test.08Jun17.d8b.vcf.gz ***"
-    wget http://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz
+    echo "*** Downloading some 1000 Genomes Project data to file: test.15Sep18.8a0.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.08Jun17.d8b.vcf.gz target.08Jun17.d8b.vcf.gz ***"
+echo "*** Creating test files: ref.15Sep18.8a0.vcf.gz target.15Sep18.8a0.vcf.gz ***"
 echo
-zcat test.08Jun17.d8b.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.08Jun17.d8b.vcf.gz
-zcat test.08Jun17.d8b.vcf.gz | cut -f1-9,191-200 | gzip > target.08Jun17.d8b.vcf.gz
-
+zcat test.15Sep18.8a0.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.15Sep18.8a0.vcf.gz
+zcat test.15Sep18.8a0.vcf.gz | cut -f1-9,191-200 | gzip > target.15Sep18.8a0.vcf.gz
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.08Jun17.d8b.jar gt=test.08Jun17.d8b.vcf.gz out=out.gt
-
-echo
-echo "*** Running test analysis with \"gl=\" argument ***"
-echo
-java -jar beagle.08Jun17.d8b.jar gl=test.08Jun17.d8b.vcf.gz out=out.gl
+java -jar beagle.15Sep18.8a0.jar gt=test.15Sep18.8a0.vcf.gz out=out.gt
 
 echo
-echo "*** Running test analysis with \"ref=\" argument ***"
+echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
 echo
-java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.vcf.gz gt=target.08Jun17.d8b.vcf.gz out=out.ref
+java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.vcf.gz gt=target.15Sep18.8a0.vcf.gz out=out.ref
 
 echo
-echo "*** Making \"bref\" file ***"
+echo "*** Making \"bref3\" file ***"
 echo
-java -jar bref.08Jun17.d8b.jar ref.08Jun17.d8b.vcf.gz
+java -jar bref3.15Sep18.8a0.jar ref.15Sep18.8a0.vcf.gz > ref.15Sep18.8a0.bref3
 
 echo
-echo "*** Running test analysis with \"bref=\" argument ***"
+echo "*** Running test analysis with \"bref3\" file ***"
 echo
-java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.bref gt=target.08Jun17.d8b.vcf.gz out=out.bref
+java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.bref3 gt=target.15Sep18.8a0.vcf.gz out=out.bref3
 

imp/ImputedRecBuilder.java

@@ -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

@@ -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

@@ -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

@@ -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;