Changeset 4019


Ignore:
Timestamp:
Nov 6, 2020, 2:55:37 AM (6 months ago)
Author:
Peter
Message:

merge 0.18 into trunk

Location:
trunk
Files:
4 deleted
17 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/NEWS

    r4001 r4019  
    1010yat 0.18.x series from http://dev.thep.lu.se/yat/svn/branches/0.18-stable
    1111
    12 version 0.18 (released NOT YET)
     12version 0.18 (released 6 November 2020)
    1313  - regression::NegativeBinomial now inherits from
    1414    regression::Multivariate (ticket #957)
  • trunk/build_support/Makefile.am

    r3987 r4019  
    8989  --exec-prefix="$(exec_prefix)" \
    9090  --libdir="$(libdir)" --includedir="$(includedir)" \
    91   --input="../$(srcdir)/build_support/yat.pc.in" > yat.pc-t \
     91  --input="$(abs_srcdir)/build_support/yat.pc.in" > yat.pc-t \
    9292  && mv yat.pc-t yat.pc
  • trunk/doc/Makefile.am

    r3987 r4019  
    4747EXTRA_DIST += doc/doxygen.config.in
    4848
    49 doc/doxygen.config: doc/doxygen.config.in
     49# config file needs to be updated when $(DOXYGEN_INPUT) is
     50# changed. That variable is set in various Makefile.am, but instead we
     51# depend on Makefile.in, since that dependency is easier to maintain.
     52doc/doxygen.config: doc/doxygen.config.in $(srcdir)/Makefile.in
    5053  $(AM_V_GEN)echo "# $@ generated by make from doc/doxygen.config.in." \
    5154  > $@-t \
  • trunk/m4/version.m4

    r4001 r4019  
    9595# yat-0.17.1 14:1:0
    9696# yat-0.17.2 14:2:0
     97# yat-0.18   15:0:0
    9798#
    9899# *Accidently, the libtool number was not updated for yat 0.5
  • trunk/m4/yat_check_libs.m4

    r3884 r4019  
    11## $Id$
    22#
    3 # serial 2 (yat 0.18)
     3# serial 3 (yat 0.18)
    44#
    55# see http://www.gnu.org/software/automake/manual/automake.html#Serials
     
    4242AC_DEFUN([YAT_CHECK_LIBS],
    4343[
    44   m4_pushdef([yat_message], [$1])
    45   m4_pushdef([yat_cache], [$2])
    46   m4_pushdef([yat_search_libs], [$3])
     44  m4_pushdef([yat_MESSAGE], [$1])
     45  m4_pushdef([yat_CACHE], [$2])
     46  m4_pushdef([yat_SEARCH_LIBS], [$3])
     47  m4_pushdef([yat_DEFAULT_RESULT], ["none required"])
    4748  AC_LANG_CONFTEST([$4])
    48   AC_CACHE_CHECK([yat_message], [$2], [
     49  AC_CACHE_CHECK([yat_MESSAGE], [yat_CACHE], [
    4950    save_LIBS=$LIBS
    50     for yat_lib in '' yat_search_libs; do
     51    for yat_lib in '' yat_SEARCH_LIBS; do
    5152      AS_VAR_IF([yat_lib], [''],[
    52         yat_result="non required"
     53        yat_result=yat_DEFAULT_RESULT
    5354      ], [
    5455        yat_result=-l$yat_lib
    5556        LIBS="-l$yat_lib $save_LIBS"
    5657      ])
    57       AC_LINK_IFELSE([], [yat_cache=$yat_result])
    58       AS_VAR_SET_IF([yat_cache], [break])
     58      AC_LINK_IFELSE([], [yat_CACHE=$yat_result])
     59      AS_VAR_SET_IF([yat_CACHE], [break])
    5960    done
    60     AS_VAR_SET_IF([yat_cache], [], [yat_cache=no])
     61    AS_VAR_SET_IF([yat_CACHE], [], [yat_CACHE=no])
    6162    rm conftest.$ac_ext
    6263    LIBS=$save_LIBS
    6364  ])
    64   yat_result=$yat_cache
     65  yat_result=$yat_CACHE
    6566
    6667  # action
    6768  AS_VAR_IF([yat_result], [no], [$6], [
    68     AS_VAR_IF([yat_result], ["none required"], [], [LIBS="$yat_result $LIBS"])
     69    AS_VAR_IF([yat_result], [yat_DEFAULT_RESULT], [],
     70              [LIBS="$yat_result $LIBS"])
    6971    $5
    7072  ])
    7173
    72 
    73   m4_popdef([yat_message])
    74   m4_popdef([yat_cache])
    75   m4_popdef([yat_search_libs])
     74  m4_popdef([yat_MESSAGE])
     75  m4_popdef([yat_CACHE])
     76  m4_popdef([yat_SEARCH_LIBS])
     77  m4_popdef([yat_DEFAULT_RESULT])
    7678])
  • trunk/test/Makefile.am

    r3987 r4019  
    101101  test/poisson.test \
    102102  test/queue.test test/queue2.test \
    103   test/random_distribution.test \
    104103  test/range.test test/regression.test test/rnd.test \
    105104  test/rng-mt.test \
  • trunk/test/yat_pc_test.sh

    r3966 r4019  
    8181CXX = `yat-config --cxx`
    8282# add -I flags to include local header files; 2nd term needed for VPATH build
    83 CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir/yat/utility \
     83CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir \
     84-I$abs_top_builddir/yat/utility \
    8485`$PKG_CONFIG yat --cflags-only-I`
    8586CXXFLAGS = `$PKG_CONFIG yat --cflags-only-other`
  • trunk/yat/classifier/KernelLookup.h

    r3330 r4019  
    88  Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
    99  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    10   Copyright (C) 2010, 2012 Peter Johansson
     10  Copyright (C) 2010, 2012, 2020 Peter Johansson
    1111
    1212  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3232#include "yat/utility/StrideIterator.h"
    3333
    34 #include <boost/shared_ptr.hpp>
     34#include <memory>
    3535
    3636namespace theplu {
     
    324324
    325325    utility::Index column_index_;
    326     boost::shared_ptr<const Kernel> kernel_;
     326    std::shared_ptr<const Kernel> kernel_;
    327327    utility::Index row_index_;
    328328  }; // class KernelLookup
  • trunk/yat/classifier/MatrixLookup.h

    r3330 r4019  
    88  Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
    99  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    10   Copyright (C) 2009, 2010, 2012 Peter Johansson
     10  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
    1111
    1212  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3333
    3434#include <boost/iterator/permutation_iterator.hpp>
    35 #include <boost/shared_ptr.hpp>
    3635
    3736#include <iosfwd>
     37#include <memory>
    3838#include <vector>
    3939
     
    327327
    328328    utility::Index column_index_;
    329     typedef boost::shared_ptr<const utility::Matrix> MatrixP;
     329    typedef std::shared_ptr<const utility::Matrix> MatrixP;
    330330    MatrixP data_;
    331331    utility::Index row_index_;
  • trunk/yat/classifier/MatrixLookupWeighted.h

    r3330 r4019  
    77  Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
    88  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    9   Copyright (C) 2009, 2010, 2012 Peter Johansson
     9  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
    1010
    1111  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3333
    3434#include <boost/iterator/permutation_iterator.hpp>
    35 #include <boost/shared_ptr.hpp>
    3635
    3736#include <iosfwd>
     37#include <memory>
    3838#include <utility>
    3939#include <vector>
     
    296296
    297297  private:
    298     typedef boost::shared_ptr<const utility::MatrixWeighted> MatrixWP;
     298    typedef std::shared_ptr<const utility::MatrixWeighted> MatrixWP;
    299299    utility::Index column_index_;
    300300    MatrixWP data_;
  • trunk/yat/omic/BamPairIterator.h

    r3999 r4019  
    3232#include <boost/iterator/iterator_concepts.hpp>
    3333#include <boost/iterator/iterator_facade.hpp>
    34 #include <boost/shared_ptr.hpp>
    3534
    3635#include <iterator>
    3736#include <map>
     37#include <memory>
    3838#include <utility>
    3939
     
    115115    Base end_;
    116116    const BamRead* mate_;
    117     boost::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
     117    std::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
    118118    typedef std::pair<int32_t, int32_t> Position;
    119     boost::shared_ptr<std::multimap<Position, BamRead> > reads_;
     119    std::shared_ptr<std::multimap<Position, BamRead> > reads_;
    120120    friend class boost::iterator_core_access;
    121121
  • trunk/yat/omic/BamPairIterator2.h

    r3881 r4019  
    3232#include <boost/iterator/iterator_concepts.hpp>
    3333#include <boost/iterator/iterator_facade.hpp>
    34 #include <boost/shared_ptr.hpp>
    3534
    3635#include <iterator>
    3736#include <map>
     37#include <memory>
    3838#include <utility>
    3939
     
    118118    // multimap with reads' position as key
    119119    typedef std::multimap<Position, BamRead> MultiMap;
    120     boost::shared_ptr<MultiMap> reads_;
     120    std::shared_ptr<MultiMap> reads_;
    121121    MultiMap::iterator first_;
    122122    MultiMap::iterator second_;
  • trunk/yat/omic/Fasta.cc

    r3999 r4019  
    166166  {
    167167    // allocate a new char*
    168     boost::shared_array<char> ptr(new char[seq.size()+1]);
     168    std::shared_ptr<char> ptr(new char[seq.size()+1],
     169                              std::default_delete<char[]>());
    169170    std::copy(seq.seq_.get(), seq.seq_.get()+seq.size(), ptr.get());
    170171    // calculate reverse complement
  • trunk/yat/omic/Fasta.h

    r3999 r4019  
    2121#include <htslib/faidx.h>
    2222
    23 #include <boost/shared_array.hpp>
    24 #include <boost/shared_ptr.hpp>
    25 
    2623#include <iosfwd>
    2724#include <map>
     25#include <memory>
    2826#include <string>
    2927#include <vector>
     
    114112      friend class Fasta;
    115113      friend Sequence reverse_complement(const Fasta::Sequence&);
    116       boost::shared_array<const char> seq_;
     114      std::shared_ptr<char> seq_;
    117115      int size_;
    118116    };
     
    134132
    135133  private:
    136     boost::shared_ptr<faidx_t> faidx_;
     134    std::shared_ptr<faidx_t> faidx_;
    137135    // using compiler generated copy
    138136    //FastaIndex(const FastaIndex& other);
  • trunk/yat/omic/Pileup.h

    r3999 r4019  
    3131#include <boost/iterator/iterator_concepts.hpp>
    3232#include <boost/concept/assert.hpp>
    33 #include <boost/shared_ptr.hpp>
    3433
    3534#include <algorithm>
    3635#include <list>
     36#include <memory>
    3737
    3838namespace theplu {
     
    139139      size_t qpos(void) const { return qpos_; }
    140140    private:
    141       boost::shared_ptr<BamRead> bam_;
     141      std::shared_ptr<BamRead> bam_;
    142142      // index of base pointed to
    143143      size_t qpos_;
  • trunk/yat/random/Makefile.am

    r3999 r4019  
    2222yat_libyat_la_SOURCES += yat/random/random.cc
    2323
    24 nobase_include_HEADERS += $(srcdir)/yat/random/ContinuousDistribution.h
    2524nobase_include_HEADERS += $(srcdir)/yat/random/copy_k_of_n.h
    26 nobase_include_HEADERS += $(srcdir)/yat/random/DiscreteDistribution.h
    27 nobase_include_HEADERS += $(srcdir)/yat/random/Distribution.h
    2825nobase_include_HEADERS += $(srcdir)/yat/random/random.h
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