debian/changelog

+mauve-aligner (2.4.0+4736-1) unstable; urgency=medium
+
+  * New upstream SVN checkout
+  * Fake watch file
+  * d/rules: do not uselessly parse d/changelog
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Jul 2018 22:48:39 +0200
+
 mauve-aligner (2.4.0+4734-3) unstable; urgency=high
 
   * Add explicit dependency on libbiojava-java to enable

debian/compat

-9
+11

debian/control

 Source: mauve-aligner
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders:
-	Andreas Tille <tille@debian.org>,
-	Afif Elghraoui <afif@ghraoui.name>,
+Uploaders: Andreas Tille <tille@debian.org>,
+           Afif Elghraoui <afif@ghraoui.name>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                default-jdk,
                ant,
@@ -17,10 +16,10 @@ Build-Depends: debhelper (>= 9),
                libzeus-jscl-java,
                icedtea-netx-common,
                libunixsocket-java,
-	       imagemagick,
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mauve-aligner.git
-Vcs-Git: git://anonscm.debian.org/debian-med/mauve-aligner.git
+               imagemagick
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/mauve-aligner
+Vcs-Git: https://salsa.debian.org/med-team/mauve-aligner.git
 Homepage: http://darlinglab.org/mauve/
 
 Package: mauve-aligner
@@ -28,7 +27,7 @@ Architecture: any
 Depends: ${java:Depends},
          java-wrappers,
          ${misc:Depends},
-	 libbiojava-java,
+         libbiojava-java,
          progressivemauve
 Recommends: ${java:Recommends}
 Description: multiple genome alignment

debian/rules

@@ -6,8 +6,6 @@
 
 #export DH_VERBOSE=1
 
-PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-
 JAVA_HOME  := /usr/lib/jvm/default-java
 
 DEBJAR    := /usr/share/java

debian/watch

-# There is no tarball download location, libMuscle is only available in SVN
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+  https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz

src/org/gel/mauve/analysis/SnpExporter.java

@@ -130,6 +130,7 @@ public class SnpExporter {
 		for (int i = 0; i < snps.length; i++){
 			output.write(snps[i].toString()+"\n");
 		}
+        output.flush(); // don't forget to flush!
 	}
 	
 	public static void exportGaps(XmfaViewerModel model, XMFAAlignment xmfa, BufferedWriter output) throws IOException {
@@ -139,6 +140,7 @@ public class SnpExporter {
 		for (Gap[] ar: gaps)
 			for (Gap g: ar)
 				output.write(g.toString()+"\n");
+        output.flush(); // don't forget to flush!
 	}
 	
 	public static SNP[] getSNPs(XmfaViewerModel model){