gnu: freebayes: Update to 1.3.5.
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.master
Efraim Flashner
parent
1fd8819fac
commit
b65c02e2d3
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@ -1019,7 +1019,6 @@ dist_patch_DATA = \
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%D%/packages/patches/fpc-reproducibility.patch \
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%D%/packages/patches/fplll-std-fenv.patch \
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%D%/packages/patches/freedink-engine-fix-sdl-hints.patch \
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%D%/packages/patches/freebayes-devendor-deps.patch \
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%D%/packages/patches/freeimage-unbundle.patch \
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%D%/packages/patches/fuse-overlapping-headers.patch \
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%D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \
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@ -13572,7 +13572,7 @@ manipulations on VCF files.")
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(define-public freebayes
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(package
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(name "freebayes")
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(version "1.3.3")
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(version "1.3.5")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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@ -13580,8 +13580,7 @@ manipulations on VCF files.")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
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(patches (search-patches "freebayes-devendor-deps.patch"))
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(base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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@ -13593,8 +13592,7 @@ manipulations on VCF files.")
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("htslib" ,htslib)
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("smithwaterman" ,smithwaterman)
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("tabixpp" ,tabixpp)
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("vcflib" ,vcflib)
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("zlib" ,zlib)))
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("vcflib" ,vcflib)))
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(native-inputs
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`(("bash-tap" ,bash-tap)
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("bc" ,bc)
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@ -13627,13 +13625,13 @@ manipulations on VCF files.")
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(string-append bash-tap "/bin/bash-tap-bootstrap"))
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(("source.*bash-tap-bootstrap")
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(string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
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(substitute* "meson.build"
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;; Some inputs aren't actually needed.
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((".*bamtools/src.*") "")
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((".*multichoose.*") ""))
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(substitute* '("src/BedReader.cpp"
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"src/BedReader.h")
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(("../intervaltree/IntervalTree.h") "IntervalTree.h"))
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(substitute* "meson.build"
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;; Our pkg-config file is vcflib.pc
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(("libvcflib") "vcflib")
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(("vcflib_inc,") ""))
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#t)))
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(add-after 'unpack 'unpack-submodule-sources
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(lambda* (#:key inputs #:allow-other-keys)
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@ -1,152 +0,0 @@
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This patch is original to Guix, ongoing work to upstream bits as possible.
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From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
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From: Efraim Flashner <efraim@flashner.co.il>
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Date: Sun, 17 Jan 2021 13:27:17 +0200
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Subject: [PATCH] devendor-dependants
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---
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meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
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1 file changed, 66 insertions(+), 18 deletions(-)
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diff --git a/meson.build b/meson.build
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index f6bf242..bded4af 100644
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--- a/meson.build
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+++ b/meson.build
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@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
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zlib_dep = dependency('zlib')
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lzma_dep = dependency('liblzma')
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+simde_dep = dependency('simde')
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bzip2_dep = dependency('bz2lib', required: false)
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htslib_dep = dependency('htslib', required : false)
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+tabixpp_dep = dependency('tabixpp', required : false)
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+fastahack_dep = dependency('fastahack', required : false)
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+smithwaterman_dep = dependency('smithwaterman', required : false)
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+vcflib_dep = dependency('vcflib', required: false)
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thread_dep = dependency('threads')
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if htslib_dep.found()
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@@ -59,6 +64,56 @@ else
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]
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endif
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+if tabixpp_dep.found()
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+ tabixpp_includes = ''
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+ tabixpp_src = []
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+else
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+ tabixpp_includes = [
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+ 'vcflib/tabixpp',
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+ ]
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+ tabixpp_src = [
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+ 'vcflib/tabixpp/tabix.cpp',
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+ ]
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+endif
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+
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+if vcflib_dep.found()
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+ vcflib_includes = ''
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+ vcflib_src = []
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+else
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+ vcflib_includes = [
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+ 'vcflib/src',
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+ 'vcflib/multichoose',
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+ 'vcflib/filevercmp',
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+ ]
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+ vcflib_src = [
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+ 'vcflib/src/Variant.cpp',
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+ ]
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+endif
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+
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+if fastahack_dep.found()
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+ fastahack_src = []
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+else
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+ fastahack_src = [
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+ 'vcflib/fastahack/Fasta.cpp',
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+ 'vcflib/src/split.cpp',
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+ ]
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+endif
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+
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+if smithwaterman_dep.found()
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+ smithwaterman_includes = ''
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+ smithwaterman_src = []
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+else
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+ smithwaterman_includes = [
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+ 'vcflib/smithwaterman',
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+ ]
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+ smithwaterman_src = [
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+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
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+ 'vcflib/smithwaterman/disorder.cpp',
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+ 'vcflib/smithwaterman/Repeats.cpp',
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+ 'vcflib/smithwaterman/LeftAlign.cpp',
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+ 'vcflib/smithwaterman/IndelAllele.cpp',
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+ ]
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+endif
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#
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@@ -105,23 +160,18 @@ seqlib_src = [
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]
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vcflib_src = [
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- 'vcflib/tabixpp/tabix.cpp',
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- 'vcflib/src/Variant.cpp',
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- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
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- 'vcflib/smithwaterman/disorder.cpp',
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- 'vcflib/smithwaterman/Repeats.cpp',
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- 'vcflib/smithwaterman/LeftAlign.cpp',
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- 'vcflib/smithwaterman/IndelAllele.cpp',
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+ vcflib_src,
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+ tabixpp_src,
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+ smithwaterman_src,
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]
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bamleftalign_src = [
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'src/bamleftalign.cpp',
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'src/IndelAllele.cpp',
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'contrib/SeqLib/src/BamWriter.cpp',
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- 'vcflib/fastahack/Fasta.cpp',
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- 'vcflib/smithwaterman/LeftAlign.cpp',
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- 'vcflib/smithwaterman/IndelAllele.cpp',
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- 'vcflib/src/split.cpp',
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+ fastahack_src,
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+ smithwaterman_src,
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+ vcflib_src,
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'src/LeftAlign.cpp',
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]
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@@ -134,11 +184,9 @@ incdir = include_directories(
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'ttmath',
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'contrib',
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'contrib/SeqLib',
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- 'vcflib/src',
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- 'vcflib/tabixpp',
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- 'vcflib/smithwaterman',
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- 'vcflib/multichoose',
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- 'vcflib/filevercmp')
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+ tabixpp_includes,
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+ smithwaterman_includes,
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+ vcflib_includes)
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c_args = ['-fpermissive','-w']
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cpp_args = ['-fpermissive','-w','-Wc++14-compat']
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@@ -152,7 +200,7 @@ executable('freebayes',
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include_directories : incdir,
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cpp_args : cpp_args,
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c_args : c_args,
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- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
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+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
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install: true
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)
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@@ -165,7 +213,7 @@ executable('bamleftalign',
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include_directories : incdir,
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cpp_args : cpp_args,
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c_args : c_args,
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- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
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+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
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install: true
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)
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--
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2.30.0
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