debian/changelog

+libbio-coordinate-perl (1.7.1-3) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * s/Conflicts/Breaks/
+  * Fix spelling
+
+ -- Andreas Tille <tille@debian.org>  Mon, 24 Sep 2018 13:07:25 +0200
+
 libbio-coordinate-perl (1.7.1-2) unstable; urgency=medium
 
   * Team upload

debian/compat

-10
+11

debian/control

@@ -2,21 +2,22 @@ Source: libbio-coordinate-perl
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: perl
+Testsuite: autopkgtest-pkg-perl
 Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 11~)
 Build-Depends-Indep: bioperl (>= 1.7.1),
                      perl
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbio-coordinate-perl.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libbio-coordinate-perl.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/libbio-coordinate-perl
+Vcs-Git: https://salsa.debian.org/med-team/libbio-coordinate-perl.git
 Homepage: https://metacpan.org/release/Bio-Coordinate
-Testsuite: autopkgtest-pkg-perl
 
 Package: libbio-coordinate-perl
 Architecture: all
-Depends: ${perl:Depends}, ${misc:Depends},
+Depends: ${perl:Depends},
+         ${misc:Depends},
          bioperl (>= 1.7.1)
-Conflicts: bioperl (<= 1.7.0)
+Breaks: bioperl (<= 1.7.0)
 Description: BioPerl modules for working with biological coordinates
  The Bioperl project is a coordinated effort to collect computational methods
  routinely used in bioinformatics into a set of standard CPAN-style,

debian/patches/series

+spelling.patch

debian/patches/spelling.patch

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 24 Sep 2018 11:57:17 +0200
+
+--- a/lib/Bio/Coordinate/Collection.pm
++++ b/lib/Bio/Coordinate/Collection.pm
+@@ -367,7 +367,7 @@ are left to the calling code.
+ 
+  Title   : _is_sorted
+  Usage   : $newpos = $obj->_is_sorted;
+- Function: toggle for whether the (internal) coodinate mapper data are sorted
++ Function: toggle for whether the (internal) coordinate mapper data are sorted
+  Example :
+  Returns : boolean
+  Args    : boolean
+--- a/lib/Bio/Coordinate/ExtrapolatingPair.pm
++++ b/lib/Bio/Coordinate/ExtrapolatingPair.pm
+@@ -180,7 +180,7 @@ can do that and set strict() to true.
+  Function: Map the location from the input coordinate system
+            to a new value in the output coordinate system.
+ 
+-           In extrapolating coodinate system there is no location zero.
++           In extrapolating coordinate system there is no location zero.
+            Locations are...
+  Example :
+  Returns : new location in the output coordinate system or undef
+--- a/lib/Bio/Coordinate/GeneMapper.pm
++++ b/lib/Bio/Coordinate/GeneMapper.pm
+@@ -1004,7 +1004,7 @@ version 1.007001
+ =head1 DESCRIPTION
+ 
+ Bio::Coordinate::GeneMapper is a module for simplifying the mappings
+-of coodinate locations between various gene related locations in human
++of coordinate locations between various gene related locations in human
+ genetics. It also adds a special human genetics twist to coordinate
+ systems by making it possible to disable the use of zero
+ (0). Locations before position one start from -1. See method