configure.ac: making htslib on by default and adding check for libdeflate

Author: andrewdavidsmith

configure.ac

@@ -1,23 +1,27 @@
 dnl This file is part of preseq
 dnl
-dnl Copyright (C) 2018-2024: Andrew D. Smith
+dnl Copyright (C) 2018-2025: Andrew D. Smith
 dnl
 dnl Authors: Andrew D. Smith
 dnl
-dnl This is free software: you can redistribute it and/or modify it
-dnl under the terms of the GNU General Public License as published by
-dnl the Free Software Foundation, either version 3 of the License, or
-dnl (at your option) any later version.
+dnl This is free software: you can redistribute it and/or modify it under the
+dnl terms of the GNU General Public License as published by the Free Software
+dnl Foundation, either version 3 of the License, or (at your option) any later
+dnl version.
 dnl
-dnl This software is distributed in the hope that it will be useful,
-dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
-dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-dnl General Public License for more details.
-
-AC_INIT([preseq], [3.2.0], [andrewds@usc.edu],
-        [preseq], [https://github.com/smithlabcode/preseq])
-dnl the config.h is not currently #included in the source, and only
-dnl used to keep command lines short.
+dnl This software is distributed in the hope that it will be useful, but
+dnl WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+dnl or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+dnl for more details.
+
+AC_INIT([preseq],
+        [3.2.0],
+        [andrewds@usc.edu],
+        [preseq],
+        [https://github.com/smithlabcode/preseq])
+
+dnl the config.h is not currently #included in the source, and only used to
+dnl keep command lines short.
 AC_CONFIG_HEADERS([config.h])
 AM_INIT_AUTOMAKE([subdir-objects foreign])
 
@@ -33,16 +37,29 @@ hts_fail_msg="
 Failed to locate HTSLib on your system. Please use the LDFLAGS and
 CPPFLAGS variables to specify the directories where the HTSLib library
 and headers can be found.
+
+If you want to disable HTSLib when building preseq, use the --disable-htslib
+argument to the configure script.
 "
 AC_ARG_ENABLE([hts],
-  [AS_HELP_STRING([--enable-hts], [Enable HTSLib @<:@yes@:>@])],
-  [enable_hts=yes], [enable_hts=no])
+  [AS_HELP_STRING([--disable-hts], [Enable HTSLib @<:@yes@:>@])],
+  [enable_hts=no], [enable_hts=yes])
 AS_IF([test "x$enable_hts" = "xyes"],
   [AC_CHECK_LIB([hts], [hts_version], [],
   [AC_MSG_FAILURE([$hts_fail_msg])])]
 )
 AM_CONDITIONAL([ENABLE_HTS], [test "x$enable_hts" = "xyes"])
 
+dnl arg for using libdeflate, which might happen by default anyway
+AC_ARG_WITH([libdeflate],
+  [AS_HELP_STRING([--with-libdeflate], [use libdeflate for reading BAM files])],
+  [with_libdeflate=yes], [with_libdeflate=no])
+AS_IF([test "x$with_libdeflate" = "xyes"],
+  [
+    AC_SEARCH_LIBS([libdeflate_deflate_compress], [deflate], [],
+                   [AC_MSG_ERROR([--with-libdeflate specified but libdeflate not found])])
+  ])
+
 AC_CONFIG_FILES([Makefile])
 
 dnl make the test data files available in the build tree