Changeset 3130 for trunk


Ignore:
Timestamp:
Nov 18, 2013, 8:38:59 AM (8 years ago)
Author:
Peter
Message:

merge release 0.11 into trunk

Location:
trunk
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/NEWS

    r3117 r3130  
    1010yat 0.11.x series from http://dev.thep.lu.se/yat/svn/branches/0.11-stable
    1111
    12 version 0.11 (released NOT YET)
     12version 0.11 (released 18 November 2013)
    1313  - Fisher::one_sided_p(void) is now deprecated (ticket #689)
    1414  - PearsonCorrelation::one_sided_p(void) is now deprecated (ticket #689)
     
    2020  - #defines HAVE_BAM_H, HAVE_BAM_BAM_H, and HAVE_SAMTOOLS_BAM_H have been
    2121    replaced with corresponding macros with prefix 'YAT_' (see ticket #766)
     22  - Bam interface is now more complete (see tickets #746 and #739)
    2223
    2324  A complete list of closed tickets can be found here [[br]]
  • trunk/doc/namespaces.doxygen

    r2608 r3130  
    55  Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
    66  Copyright (C) 2010, 2011 Peter Johansson
     7  Copyright (C) 2013 Jari Häkkinen
    78
    89  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    8384/// All classes and functions related to statistical methods or
    8485/// functions are defined within this namespace. See
    85 /// \ref weighted_statistics<br>.
     86/// \ref weighted_statistics.
    8687///
    8788/// @brief Statistical methods, classes, and functions.
  • trunk/m4/version.m4

    r3117 r3130  
    7373# yat-0.10.2 7:2:0
    7474# yat-0.10.3 7:3:0
     75# yat-0.11   8:0:0
    7576#
    7677# *Accidently, the libtool number was not updated for yat 0.5
  • trunk/m4/yat_check_libbam.m4

    r3068 r3130  
    11## $Id$
    22#
    3 # serial 3 (yat 0.11)
     3# serial 4 (yat 0.11)
    44#
    55#
     
    2828yat_bam_header=no
    2929# check how to #include <bam.h>
    30 m4_map_args_w([bam/bam.h bam.h samtools/bam.h],
    31               [_YAT_CHECK_HEADER_BAM(], [)
     30m4_foreach_w([myheader], [bam.h bam/bam.h samtools/bam.h],
     31             [_YAT_CHECK_HEADER_BAM(myheader)
    3232])
    3333AS_IF([test x$yat_bam_header = xyes], [$1], [$2])
  • trunk/test/Makefile.am

    r3109 r3130  
    152152  $(top_builddir)/build_support/yat-config
    153153test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
    154   test/lib/libmy-static.a test/lib/libmy-shared.la \
     154  test/lib/libmy-shared.la \
    155155  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
    156156  $(top_srcdir)/m4/yat_common.m4
  • trunk/test/gen_libmy_shared.sh

    r3106 r3130  
    2020# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2121
     22set -e
    2223. test/defs.sh || exit 99
    2324
     
    6566verbose=
    6667bootstrap
    67 ./configure --prefix=$abs_top_builddir/test || exit 1
     68./configure --libdir=$abs_top_builddir/test/lib || exit 1
    6869
    6970unset MAKEFLAGS
  • trunk/test/gen_libmy_static.sh

    r3110 r3130  
    2020# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2121
     22set -e
    2223. test/defs.sh || exit 99
    2324
  • trunk/test/static_test.sh

    r3114 r3130  
    22# $Id$
    33#
    4 # Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
     4# Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     5# Copyright (C) 2013 Jari Häkkinen, Peter Johansson
    56#
    67# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    4041EOF
    4142
    42 sed -i 's,^AM_LDFLAGS =,AM_LDFLAGS = -all-static,' Makefile.am
     43sed -i -e 's,^AM_LDFLAGS =,AM_LDFLAGS = -all-static,' Makefile.am
    4344grep '^AM_LDFLAGS' Makefile.am || exit_fail
    4445
  • trunk/test/yat_lt_link_la_ifelse_test.sh

    r3112 r3130  
    1919# along with yat. If not, see <http://www.gnu.org/licenses/>.
    2020
    21 required="autoconf automake libtool libmy-static libmy-shared"
     21required="autoconf automake libtool libmy-shared"
    2222set -e
    2323. ./test/init.sh || exit 99
     
    4949  ])
    5050
    51 LIBS=-lmy-static
    52 AC_MSG_CHECKING([whether linking against -lmy-static works])
    53 YAT_LT_LINK_LA_IFELSE([
    54 namespace theplu {
    55 namespace yat {
    56 namespace utility {
    57     int version(void);
    58 }}}
    59     int my_func(void) { return theplu::yat::utility::version(); }
    60   ],[
    61     AC_MSG_RESULT([yes])
    62     AC_MSG_FAILURE([expected configure to fail])
    63   ],[
    64     AC_MSG_RESULT([no])
    65   ])
    66 
    6751AC_CONFIG_FILES([Makefile])
    6852AC_OUTPUT
  • trunk/test/yat_msg_error_test.sh

    r3114 r3130  
    22# $Id$
    33#
    4 # Copyright (C) 2011, 2012, 2013 Peter Johansson
     4# Copyright (C) 2011, 2012 Peter Johansson
     5# Copyright (C) 2013 Jari Häkkinen, Peter Johansson
    56#
    67# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3233cat >> configure.ac <<EOF
    3334YAT_MSG_ERROR([$specific_msg])
    34 AC_PREREQ([2.64])
     35AC_PREREQ([2.63])
    3536AC_MSG_CHECKING([for something more])
    3637AC_MSG_RESULT([no])
  • trunk/test/yat_msg_error_test2.sh

    r3114 r3130  
    22# $Id$
    33#
    4 # Copyright (C) 2011, 2012, 2013 Peter Johansson
     4# Copyright (C) 2011, 2012 Peter Johansson
     5# Copyright (C) 2013 Jari Häkkinen, Peter Johansson
    56#
    67# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3031
    3132cat >> configure.ac <<EOF
    32 AC_PREREQ([2.64])
     33AC_PREREQ([2.63])
    3334AS_IF([test x = x], [], [YAT_MSG_ERROR([some message])])
    3435AC_CONFIG_FILES([Makefile])
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