debian/changelog

-libbiod (0.1.0-6) UNRELEASED; urgency=medium
+libbiod (0.1.0-6) unstable; urgency=medium
 
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.2.1
+  * Cherry pick patch from upstream (thanks for the hint to Matthias Klumpp)
+    Closes: #907451
 
- -- Andreas Tille <tille@debian.org>  Tue, 28 Aug 2018 09:57:33 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 29 Aug 2018 20:38:20 +0200
 
 libbiod (0.1.0-5) unstable; urgency=medium
 

debian/patches/0017_fix_expression_conversion.patch

+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Sat, 28 Jul 2018 00:05:29 +0000
+Origin: https://github.com/biod/BioD/commit/dd07f3497979b5d7f32ad32476da5108ffc5121e
+Bug-Debian: https://bugs.debian.org/907451
+Subject: [PATCH] Fixes:
+
+BioD/bio/maf/reader.d(53): Error: cannot implicitly convert expression `this._f.byLine(cast(Flag)true, '\x0a')` of type `ByLineImpl!(char, char)` to `ByLine!(char, char)`
+
+See https://github.com/bioconda/bioconda-recipes/pull/8787#issuecomment-389195848
+---
+ bio/maf/reader.d | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/bio/maf/reader.d b/bio/maf/reader.d
+index 708c5b3..c57decd 100644
+--- a/bio/maf/reader.d
++++ b/bio/maf/reader.d
+@@ -1,6 +1,7 @@
+ /*
+     This file is part of BioD.
+     Copyright (C) 2013    Artem Tarasov <lomereiter@gmail.com>
++    Copyright (C) 2018    Pjotr Prins <pjotr.prins@thebird.nl>
+ 
+     Permission is hereby granted, free of charge, to any person obtaining a
+     copy of this software and associated documentation files (the "Software"),
+@@ -8,10 +9,10 @@
+     the rights to use, copy, modify, merge, publish, distribute, sublicense,
+     and/or sell copies of the Software, and to permit persons to whom the
+     Software is furnished to do so, subject to the following conditions:
+-    
++
+     The above copyright notice and this permission notice shall be included in
+     all copies or substantial portions of the Software.
+-    
++
+     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+@@ -50,7 +51,7 @@ struct MafBlockRange {
+ 
+     this(string fn) {
+         _f = File(fn);
+-        _lines = _f.byLine(KeepTerminator.yes);
++        _lines = cast(LineRange)_f.byLine(KeepTerminator.yes);
+         skipHeader();
+         popFront();
+     }
+@@ -85,7 +86,7 @@ struct MafBlockRange {
+ 
+ ///
+ class MafReader {
+- 
++
+     private string _fn;
+ 
+     ///

debian/patches/series

@@ -12,3 +12,4 @@
 0014-Add-compareCoordinatesAndStrand-to-fix-sorting-test-.patch
 0015-Add-Meson-build-definition.patch
 0016-fix-type-conversion.patch
+0017_fix_expression_conversion.patch