Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 22 Jan 2020 20:12:46 +0100
Description: Latest libpbihdf and libpbdata are header only libs and
 there is no library to link with

--- a/configure.py
+++ b/configure.py
@@ -90,8 +90,6 @@ HDF_HEADERS:=%(HDF_HEADERS)s
 #HDF5_INCLUDE?=${HDF_HEADERS}/src
 CPPFLAGS+=-I${HDF_HEADERS}/src -I${HDF_HEADERS}/c++/src
 CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
-LIBPBDATA_LIB     ?=../pbdata/libpbdata.so
-LIBPBIHDF_LIB     ?=../pbdata/libpbihdf.so
 LIBBLASR_LIB      ?=../pbdata/libblasr.so
 """%(dict(thisdir=thisdir, HDF_HEADERS=HDF_HEADERS))
 
@@ -102,11 +100,7 @@ def compose_defines():
     """
     thisdir = os.path.dirname(os.path.abspath(__file__))
     return """
-LIBPBDATA_INCLUDE ?=../pbdata
-LIBPBIHDF_INCLUDE ?=../hdf
 LIBBLASR_INCLUDE  ?=../alignment
-LIBPBDATA_LIB     ?=%(thisdir)s/pbdata/libpbdata.so
-LIBPBIHDF_LIB     ?=%(thisdir)s/pbdata/libpbihdf.so
 LIBBLASR_LIB      ?=%(thisdir)s/pbdata/libblasr.so
 nohdf             ?=1
 """%(dict(thisdir=thisdir))
@@ -232,7 +226,6 @@ def parse_args(args):
 
 def set_defs_defaults(env, nopbbam):
     defaults = {
-        'LIBPBDATA_LIBFLAGS': '-lpbdata',
         'LIBBLASR_LIBFLAGS':  '-lblasr',
         'SHELL': 'bash -xe',
         'DAZZ_DB_SRC': os.path.join(ROOT, '..', 'DAZZ_DB'),
@@ -242,7 +235,6 @@ def set_defs_defaults(env, nopbbam):
         'PTHREAD_LIBFLAGS': '-lpthread',
     }
     pbbam_defaults = {
-        'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
         'PBBAM_LIBFLAGS': '-lpbbam',
         'HTSLIB_LIBS': '-lhts',
         'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
@@ -264,7 +256,6 @@ def set_defs_submodule_defaults(env, nop
         'LIBPBDATA_INCLUDE': os.path.join(libcpp, 'pbdata'),
         'LIBBLASR_INCLUDE':  os.path.join(libcpp, 'alignment'),
         'LIBPBIHDF_INCLUDE': '' if nopbbam else os.path.join(libcpp, 'hdf'),
-        'LIBPBDATA_LIB': os.path.join(libcpp, 'pbdata'),
         'LIBBLASR_LIB':  os.path.join(libcpp, 'alignment'),
         'LIBPBIHDF_LIB': '' if nopbbam else os.path.join(libcpp, 'hdf'),
         'DALIGNER_SRC': daligner,