Changeset 3561 for trunk


Ignore:
Timestamp:
Jan 4, 2017, 1:55:10 AM (5 years ago)
Author:
Peter
Message:

Merged release 0.13.1 into trunk

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/NEWS

    r3550 r3561  
    1919
    2020yat 0.13.x series from http://dev.thep.lu.se/yat/svn/branches/0.13-stable
     21
     22version 0.13.1 (released 4 January 2017)
     23  - fixed bug in pkg-config file 'yat.pc' (bug #850)
     24  - improved detection of boost thread detection (bug #863)
     25
     26  A complete list of closed tickets can be found here [[br]]
     27  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.13
    2128
    2229version 0.13 (released 20 November 2015)
  • trunk/configure.ac

    r3550 r3561  
    247247# skip boost link tests if boost is not wanted (--without-boost)
    248248AS_IF([test x"$want_boost" = x"yes"],[
     249  AX_BOOST_SYSTEM
     250  LIBS="$BOOST_SYSTEM_LIB $LIBS"
    249251  AX_BOOST_THREAD
    250   AX_BOOST_SYSTEM
    251252  YAT_CPP_ADD_FLAG([CPPFLAGS], [$BOOST_CPPFLAGS])
    252253  YAT_LD_ADD_FLAG([LDFLAGS], [$BOOST_LDFLAGS])
    253   # boost tests above only test compilation, so let's try link in the libs
    254   LIBS="$LIBS $BOOST_THREAD_LIB $BOOST_SYSTEM_LIB"
     254  LIBS="$BOOST_THREAD_LIB $LIBS"
     255  # linking tests in AX_BOOST_SYSTEM occasionaly miss to detect
     256  # missing lib (see ticket #719), so link specifically here to catch
     257  # that case.
    255258  AC_MSG_CHECKING([for boost::thread_specific_ptr])
    256259  AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@include <boost/thread/tss.hpp>],
     
    533536AS_IF([test x$with_htslib != x"no"], [
    534537  # htslib comes with a pc file, so we can require htslib in yat.pc
    535   AS_IF([test x$with_hts = x"yes"], [
     538  AS_IF([test x$have_hts = x"yes"], [
    536539    YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$BAM_LIBS -lz])
    537540    YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lhts], [
     
    544547    # require zlib
    545548    YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [-lz])
    546     YAT_PC_REQUIRES="$YAT_PC_REQUIRES zlib"
    547549    YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lz], [
    548550      YAT_PC_REQUIRES_PRIVATE="$YAT_PC_REQUIRES_PRIVATE zlib"
  • trunk/doc/first_page.doxygen.in

    r3210 r3561  
    55  Copyright (C) 2003, 2004 Jari Häkkinen
    66  Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
    7   Copyright (C) 2010, 2013, 2014 Peter Johansson
     7  Copyright (C) 2010, 2013, 2014, 2015 Peter Johansson
    88
    99  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    5454
    5555   <li> Wrapper classes for <a
    56    href="http://samtools.sourceforge.net/">samtools</a> allowing
     56   href="http://www.htslib.org//">htslib</a> allowing
    5757   handling BAM reads with <a
    5858   href="http://www.sgi.com/tech/stl/table_of_contents.html">Standard
  • trunk/m4/version.m4

    r3419 r3561  
    22#
    33# Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
    4 # Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015 Peter Johansson
     4# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    8080# yat-0.12.2 9:2:0
    8181# yat-0.13   10:0:0
     82# yat-0.13.1 10:1:0
    8283#
    8384# *Accidently, the libtool number was not updated for yat 0.5
  • trunk/yat/statistics/Fisher.h

    r3455 r3561  
    7373    /// chi-squared calculation
    7474    ///
     75    /// \since Constructor with argument was introduced in yat 0.13
     76    ///
    7577    Fisher(bool yates=false);
    7678
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