try to update htslib

.github/workflows/build.yml

@@ -28,7 +28,7 @@ jobs:
         cd htslib
         autoheader && autoconf && autoreconf --install
         ./configure --enable-s3 --disable-lzma --disable-bz2
-        make
+        make version.h && make
         cd ..
         CYTHONIZE=1 python setup.py build_ext -i
     - name: Test

MANIFEST.in

@@ -10,3 +10,4 @@ include htslib/*.h
 include htslib/htslib/*.h
 include htslib/cram/*.c
 include htslib/cram/*.h
+include htslib/htscodecs/htscodecs/varint.h

requirements.txt

@@ -1,4 +1,4 @@
-cython>=0.23.3
+cython>=0.23.3,<3.0.0
 numpy
 coloredlogs
 click

setup.py

@@ -48,7 +48,11 @@ def no_cythonize(extensions, **_ignore):
     if not any(e in x for e in ['irods', 'plugin'])
 ]
 sources += glob.glob('htslib/cram/*.c')
-sources += glob.glob('htslib/htscodecs/htscodecs/*.c')
+sources += ['htslib/htscodecs/htscodecs/%s' % s for s in ['rle.c', 'arith_dynamic.c', 'pack.c', 'utils.c',
+                                                          'htscodecs.c', 'fqzcomp_qual.c',
+                                                          #'rANS_static.c',
+                                                          'rANS_static4x16pr.c']]
+
 # Exclude the htslib sources containing main()'s
 sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]
 sources.append('cyvcf2/helpers.c')
@@ -65,7 +69,7 @@ def no_cythonize(extensions, **_ignore):
                         extra_compile_args=["-Wno-sign-compare", "-Wno-unused-function",
                             "-Wno-strict-prototypes",
                             "-Wno-unused-result", "-Wno-discarded-qualifiers"],
-                        include_dirs=['htslib', 'cyvcf2', np.get_include()])]
+                        include_dirs=['htslib', 'cyvcf2', 'htslib/htscodecs/htscodecs', np.get_include()])]
 
 
 CYTHONIZE = bool(int(os.getenv("CYTHONIZE", 0)))