Changeset 3400

Timestamp:

Mar 30, 2015, 10:13:35 AM (8 years ago)

Author:

Peter

Message:

refs #794

Deprecate configure option --without-samtools and add new option
--without-htslib that does the same thing.

Prefer variable names with htslib rather than samtools or libbam in
autotool files.

Location:

trunk

Files:

• Makefile.am (modified) (1 diff)
• NEWS (modified) (1 diff)
• configure.ac (modified) (5 diffs)
• test/defs.sh.in (modified) (1 diff)
• test/yat_m4_with_bam_test.sh (modified) (1 diff)
• test/yat_pc_test.sh (modified) (1 diff)
• yat/omic/Makefile.am (modified) (1 diff)

trunk/Makefile.am

@@ -164 +164 @@
 
 # run within maintainer-check
-# try ./configure --without-samtools; make; make check
+# try ./configure --without-htslib; make; make check
 mc_without_samtools:
-  @rm -rf _mc_without_samtools
-  mkdir _mc_without_samtools
-  cd _mc_without_samtools \
-  && ../$(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) --without-samtools \
+  @rm -rf _mc_without_htslib
+  mkdir _mc_without_htslib
+  cd _mc_without_htslib \
+  && ../$(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) --without-htslib \
   && $(MAKE) $(AM_MAKEFLAGS) && $(MAKE) check $(AM_MAKEFLAGS)

trunk/NEWS

@@ -11 +11 @@
     boost::random_access_traversal_tag (see ticket #803, r3393)
   - StrideIterator is now tagged with use_default (see ticket #803, r3393)
+  - configure option --without-samtools is deprecated; use --without-htslib
 
   A complete list of closed tickets can be found here [[br]]

trunk/configure.ac

@@ -348 +348 @@
 AC_ARG_WITH([samtools],
             [AS_HELP_STRING([--without-samtools],
-                            [disable samtools support])],
+                            [disable samtools support (deprecated)])],
             [],
             [with_samtools=yes])
 
-AS_IF([test x"$with_samtools" != x"no"], [
+# HTSLIB API available from http://www.htslib.org/
+AC_ARG_WITH([htslib],
+            [AS_HELP_STRING([--without-htslib], [disable htslib support])],
+            [],
+            [with_htslib=$with_samtools])
+
+AS_IF([test x"$with_htslib" != x"no"], [
   AC_CHECK_HEADER([zlib.h], [],
     [AC_MSG_FAILURE([header file 'zlib.h' was not found])])
@@ -375 +381 @@
   YAT_CHECK_LIBBAM([LIBS="$BAM_LIBS $LIBS"
                     AC_DEFINE([YAT_HAVE_LIBBAM], [1],
-                              [Define to 1 if libhts or libbam is available])],
+                              [Define to 1 if libbam is available])],
     [AC_MSG_FAILURE([library 'libbam' was not found])])
   YAT_CHECK_LA_LIBS([
@@ -395 +401 @@
   SAMTOOLS=false
 ])
-AM_CONDITIONAL([HAVE_LIBBAM], [test x"$with_samtools" = x"yes"])
-have_libbam=$with_samtools
-AC_SUBST([have_libbam])
+AM_CONDITIONAL([HAVE_HTSLIB], [test x"$with_htslib" = x"yes"])
+have_htslib=$with_htslib
+AC_SUBST([have_htslib])
 AM_CONDITIONAL([HAVE_SAMTOOLS], [test x"$SAMTOOLS" != x"false"])
 AC_SUBST([SAMTOOLS])
@@ -585 +591 @@
 ])
 
-# ignore this whole bam thing if --without-samtools
-AS_IF([test x$with_samtools != x"no"], [
+# ignore this whole bam thing if --without-htslib
+AS_IF([test x$with_htslib != x"no"], [
   # htslib comes with a pc file, so we can require htslib in yat.pc
   AS_IF([test x$with_hts = x"yes"], [
@@ -682 +688 @@
   Build Static Library: $enable_static
   Build Documentation:  $doxygen_message
-  With Bam Support:     $with_samtools
+  With Bam Support:     $with_htslib
 
 Options used to compile and link:

trunk/test/defs.sh.in

@@ -81 +81 @@
       test @have_doxygen@ = "yes" || exit_skip no doxygen
       ;;
-      libbam)
-      test @have_libbam@ = "yes" || exit_skip no libbam
+      htslib)
+      test @have_htslib@ = "yes" || exit_skip no libbam
       ;;
       libmy-shared)

trunk/test/yat_m4_with_bam_test.sh

@@ -19 +19 @@
 # along with yat. If not, see <http://www.gnu.org/licenses/>.
 
-required="autoconf automake libtool libbam"
+required="autoconf automake libtool htslib"
 
 set -e

trunk/test/yat_pc_test.sh

@@ -21 +21 @@
 # testing that pkg-config works with yat.pc
 
-required="pkg-config libbam"
+required="pkg-config htslib"
 
 set -e

trunk/yat/omic/Makefile.am

@@ -18 +18 @@
 # along with yat. If not, see <http://www.gnu.org/licenses/>.
 
-if HAVE_LIBBAM
+if HAVE_HTSLIB
 yat_libyat_la_SOURCES += yat/omic/BamFile.cc
 yat_libyat_la_SOURCES += yat/omic/BamHeader.cc