From 877ab0266c69858a9d4554dffba89dc5300a0736 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 1 Feb 2021 18:18:42 +0200
Subject: gnu: vcflib: Fix generated pkg-config file.

* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
---
 gnu/packages/bioinformatics.scm                    | 8 ++++----
 gnu/packages/patches/freebayes-devendor-deps.patch | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b14e765de..39611d23f4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15209,18 +15209,18 @@ library automatically handles index file generation and use.")
              (let* ((out (assoc-ref outputs "out"))
                     (pkgconfig (string-append out "/lib/pkgconfig")))
                (mkdir-p pkgconfig)
-               (with-output-to-file (string-append pkgconfig "/libvcflib.pc")
+               (with-output-to-file (string-append pkgconfig "/vcflib.pc")
                  (lambda _
                    (format #t "prefix=~a~@
                            exec_prefix=${prefix}~@
                            libdir=${exec_prefix}/lib~@
                            includedir=${prefix}/include~@
                            ~@
-                           Name: libvcflib~@
+                           Name: vcflib~@
                            Version: ~a~@
-                           Requires: smithwaterman, fastahack~@
+                           Requires: smithwaterman, fastahack, tabixpp~@
                            Description: C++ library for parsing and manipulating VCF files~@
-                           Libs: -L${libdir} -llibvcflib~@
+                           Libs: -L${libdir} -lvcflib~@
                            Cflags: -I${includedir}~%"
                            out ,version)))
                  #t))))))
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
index 7e84666b85..9886de11fb 100644
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -23,7 +23,7 @@ index f6bf242..bded4af 100644
 +tabixpp_dep = dependency('tabixpp', required : false)
 +fastahack_dep = dependency('fastahack', required : false)
 +smithwaterman_dep = dependency('smithwaterman', required : false)
-+vcflib_dep = dependency('libvcflib', required: false)
++vcflib_dep = dependency('vcflib', required: false)
  thread_dep = dependency('threads')
  
  if htslib_dep.found()
-- 
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