beagleutil/Samples.java

@@ -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 {

debian/changelog

+beagle (5.0-190712+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <daissi@debian.org>  Sat, 13 Jul 2019 17:09:59 +0200
+
 beagle (5.0-190703+dfsg-1) unstable; urgency=medium
 
   * New upstream release.

debian/upstream.docs/README

 # Author: Dylan Assi <daissi@debian.org>
-# Last-Update: 2019-07-04
+# Last-Update: 2019-07-13
 # 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/beagle5_release_notes -O release_notes
 	wget https://faculty.washington.edu/browning/beagle/beagle_5.0_03Jul19.pdf -O beagle_5.0.pdf
-	wget https://faculty.washington.edu/browning/beagle/run.beagle.03Jul19.b33.example -O run.beagle.example
-	wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz -O test.vcf.gz && \
+	wget https://faculty.washington.edu/browning/beagle/run.beagle.12Jul19.0df.example -O run.beagle.example
+	wget http://faculty.washington.edu/browning/beagle/test.12Jul19.0df.vcf.gz -O test.vcf.gz && \
 		gunzip test.vcf.gz

debian/upstream.docs/release_notes

@@ -59,3 +59,8 @@ Beagle 5.0 (16May19.351) release notes
 Beagle 5.0 (03Jul19.b33) release notes
 =============================================
 * Fixed a bug when analysis includes multiple chromosomes
+
+Beagle 5.0 (12Jul19.0df) release notes
+=============================================
+* Improved an error message
+* Improved handling of inconsistent marker order in ref and gt files

debian/upstream.docs/run.beagle.example

 #!/bin/bash
-if [ ! -f beagle.03Jul19.b33.jar ]; then
+if [ ! -f beagle.12Jul19.0df.jar ]; then
   echo
-  echo "Downloading beagle.03Jul19.b33.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.03Jul19.b33.jar
+  echo "Downloading beagle.12Jul19.0df.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar
 fi
 
-if [ ! -f bref3.03Jul19.b33.jar ]; then
+if [ ! -f bref3.12Jul19.0df.jar ]; then
   echo
-  echo "Downloading bref3.03Jul19.b33.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref3.03Jul19.b33.jar
+  echo "Downloading bref3.12Jul19.0df.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar
 fi
 
 echo
 
-if [ ! -f test.03Jul19.b33.vcf.gz ]; then
+if [ ! -f test.12Jul19.0df.vcf.gz ]; then
     echo
-    echo "*** Downloading some 1000 Genomes Project data to file: test.03Jul19.b33.vcf.gz ***"
-    wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz
+    echo "*** Downloading some 1000 Genomes Project data to file: test.12Jul19.0df.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.12Jul19.0df.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.03Jul19.b33.vcf.gz target.03Jul19.b33.vcf.gz ***"
+echo "*** Creating test files: ref.12Jul19.0df.vcf.gz target.12Jul19.0df.vcf.gz ***"
 echo
-zcat test.03Jul19.b33.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.03Jul19.b33.vcf.gz
-zcat test.03Jul19.b33.vcf.gz | cut -f1-9,191-200 | gzip > target.03Jul19.b33.vcf.gz
+zcat test.12Jul19.0df.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.12Jul19.0df.vcf.gz
+zcat test.12Jul19.0df.vcf.gz | cut -f1-9,191-200 | gzip > target.12Jul19.0df.vcf.gz
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.03Jul19.b33.jar gt=test.03Jul19.b33.vcf.gz out=out.gt
+java -jar beagle.12Jul19.0df.jar gt=test.12Jul19.0df.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
 echo
-java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.vcf.gz gt=target.03Jul19.b33.vcf.gz out=out.ref
+java -jar beagle.12Jul19.0df.jar ref=ref.12Jul19.0df.vcf.gz gt=target.12Jul19.0df.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref3\" file ***"
 echo
-java -jar bref3.03Jul19.b33.jar ref.03Jul19.b33.vcf.gz > ref.03Jul19.b33.bref3
+java -jar bref3.12Jul19.0df.jar ref.12Jul19.0df.vcf.gz > ref.12Jul19.0df.bref3
 
 echo
 echo "*** Running test analysis with \"bref3\" file ***"
 echo
-java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.bref3 gt=target.03Jul19.b33.vcf.gz out=out.bref3
+java -jar beagle.12Jul19.0df.jar ref=ref.12Jul19.0df.bref3 gt=target.12Jul19.0df.vcf.gz out=out.bref3
 

main/Main.java

@@ -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);