debian/README.source

@@ -2,7 +2,7 @@ How to rename the upstream sources
 =============================================
 
 uscan
-mv beagle_180703+dfsg.orig.tar.xz \
-   beagle_5.0-180703+dfsg.orig.tar.xz
+mv beagle_190921+dfsg.orig.tar.xz \
+   beagle_5.1-190921+dfsg.orig.tar.xz
 
  -- Dylan Aïssi <bob.dybian@gmail.com>  Tue, 30 Jan 2018 23:28:16 +0100

debian/changelog

+beagle (5.1-190921+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+  * Standards-Version: 4.4.1 (no changes needed).
+
+ -- Dylan Aïssi <daissi@debian.org>  Mon, 14 Oct 2019 21:31:05 +0200
+
 beagle (5.1-190824+dfsg-2) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12),
                javahelper
 Build-Depends-Indep: default-jdk,
                      libhtsjdk-java
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/beagle
 Vcs-Git: https://salsa.debian.org/med-team/beagle.git
 Homepage: https://faculty.washington.edu/browning/beagle/beagle.html

debian/upstream.docs/README

@@ -5,6 +5,6 @@
 
 	wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
 	wget https://faculty.washington.edu/browning/beagle/beagle_5.1_12Aug19.pdf -O beagle_5.1.pdf
-	wget https://faculty.washington.edu/browning/beagle/run.beagle.24Aug19.3e8.example -O run.beagle.example
-	wget https://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz -O test.vcf.gz && \
+	wget https://faculty.washington.edu/browning/beagle/run.beagle.21Sep19.ec3.example -O run.beagle.example
+	wget https://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz -O test.vcf.gz && \
 		gunzip test.vcf.gz

debian/upstream.docs/release_notes

@@ -73,3 +73,8 @@ Beagle 5.1 (13Aug19.a31) release notes
 Beagle 5.1 (24Aug19.3e8) release notes
 ============================================
 * Fixed a bug that can arise when phasing inbred samples
+
+Beagle 5.1 (21Sep19.ec3) release notes
+============================================
+* Fixed bugs when phasing or imputing using a reference panel
+

debian/upstream.docs/run.beagle.example

 #!/bin/bash
-if [ ! -f beagle.24Aug19.3e8.jar ]; then
+if [ ! -f beagle.21Sep19.ec3.jar ]; then
   echo
-  echo "Downloading beagle.24Aug19.3e8.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.24Aug19.3e8.jar
+  echo "Downloading beagle.21Sep19.ec3.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.21Sep19.ec3.jar
 fi
 
-if [ ! -f bref3.24Aug19.3e8.jar ]; then
+if [ ! -f bref3.21Sep19.ec3.jar ]; then
   echo
-  echo "Downloading bref3.24Aug19.3e8.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref3.24Aug19.3e8.jar
+  echo "Downloading bref3.21Sep19.ec3.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref3.21Sep19.ec3.jar
 fi
 
 echo
 
-if [ ! -f test.24Aug19.3e8.vcf.gz ]; then
+if [ ! -f test.21Sep19.ec3.vcf.gz ]; then
     echo
-    echo "*** Downloading some 1000 Genomes Project data to file: test.24Aug19.3e8.vcf.gz ***"
-    wget http://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz
+    echo "*** Downloading some 1000 Genomes Project data to file: test.21Sep19.ec3.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.24Aug19.3e8.vcf.gz target.24Aug19.3e8.vcf.gz ***"
+echo "*** Creating test files: ref.21Sep19.ec3.vcf.gz target.21Sep19.ec3.vcf.gz ***"
 echo
-zcat test.24Aug19.3e8.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.24Aug19.3e8.vcf.gz
-zcat test.24Aug19.3e8.vcf.gz | cut -f1-9,191-200 | gzip > target.24Aug19.3e8.vcf.gz
+zcat test.21Sep19.ec3.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.21Sep19.ec3.vcf.gz
+zcat test.21Sep19.ec3.vcf.gz | cut -f1-9,191-200 | gzip > target.21Sep19.ec3.vcf.gz
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.24Aug19.3e8.jar gt=test.24Aug19.3e8.vcf.gz out=out.gt
+java -jar beagle.21Sep19.ec3.jar gt=test.21Sep19.ec3.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
 echo
-java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.vcf.gz gt=target.24Aug19.3e8.vcf.gz out=out.ref
+java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.vcf.gz gt=target.21Sep19.ec3.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref3\" file ***"
 echo
-java -jar bref3.24Aug19.3e8.jar ref.24Aug19.3e8.vcf.gz > ref.24Aug19.3e8.bref3
+java -jar bref3.21Sep19.ec3.jar ref.21Sep19.ec3.vcf.gz > ref.21Sep19.ec3.bref3
 
 echo
 echo "*** Running test analysis with \"bref3\" file ***"
 echo
-java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.bref3 gt=target.24Aug19.3e8.vcf.gz out=out.bref3
+java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.bref3 gt=target.21Sep19.ec3.vcf.gz out=out.bref3