src/analysis/nanopore.cpp src/dnmtools.cpp src/CMakeLists.txt configure.ac and Makefile.am: adding condition to build for nanopore if htslib version is recent enough to support mods and user requests it

Author: andrewdavidsmith

Makefile.am

@@ -22,7 +22,13 @@ ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp src/abismal
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
+AM_CPPFLAGS = \
+	-I $(top_srcdir)/src/common \
+	-I $(top_srcdir)/src/smithlab_cpp \
+	-I $(top_srcdir)/src/bamxx
+if BUILD_NANOPORE
+AM_CPPFLAGS += -DBUILD_NANOPORE
+endif
 
 AM_CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
 

configure.ac

@@ -55,6 +55,11 @@ AC_ARG_WITH([libdeflate],
   [AS_HELP_STRING([--with-libdeflate], [use libdeflate for BAM output])],
   [with_libdeflate=yes], [with_libdeflate=no])
 
+dnl arg for building with mods support in 'counts'
+AC_ARG_WITH([htsmods],
+  [AS_HELP_STRING([--with-htsmods], [use HTSLib 'mods' to support Nanopore])],
+  [with_htsmods=yes], [with_htsmods=no])
+
 dnl check for required libraries
 AC_SEARCH_LIBS([pthread_create], [pthread], [], [AC_MSG_FAILURE(["pthread library not found"])])
 AC_SEARCH_LIBS([gzopen], [z], [], [AC_MSG_FAILURE(["Zlib library not found"])])
@@ -66,18 +71,22 @@ AS_IF([test "x$with_libdeflate" = "xyes"],
 AC_SEARCH_LIBS([hts_version], [hts], [], [AC_MSG_FAILURE([$hts_fail_msg])])
 AC_CHECK_HEADERS([htslib/hts.h], [], [AC_MSG_ERROR([hts.h not found])])
 # Require HTS_VERSION >= 102000
-AC_COMPILE_IFELSE(
-  [AC_LANG_PROGRAM([[
-     #include <htslib/hts.h>
-     #if !defined(HTS_VERSION)
-     # error HTS_VERSION not defined
-     #endif
-     #if HTS_VERSION < 102000
-     # error htslib library too old
-     #endif
-  ]], [[]])],
-  [have_hts=yes],
-  [have_hts=no]
+AS_IF([test "x$with_htsmods" = "xyes"],
+  [
+    AC_COMPILE_IFELSE(
+      [
+        AC_LANG_PROGRAM([[
+          #include <htslib/hts.h>
+          #if !defined(HTS_VERSION)
+          # error HTS_VERSION not defined
+          #endif
+          #if HTS_VERSION < 102000
+          # error htslib library too old
+          #endif
+        ]], [[]])
+      ], [have_htsmods_version=yes], [have_htsmods_version=no])
+  ],
+  [have_htsmods_version=yes]
 )
 
 AC_COMPUTE_INT(
@@ -87,8 +96,13 @@ AC_COMPUTE_INT(
   [AC_MSG_ERROR([Could not compute HTS_VERSION])]
 )
 AC_MSG_NOTICE([Detected htslib version: $hts_version_macro])
-AS_IF([test "x$have_hts" != "xyes"],
-      [AC_MSG_ERROR([Required htslib version must be at least 102000 (v1.20)])])
+
+AS_IF([test "x$have_htsmods_version" != "xyes"], [
+  AC_MSG_ERROR([
+    HTSLib version must be at least 102000 (v1.20) for mods support
+  ])
+])
+AM_CONDITIONAL([BUILD_NANOPORE], [test "x$with_htsmods" = "xyes"])
 
 AC_SEARCH_LIBS([cblas_dgemm], [gslcblas], [], [AC_MSG_FAILURE([$gsl_fail_msg])])
 AC_SEARCH_LIBS([gsl_blas_dgemm], [gsl], [], [AC_MSG_FAILURE([$gsl_fail_msg])])

src/CMakeLists.txt

@@ -13,7 +13,12 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <https://www.gnu.org/licenses/>.
 
-find_package(HTSLIB 1.20 REQUIRED)
+if(BUILD_NANOPORE)
+  find_package(HTSLIB 1.20 REQUIRED)
+  add_compile_definitions(BUILD_NANOPORE)
+else()
+  find_package(HTSLIB REQUIRED)
+endif()
 find_package(Threads REQUIRED)
 
 if(NOT TARGET bamxx)

src/analysis/nanopore.cpp

@@ -16,6 +16,8 @@
  * more details.
  */
 
+#ifdef BUILD_NANOPORE
+
 #include "counts_header.hpp"
 
 #include "OptionParser.hpp"
@@ -1085,3 +1087,5 @@ main_nanocount(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
 }
 
 // NOLINTEND(*-narrowing-conversions,*-pointer-arithmetic)
+
+#endif

src/dnmtools.cpp

@@ -74,8 +74,6 @@ simreads(int argc, char *argv[]);
 int
 main_counts(int argc, char *argv[]);
 int
-main_nanocount(int argc, char *argv[]);
-int
 main_allelicmeth(int argc, char *argv[]);
 int
 main_amrfinder(int argc, char *argv[]);
@@ -153,6 +151,10 @@ int
 kmersites(int argc, char *argv[]);
 int
 main_summary(int argc, char *argv[]);
+#ifdef BUILD_NANOPORE
+int
+main_nanocount(int argc, char *argv[]);
+#endif
 // NOLINTEND(*-avoid-c-arrays)
 
 void
@@ -188,7 +190,9 @@ main(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
           {"uniq",      "remove duplicate reads from sorted mapped reads",           main_uniq},
           {"bsrate",    "compute the BS conversion rate from BS-seq reads mapped to a genome",  main_bsrate},
           {"counts",    "get methylation levels from mapped WGBS reads",             main_counts},
+#ifdef BUILD_NANOPORE
           {"counts-nano", "get methylation levels from mapped nanopore reads",       main_nanocount},
+#endif
           {"sym",       "get CpG sites and make methylation levels symmetric",       main_symmetric_cpgs},
           {"levels",    "compute methylation summary statistics from a counts file", main_levels}}}},