htslib: update to 1.22.1

Signed-off-by: Rosen Penev <[email protected]>

Author: neheb

releases.json

@@ -1515,6 +1515,7 @@
       "htslib"
     ],
     "versions": [
+      "1.22.1-1",
       "1.22-1",
       "1.21-2",
       "1.21-1",

subprojects/htslib.wrap

@@ -1,9 +1,9 @@
 [wrap-file]
-directory = htslib-1.22
-source_url = https://github.com/samtools/htslib/releases/download/1.22/htslib-1.22.tar.bz2
-source_filename = htslib-1.22.tar.bz2
-source_hash = 6250c1df297db477516e60ac8df45ed75a652d1f25b0f37f12f5b17269eafde9
+directory = htslib-1.22.1
+source_url = https://github.com/samtools/htslib/releases/download/1.22.1/htslib-1.22.1.tar.bz2
+source_filename = htslib-1.22.1.tar.bz2
+source_hash = 3dfa6eeb71db719907fe3ef7c72cb2ec9965b20b58036547c858c89b58c342f7
 patch_directory = htslib
 
 [provide]
-htslib = htslib_dep
+dependency_names = htslib

subprojects/packagefiles/htslib/htslib/meson.build

@@ -0,0 +1,31 @@
+install_headers(
+  'bgzf.h',
+  'cram.h',
+  'faidx.h',
+  'hfile.h',
+  'hts_defs.h',
+  'hts_endian.h',
+  'hts_expr.h',
+  'hts.h',
+  'hts_log.h',
+  'hts_os.h',
+  'kbitset.h',
+  'kfunc.h',
+  'khash.h',
+  'khash_str2int.h',
+  'klist.h',
+  'knetfile.h',
+  'kroundup.h',
+  'kseq.h',
+  'ksort.h',
+  'kstring.h',
+  'regidx.h',
+  'sam.h',
+  'synced_bcf_reader.h',
+  'tbx.h',
+  'thread_pool.h',
+  'vcf.h',
+  'vcf_sweep.h',
+  'vcfutils.h',
+  subdir: 'htslib',
+)

subprojects/packagefiles/htslib/meson.build

@@ -1,45 +1,46 @@
 project(
   'htslib',
   'c',
-  version: '1.22',
-  default_options: ['warning_level=0', 'c_std=c99', 'b_ndebug=if-release'],
+  version: '1.22.1',
   license: 'MIT',
-  meson_version: '>= 0.50.0',
+  meson_version: '>= 0.54.0',
 )
 
 cc = meson.get_compiler('c')
 if cc.get_argument_syntax() == 'msvc'
   error('MSVC is unsupported. Only MinGW.')
 endif
 
-# htslib uses
-#   - usleep()
-#   - strdup()
-#   - M_LN10/M_LN2
-add_project_arguments(
-  '-D_XOPEN_SOURCE=600',
-  language: 'c',
-)
+thread_dep = dependency('threads')
+zlib_dep = dependency('zlib')
 
 if meson.version().version_compare('>= 0.62')
   dl_dep = dependency('dl')
 else
   dl_dep = cc.find_library('dl')
 endif
-libm_dep = cc.find_library(
-  'm',
-  required: false,
-)
-regex_dep = dependency(
-  'regex',
-  required: host_machine.system() == 'windows',
-)
-thread_dep = dependency('threads')
-ws_dep = cc.find_library(
-  'ws2_32',
-  required: host_machine.system() == 'windows',
-)
-zlib_dep = dependency('zlib')
+
+if cc.links('#include <math.h>\nint main(){log(0);}')
+  libm_dep = declare_dependency()
+else
+  libm_dep = cc.find_library('m')
+endif
+
+if cc.links('#include <regex.h>\nint main(){regfree(0);}')
+  regex_dep = declare_dependency()
+else
+  regex_dep = dependency('regex')
+endif
+
+if host_machine.system() == 'windows'
+  ws_dep = cc.find_library('ws2_32')
+else
+  if cc.has_function('recv')
+    ws_dep = declare_dependency()
+  else
+    ws_dep = cc.find_library('socket')
+  endif
+endif
 
 htslib_sources = files(
   'bcf_sr_sort.c',
@@ -130,22 +131,23 @@ configure_file(
   configuration: htslib_version_h_config,
 )
 
-# install library if
-# - either running as a proper project
-# - or linking to shared libraries
-htslib_lib_install = (not meson.is_subproject()) or (get_option(
-  'default_library',
-) != 'static')
-
 htslib_lib = library(
   'hts',
   htslib_sources,
+  c_args: '-D_XOPEN_SOURCE=600',
   soversion: 3,
   version: meson.project_version(),
-  install: htslib_lib_install,
+  install: true,
   dependencies: [dl_dep, libm_dep, regex_dep, thread_dep, ws_dep, zlib_dep],
   gnu_symbol_visibility: 'hidden',
-  override_options: ['warning_level=0', 'c_std=c99'],
+  override_options: 'c_std=c99',
+)
+
+pc = import('pkgconfig')
+pc.generate(
+  htslib_lib,
+  name: 'htslib',
+  description: 'C library for high-throughput sequencing data format',
 )
 
 ###################
@@ -155,14 +157,28 @@ htslib_lib = library(
 htslib_dep = declare_dependency(
   include_directories: '.',
   link_with: htslib_lib,
-  version: meson.project_version(),
 )
 
+meson.override_dependency('htslib', htslib_dep)
+
+subdir('htslib')
+
+foreach e : ['annot-tsv', 'bgzip', 'htsfile', 'tabix']
+  executable(
+    e,
+    '@[email protected]'.format(e),
+    dependencies: htslib_dep,
+    install: true,
+  )
+endforeach
+
+subdir('ref_cache')
+
+#mangix/usr/local/bin/ref-cache
+
 #########
 # tests #
 #########
 
-if get_option('tests')
-  htslib_source_root = meson.current_source_dir()
-  subdir('test')
-endif
+htslib_source_root = meson.current_source_dir()
+subdir('test')

subprojects/packagefiles/htslib/meson_options.txt

@@ -1,3 +1,9 @@
+option(
+    'raf-cache',
+    type: 'feature',
+    description: 'raf-cache utility',
+)
+
 option(
     'tests',
     type: 'boolean',

subprojects/packagefiles/htslib/ref_cache/meson.build

@@ -0,0 +1,38 @@
+socket = cc.has_header(
+  'sys/socket.h',
+  required: get_option('raf-cache'),
+)
+
+if not socket
+  subdir_done()
+endif
+
+curl_dep = dependency(
+  'libcurl',
+  required: get_option('raf-cache'),
+)
+
+if not curl_dep.found()
+  subdir_done()
+endif
+
+executable(
+  'ref-cache',
+  'cmsg_wrap.c',
+  'http_parser.c',
+  'listener.c',
+  'log_files.c',
+  'main.c',
+  'misc.c',
+  'ping.c',
+  'poll_wrap_epoll.c',
+  'poll_wrap_poll.c',
+  'ref_files.c',
+  'request_handler.c',
+  'sendfile_wrap.c',
+  'server.c',
+  'transaction.c',
+  'upstream.c',
+  '../cram/pooled_alloc.c',
+  dependencies: [curl_dep, htslib_dep],
+)

subprojects/packagefiles/htslib/test/meson.build

@@ -1,3 +1,7 @@
+if not get_option('tests')
+  subdir_done()
+endif
+
 # tests rely on -fvisibility=hidden symbols
 htslib_test_lib = static_library(
   'statichts',