debian/changelog

-snp-sites (2.4.0-1) UNRELEASED; urgency=medium
+snp-sites (2.4.0-1) unstable; urgency=medium
 
   * New upstream version.
   * Adjust watchfile to allow 'v' in version tags.
   * Update upstream metadata (thanks Steffen Moeller).
+  * Remove obsolete autotools Build-Depends.
+  * Use debhelper 11.
+  * Bump Standards-Version.
+  * Use secure copyright format URL.
 
  -- Sascha Steinbiss <satta@debian.org>  Thu, 14 Jun 2018 17:29:53 +0200
 

debian/compat

-9
+11

debian/control

@@ -5,18 +5,15 @@ Uploaders: Jorge Soares <j.s.soares@gmail.com>,
            Sascha Steinbiss <satta@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9.0.0),
-               autotools-dev,
+Build-Depends: debhelper (>= 11),
                zlib1g-dev,
                check,
                pkg-config,
-               dh-autoreconf,
                d-shlibs,
                asciidoctor
-Standards-Version: 3.9.8
-Testsuite: autopkgtest
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snp-sites.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/snp-sites.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/snp-sites
+Vcs-Git: https://salsa.debian.org/med-team/snp-sites.git
 Homepage: https://github.com/sanger-pathogens/snp-sites
 
 Package: snp-sites

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: snp-sites
 Source: https://github.com/sanger-pathogens/snp-sites
 

debian/patches/add_lib_subunit.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 16 Sep 2015 15:08:04 +0200
-Bug-Debian: http://bugs.debian.org/799164
-Description: Add missing lib subunit
-

debian/patches/fix_manpage.patch

-Description: Fix manpage
-Author: Sascha Steinbiss <sascha@steinbiss.name>
-Forwarded: https://github.com/sanger-pathogens/snp-sites/pull/47
-Applied-Upstream: v2.2.1
---- a/snp-sites.txt
-+++ b/snp-sites.txt
-@@ -1,5 +1,5 @@
--SNP-SITESDOC(1)
--==============
-+SNP-SITES(1)
-+============
- :doctype: manpage
- 
- 
-@@ -15,10 +15,15 @@
- -----------
- This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats:
- 
--a multi fasta alignment, VCF, relaxed phylip format.
-+ - multi fasta alignment
-+ - VCF
-+ - relaxed phylip format
- 
- OPTIONS
- -------
-+*-r*::
-+	Output internal pseudo reference sequence
-+
- *-m*::
- 	Output a multi fasta alignment file (default)
- 
-@@ -32,16 +37,18 @@
- 	Specify an output filename
- 
- *-h*::
--	This document
-+	Show help message
- 
- *-V*::
- 	Show version and exit
- 
-+
- EXAMPLES
- --------
--snp-sites my-alignment.aln
- 
--snp-sites my-gzipped-alignment.aln.gz
-+ snp-sites my-alignment.aln
-+
-+ snp-sites my-gzipped-alignment.aln.gz
- 
- 
- FORMAT OF THE INPUT FILE
-@@ -49,12 +56,12 @@
- 
- Input files should look like this:
- 
-->reference_sequence
--aaccggtt
-->comparison_sequence
--AACCGGTT
-->another_comparison_sequence
--AACCGCTT
-+    >reference_sequence
-+    aaccggtt
-+    >comparison_sequence
-+    AACCGGTT
-+    >another_comparison_sequence
-+    AACCGCTT
- 
- For more examples, visit:
- https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data
-@@ -63,6 +70,13 @@
- ------
- snp-sites was originally written by Andrew Page (ap13@sanger.ac.uk)
- 
-+CITATION
-+--------
-+If you use this program, please cite:
-+"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments",
-+Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016),
-+bioRxiv doi: http://dx.doi.org/10.1101/038190
-+
- COPYING
- -------
- Wellcome Trust Sanger Institute Copyright (C) 2013 Wellcome Trust Sanger Institute

debian/patches/reproducible-build.patch

-Description: Manually set the timestamp in the manpage to the last modification time
-
---- a/snp-sites.txt
-+++ b/snp-sites.txt
-@@ -1,6 +1,7 @@
- SNP-SITES(1)
- ============
- :doctype: manpage
-+:revdate: 2015-09-03
- 
- 
- NAME