gnu/packages/patches/freebayes-devendor-deps.patch

   1 This patch is original to Guix, ongoing work to upstream bits as possible.
   2
   3 From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
   4 From: Efraim Flashner <efraim@flashner.co.il>
   5 Date: Sun, 17 Jan 2021 13:27:17 +0200
   6 Subject: [PATCH] devendor-dependants
   7
   8 ---
   9  meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
  10  1 file changed, 66 insertions(+), 18 deletions(-)
  11
  12 diff --git a/meson.build b/meson.build
  13 index f6bf242..bded4af 100644
  14 --- a/meson.build
  15 +++ b/meson.build
  16 @@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
  17
  18  zlib_dep = dependency('zlib')
  19  lzma_dep = dependency('liblzma')
  20 +simde_dep = dependency('simde')
  21  bzip2_dep = dependency('bz2lib', required: false)
  22  htslib_dep = dependency('htslib', required : false)
  23 +tabixpp_dep = dependency('tabixpp', required : false)
  24 +fastahack_dep = dependency('fastahack', required : false)
  25 +smithwaterman_dep = dependency('smithwaterman', required : false)
  26 +vcflib_dep = dependency('vcflib', required: false)
  27  thread_dep = dependency('threads')
  28
  29  if htslib_dep.found()
  30 @@ -59,6 +64,56 @@ else
  31  ]
  32  endif
  33
  34 +if tabixpp_dep.found()
  35 +  tabixpp_includes = ''
  36 +  tabixpp_src = []
  37 +else
  38 +  tabixpp_includes = [
  39 +    'vcflib/tabixpp',
  40 +    ]
  41 +  tabixpp_src = [
  42 +    'vcflib/tabixpp/tabix.cpp',
  43 +    ]
  44 +endif
  45 +
  46 +if vcflib_dep.found()
  47 +  vcflib_includes = ''
  48 +  vcflib_src = []
  49 +else
  50 +  vcflib_includes = [
  51 +    'vcflib/src',
  52 +    'vcflib/multichoose',
  53 +    'vcflib/filevercmp',
  54 +    ]
  55 +  vcflib_src = [
  56 +    'vcflib/src/Variant.cpp',
  57 +    ]
  58 +endif
  59 +
  60 +if fastahack_dep.found()
  61 +  fastahack_src = []
  62 +else
  63 +  fastahack_src = [
  64 +    'vcflib/fastahack/Fasta.cpp',
  65 +    'vcflib/src/split.cpp',
  66 +    ]
  67 +endif
  68 +
  69 +if smithwaterman_dep.found()
  70 +  smithwaterman_includes = ''
  71 +  smithwaterman_src = []
  72 +else
  73 +  smithwaterman_includes = [
  74 +    'vcflib/smithwaterman',
  75 +    ]
  76 +  smithwaterman_src = [
  77 +    'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
  78 +    'vcflib/smithwaterman/disorder.cpp',
  79 +    'vcflib/smithwaterman/Repeats.cpp',
  80 +    'vcflib/smithwaterman/LeftAlign.cpp',
  81 +    'vcflib/smithwaterman/IndelAllele.cpp',
  82 +    ]
  83 +endif
  84
  85
  86  #
  87 @@ -105,23 +160,18 @@ seqlib_src = [
  88  ]
  89
  90  vcflib_src = [
  91 -    'vcflib/tabixpp/tabix.cpp',
  92 -    'vcflib/src/Variant.cpp',
  93 -    'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
  94 -    'vcflib/smithwaterman/disorder.cpp',
  95 -    'vcflib/smithwaterman/Repeats.cpp',
  96 -    'vcflib/smithwaterman/LeftAlign.cpp',
  97 -    'vcflib/smithwaterman/IndelAllele.cpp',
  98 +    vcflib_src,
  99 +    tabixpp_src,
 100 +    smithwaterman_src,
 101  ]
 102
 103  bamleftalign_src = [
 104      'src/bamleftalign.cpp',
 105      'src/IndelAllele.cpp',
 106      'contrib/SeqLib/src/BamWriter.cpp',
 107 -    'vcflib/fastahack/Fasta.cpp',
 108 -    'vcflib/smithwaterman/LeftAlign.cpp',
 109 -    'vcflib/smithwaterman/IndelAllele.cpp',
 110 -    'vcflib/src/split.cpp',
 111 +    fastahack_src,
 112 +    smithwaterman_src,
 113 +    vcflib_src,
 114      'src/LeftAlign.cpp',
 115  ]
 116
 117 @@ -134,11 +184,9 @@ incdir = include_directories(
 118      'ttmath',
 119      'contrib',
 120      'contrib/SeqLib',
 121 -    'vcflib/src',
 122 -    'vcflib/tabixpp',
 123 -    'vcflib/smithwaterman',
 124 -    'vcflib/multichoose',
 125 -    'vcflib/filevercmp')
 126 +    tabixpp_includes,
 127 +    smithwaterman_includes,
 128 +    vcflib_includes)
 129
 130  c_args = ['-fpermissive','-w']
 131  cpp_args = ['-fpermissive','-w','-Wc++14-compat']
 132 @@ -152,7 +200,7 @@ executable('freebayes',
 133             include_directories : incdir,
 134             cpp_args : cpp_args,
 135             c_args :   c_args,
 136 -           dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
 137 +           dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
 138             install: true
 139            )
 140
 141 @@ -165,7 +213,7 @@ executable('bamleftalign',
 142             include_directories : incdir,
 143             cpp_args : cpp_args,
 144             c_args :   c_args,
 145 -           dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
 146 +           dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
 147             install: true
 148            )
 149
 150 --
 151 2.30.0
 152