debian/changelog

+libseqlib (1.1.1+dfsg-4) unstable; urgency=medium
+
+  * Make sure also private headers of htslib will be installed and usable
+    since these are used in libseqlib-dev
+    Closes: #891745
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Mon, 05 Mar 2018 16:25:15 +0100
+
 libseqlib (1.1.1+dfsg-3) unstable; urgency=medium
 
   * Remove liblzma-dev again since it is only used for dist target

debian/compat

-10
+11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                d-shlibs,
                pkg-config,
                libhts-private-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 10),
                libbwa-dev (>= 0.7.15-3),
                libjsoncpp-dev,
                libssw-dev
-Standards-Version: 4.1.2
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libseqlib.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libseqlib.git
 Homepage: https://github.com/walaj/SeqLib
@@ -43,6 +43,7 @@ Depends: libseqlib0 (= ${binary:Version}),
          ${shlibs:Depends},
          ${misc:Depends},
          libhts-dev (>= 1.3.2-3),
+         libhts-private-dev,
          libjsoncpp-dev,
          libbwa-dev,
          libfml-dev

debian/patches/series

@@ -7,3 +7,4 @@ dynamic_lib.patch
 use_debian_packaged_jsoncpp.patch
 use_debian_packaged_ssw.patch
 pkg-config.patch
+use_private_htslib_headers.patch

debian/patches/use_private_htslib_headers.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 05 Mar 2018 15:39:42 +0100
+Bug-Debian: https://bugs.debian.org/891745
+Description: Hack around improper use of private files of htslib
+
+--- a/SeqLib/BamWalker.h
++++ b/SeqLib/BamWalker.h
+@@ -12,8 +12,8 @@
+ #endif
+ 
+ extern "C" {
+-#include "htslib/cram/cram.h"
+-#include "htslib/cram/cram_io.h"
++#include <htslib/cram/cram.h>
++#include <htslib/cram/cram_io.h>
+ }
+ 
+ struct idx_delete {
+--- a/libseqlib.pc.in
++++ b/libseqlib.pc.in
+@@ -7,5 +7,5 @@ Name: libseqlib
+ Version: @VERSION@
+ Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data
+ Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw
+-Cflags: -I${includedir}
++Cflags: -I${includedir} -I/usr/include/htslib
+