Changeset 3400


Ignore:
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:
7 edited

Legend:

Unmodified
Added
Removed
  • trunk/Makefile.am

    r3246 r3400  
    164164
    165165# run within maintainer-check
    166 # try ./configure --without-samtools; make; make check
     166# try ./configure --without-htslib; make; make check
    167167mc_without_samtools:
    168   @rm -rf _mc_without_samtools
    169   mkdir _mc_without_samtools
    170   cd _mc_without_samtools \
    171   && ../$(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) --without-samtools \
     168  @rm -rf _mc_without_htslib
     169  mkdir _mc_without_htslib
     170  cd _mc_without_htslib \
     171  && ../$(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) --without-htslib \
    172172  && $(MAKE) $(AM_MAKEFLAGS) && $(MAKE) check $(AM_MAKEFLAGS)
  • trunk/NEWS

    r3393 r3400  
    1111    boost::random_access_traversal_tag (see ticket #803, r3393)
    1212  - StrideIterator is now tagged with use_default (see ticket #803, r3393)
     13  - configure option --without-samtools is deprecated; use --without-htslib
    1314
    1415  A complete list of closed tickets can be found here [[br]]
  • trunk/configure.ac

    r3381 r3400  
    348348AC_ARG_WITH([samtools],
    349349            [AS_HELP_STRING([--without-samtools],
    350                             [disable samtools support])],
     350                            [disable samtools support (deprecated)])],
    351351            [],
    352352            [with_samtools=yes])
    353353
    354 AS_IF([test x"$with_samtools" != x"no"], [
     354# HTSLIB API available from http://www.htslib.org/
     355AC_ARG_WITH([htslib],
     356            [AS_HELP_STRING([--without-htslib], [disable htslib support])],
     357            [],
     358            [with_htslib=$with_samtools])
     359
     360AS_IF([test x"$with_htslib" != x"no"], [
    355361  AC_CHECK_HEADER([zlib.h], [],
    356362    [AC_MSG_FAILURE([header file 'zlib.h' was not found])])
     
    375381  YAT_CHECK_LIBBAM([LIBS="$BAM_LIBS $LIBS"
    376382                    AC_DEFINE([YAT_HAVE_LIBBAM], [1],
    377                               [Define to 1 if libhts or libbam is available])],
     383                              [Define to 1 if libbam is available])],
    378384    [AC_MSG_FAILURE([library 'libbam' was not found])])
    379385  YAT_CHECK_LA_LIBS([
     
    395401  SAMTOOLS=false
    396402])
    397 AM_CONDITIONAL([HAVE_LIBBAM], [test x"$with_samtools" = x"yes"])
    398 have_libbam=$with_samtools
    399 AC_SUBST([have_libbam])
     403AM_CONDITIONAL([HAVE_HTSLIB], [test x"$with_htslib" = x"yes"])
     404have_htslib=$with_htslib
     405AC_SUBST([have_htslib])
    400406AM_CONDITIONAL([HAVE_SAMTOOLS], [test x"$SAMTOOLS" != x"false"])
    401407AC_SUBST([SAMTOOLS])
     
    585591])
    586592
    587 # ignore this whole bam thing if --without-samtools
    588 AS_IF([test x$with_samtools != x"no"], [
     593# ignore this whole bam thing if --without-htslib
     594AS_IF([test x$with_htslib != x"no"], [
    589595  # htslib comes with a pc file, so we can require htslib in yat.pc
    590596  AS_IF([test x$with_hts = x"yes"], [
     
    682688  Build Static Library: $enable_static
    683689  Build Documentation:  $doxygen_message
    684   With Bam Support:     $with_samtools
     690  With Bam Support:     $with_htslib
    685691
    686692Options used to compile and link:
  • trunk/test/defs.sh.in

    r3365 r3400  
    8181      test @have_doxygen@ = "yes" || exit_skip no doxygen
    8282      ;;
    83       libbam)
    84       test @have_libbam@ = "yes" || exit_skip no libbam
     83      htslib)
     84      test @have_htslib@ = "yes" || exit_skip no libbam
    8585      ;;
    8686      libmy-shared)
  • trunk/test/yat_m4_with_bam_test.sh

    r3112 r3400  
    1919# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2020
    21 required="autoconf automake libtool libbam"
     21required="autoconf automake libtool htslib"
    2222
    2323set -e
  • trunk/test/yat_pc_test.sh

    r3383 r3400  
    2121# testing that pkg-config works with yat.pc
    2222
    23 required="pkg-config libbam"
     23required="pkg-config htslib"
    2424
    2525set -e
  • trunk/yat/omic/Makefile.am

    r3336 r3400  
    1818# along with yat. If not, see <http://www.gnu.org/licenses/>.
    1919
    20 if HAVE_LIBBAM
     20if HAVE_HTSLIB
    2121yat_libyat_la_SOURCES += yat/omic/BamFile.cc
    2222yat_libyat_la_SOURCES += yat/omic/BamHeader.cc
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