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Merge pull request #86 from jmarshall/htslib
Convert lofreq to use the HTSlib API instead of the legacy samtools API
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| # =========================================================================== | ||
| # http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html | ||
| # =========================================================================== | ||
| # | ||
| # SYNOPSIS | ||
| # | ||
| # AX_WITH_HTSLIB | ||
| # | ||
| # DESCRIPTION | ||
| # | ||
| # This macro checks whether HTSlib <http://www.htslib.org/> is installed | ||
| # or nearby, and adds a --with-htslib=DIR option to the configure script | ||
| # for specifying the location. It locates either an installation prefix | ||
| # (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as | ||
| # HTSlib is fast-moving and users may wish to use an in-development tree. | ||
| # | ||
| # Different checks occur depending on the --with-htslib argument given: | ||
| # | ||
| # With --with-htslib=DIR, checks whether DIR is a source tree or contains | ||
| # a working installation. | ||
| # By default, searches for a source tree (with a name matching htslib*) | ||
| # within or alongside $srcdir. Produces AC_MSG_ERROR if there are | ||
| # several equally-likely candidates. If there are none, checks for | ||
| # a working default installation. | ||
| # With --with-htslib=system, checks for a working default installation. | ||
| # | ||
| # If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS | ||
| # if either --enable-configure-htslib is set, or where htslib is included | ||
| # in a subdirectory (for packages that want to supply an embedded htslib). | ||
| # Unfortunately this may cause a "you should use literals" warning when | ||
| # autoconf is run. | ||
| # | ||
| # The following output variables are set by this macro: | ||
| # | ||
| # HTSDIR Directory containing HTSlib source tree | ||
| # HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib | ||
| # HTSLIB_LDFLAGS Linker flags for linking with HTSlib | ||
| # | ||
| # The following shell variables may be defined: | ||
| # | ||
| # ax_cv_htslib Set to "yes" if HTSlib was found | ||
| # ax_cv_htslib_which Set to "source", "install", or "none" | ||
| # | ||
| # LICENSE | ||
| # | ||
| # Copyright (C) 2015,2017 Genome Research Ltd | ||
| # | ||
| # Copying and distribution of this file, with or without modification, are | ||
| # permitted in any medium without royalty provided the copyright notice | ||
| # and this notice are preserved. This file is offered as-is, without any | ||
| # warranty. | ||
|
|
||
| #serial 1 | ||
|
|
||
| AC_DEFUN([AX_WITH_HTSLIB], | ||
| [AC_ARG_WITH([htslib], | ||
| [AS_HELP_STRING([--with-htslib=DIR], | ||
| [use the HTSlib source tree or installation in DIR]) | ||
| dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() | ||
| AS_HELP_STRING([--with-htslib=system], | ||
| [use only a system HTSlib installation])], | ||
| [], [with_htslib=search]) | ||
| AC_ARG_ENABLE([configure-htslib], | ||
| [AS_HELP_STRING([--enable-configure-htslib], | ||
| [run configure for htslib as well @<:@default=only_in_subdir@:>@])], | ||
| [], [enable_configure_htslib=only_in_subdir]) | ||
| case $with_htslib in | ||
| yes|search) | ||
| AC_MSG_CHECKING([location of HTSlib source tree]) | ||
| case $srcdir in | ||
| .) srcp= ;; | ||
| *) srcp=$srcdir/ ;; | ||
| esac | ||
| found= | ||
| for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* | ||
| do | ||
| if test "$dir" = "--"; then | ||
| test -n "$found" && break | ||
| elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then | ||
| found="${found}1" | ||
| HTSDIR=$dir | ||
| fi | ||
| done | ||
| if test -z "$found"; then | ||
| AC_MSG_RESULT([none found]) | ||
| ax_cv_htslib_which=system | ||
| elif test "$found" = 1; then | ||
| AC_MSG_RESULT([$HTSDIR]) | ||
| ax_cv_htslib_which=source | ||
| if test "x$enable_configure_htslib" = "xonly_in_subdir" ; then | ||
| case $HTSDIR in | ||
| "${srcp}htslib"*) enable_configure_htslib=yes ;; | ||
| *) ;; | ||
| esac | ||
| fi | ||
| else | ||
| AC_MSG_RESULT([several directories found]) | ||
| AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) | ||
| fi | ||
| ;; | ||
| no) ax_cv_htslib_which=none ;; | ||
| system) ax_cv_htslib_which=system ;; | ||
| *) | ||
| HTSDIR=$with_htslib | ||
| if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then | ||
| ax_cv_htslib_which=source | ||
| else | ||
| ax_cv_htslib_which=install | ||
| fi | ||
| ;; | ||
| esac | ||
| case $ax_cv_htslib_which in | ||
| source) | ||
| ax_cv_htslib=yes | ||
| HTSLIB_CPPFLAGS="-I$HTSDIR" | ||
| HTSLIB_LDFLAGS="-L$HTSDIR" | ||
| if test "x$enable_configure_htslib" = "xyes"; then | ||
| # We can't use a literal, because $HTSDIR is user-provided and variable | ||
| AC_CONFIG_SUBDIRS($HTSDIR) | ||
| fi | ||
| ;; | ||
| system) | ||
| AC_CHECK_HEADER([htslib/sam.h], | ||
| [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], | ||
| [ax_cv_htslib=no], [;]) | ||
| ax_cv_htslib_which=install | ||
| HTSDIR= | ||
| HTSLIB_CPPFLAGS= | ||
| HTSLIB_LDFLAGS= | ||
| ;; | ||
| install) | ||
| ax_saved_CPPFLAGS=$CPPFLAGS | ||
| ax_saved_LDFLAGS=$LDFLAGS | ||
| HTSLIB_CPPFLAGS="-I$HTSDIR/include" | ||
| HTSLIB_LDFLAGS="-L$HTSDIR/lib" | ||
| CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" | ||
| LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" | ||
| AC_CHECK_HEADER([htslib/sam.h], | ||
| [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], | ||
| [ax_cv_htslib=no], [;]) | ||
| HTSDIR= | ||
| CPPFLAGS=$ax_saved_CPPFLAGS | ||
| LDFLAGS=$ax_saved_LDFLAGS | ||
| ;; | ||
| none) | ||
| ax_cv_htslib=no | ||
| ;; | ||
| esac | ||
| AC_SUBST([HTSDIR]) | ||
| AC_SUBST([HTSLIB_CPPFLAGS]) | ||
| AC_SUBST([HTSLIB_LDFLAGS])]) |
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