debian/changelog

 beagle (5.0-190703+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream release.
+  * Standards-Version: 4.3.0 (no changes needed).
 
  -- Dylan Aïssi <daissi@debian.org>  Thu, 04 Jul 2019 07:49:33 +0200
 

debian/control

@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 11~),
                javahelper
 Build-Depends-Indep: default-jdk,
                      libhtsjdk-java
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 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

-# Author: Dylan Assi <bob.dybian@gmail.com>
-# Last-Update: 2018-09-16
+# Author: Dylan Assi <daissi@debian.org>
+# Last-Update: 2019-07-04
 # 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_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 && \
+	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 && \
 		gunzip test.vcf.gz

debian/upstream.docs/run.beagle.example

 #!/bin/bash
-if [ ! -f beagle.15Sep18.8a0.jar ]; then
+if [ ! -f beagle.03Jul19.b33.jar ]; then
   echo
-  echo "Downloading beagle.15Sep18.8a0.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.15Sep18.8a0.jar
+  echo "Downloading beagle.03Jul19.b33.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.03Jul19.b33.jar
 fi
 
-if [ ! -f bref3.15Sep18.8a0.jar ]; then
+if [ ! -f bref3.03Jul19.b33.jar ]; then
   echo
-  echo "Downloading bref3.15Sep18.8a0.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref3.15Sep18.8a0.jar
+  echo "Downloading bref3.03Jul19.b33.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref3.03Jul19.b33.jar
 fi
 
 echo
 
-if [ ! -f test.15Sep18.8a0.vcf.gz ]; then
+if [ ! -f test.03Jul19.b33.vcf.gz ]; then
     echo
-    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
+    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
 fi
 
 echo
-echo "*** Creating test files: ref.15Sep18.8a0.vcf.gz target.15Sep18.8a0.vcf.gz ***"
+echo "*** Creating test files: ref.03Jul19.b33.vcf.gz target.03Jul19.b33.vcf.gz ***"
 echo
-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
+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
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.15Sep18.8a0.jar gt=test.15Sep18.8a0.vcf.gz out=out.gt
+java -jar beagle.03Jul19.b33.jar gt=test.03Jul19.b33.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
 echo
-java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.vcf.gz gt=target.15Sep18.8a0.vcf.gz out=out.ref
+java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.vcf.gz gt=target.03Jul19.b33.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref3\" file ***"
 echo
-java -jar bref3.15Sep18.8a0.jar ref.15Sep18.8a0.vcf.gz > ref.15Sep18.8a0.bref3
+java -jar bref3.03Jul19.b33.jar ref.03Jul19.b33.vcf.gz > ref.03Jul19.b33.bref3
 
 echo
 echo "*** Running test analysis with \"bref3\" file ***"
 echo
-java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.bref3 gt=target.15Sep18.8a0.vcf.gz out=out.bref3
+java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.bref3 gt=target.03Jul19.b33.vcf.gz out=out.bref3