Changeset 3188


Ignore:
Timestamp:
Mar 25, 2014, 11:24:29 AM (9 years ago)
Author:
Peter
Message:

merge patch release 0.11.2

Location:
trunk
Files:
13 edited

Legend:

Unmodified
Added
Removed

  • trunk

  • trunk/NEWS

    r3157 r3188  
    1010
    1111yat 0.11.x series from http://dev.thep.lu.se/yat/svn/branches/0.11-stable
     12
     13version 0.11.2 (released 25 March 2014)
     14  - Fixed bug that error in OutBamFile::write was not detected (see r3163)
     15  - Fixed bug that `-lgsl` was not included in `yat-config --libs` (bug #788)
     16
     17  A complete list of closed tickets can be found here [[br]]
     18  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.11.2
    1219
    1320version 0.11.1 (released 18 December 2013)
    … …  
    339346Copyright (C) 2010, 2011 Peter Johansson
    340347Copyright (C) 2012 Jari Häkkinen, Peter Johansson
    341 Copyright (C) 2013 Peter Johansson
     348Copyright (C) 2013, 2014 Peter Johansson
    342349
    343350This file is part of yat library, http://dev.thep.lu.se/yat

  • trunk/README.developer

    r3144 r3188  
    106106'''Internal Interface'''
    107107
    108 Helper functions and classes that are not part of yat API should either be
    109 labeled with doxygen flag `\internal` or placed in sub-namespace `detail`.
     108Helper functions and classes that are not part of yat API should
     109either be labeled with doxygen flag `\internal` or placed in
     110sub-namespace `detail`. Functionality placed in namespace `detail`
     111should be excluded from doxygen input using a pattern like this:
     112
     113/// \cond IGNORE_DOXYGEN
     114namespace detail {
     115
     116<Some very detailed code here>
     117
     118}
     119/// \endcode
    110120
    111121= Build =
    … …  
    444454Copyright (C) 2004 Jari Häkkinen
    445455Copyright (C) 2006, 2007, 2008, 2009 Jari Häkkinen, Peter Johansson
    446 Copyright (C) 2010, 2011, 2012, 2013 Peter Johansson
     456Copyright (C) 2010, 2011, 2012, 2013, 2014 Peter Johansson
    447457
    448458This file is part of yat library, http://dev.thep.lu.se/yat

  • trunk/configure.ac

    r3111 r3188  
    1010# Copyright (C) 2010, 2011 Peter Johansson
    1111# Copyright (C) 2012 Jari Häkkinen, Peter Johansson
    12 # Copyright (C) 2013 Peter Johansson
     12# Copyright (C) 2013, 2014 Peter Johansson
    1313#
    1414# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    494494YAT_PC_LIBS=$YAT_LIBS
    495495# Dependency to GSL is noted via 'Requires' field
    496 YAT_VAR_REMOVE([YAT_PRIMARY_LIBS], [-lgsl $YAT_CBLAS_LIB $LIBM])
     496YAT_VAR_REMOVE([YAT_PC_LIBS], [-lgsl $YAT_CBLAS_LIB $LIBM])
    497497AC_SUBST([YAT_PC_LIBS])
    498498

  • trunk/m4/version.m4

    r3144 r3188  
    22#
    33# Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
    4 # Copyright (C) 2010, 2011, 2012, 2013 Peter Johansson
     4# Copyright (C) 2010, 2011, 2012, 2013, 2014 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    7575# yat-0.11   8:0:0
    7676# yat-0.11.1 8:1:0
     77# yat-0.11.2 8:2:0
    7778#
    7879# *Accidently, the libtool number was not updated for yat 0.5

  • trunk/test/yat_config_test.sh

    r3114 r3188  
    22# $Id$
    33#
    4 # Copyright (C) 2011, 2012, 2013 Peter Johansson
     4# Copyright (C) 2011, 2012, 2013, 2014 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    4242grep 'for more information' stderr || exit_fail
    4343
     44run sh 0 $prog --libs
     45grep lgsl stdout || exit_fail
     46
     47run sh 0 $prog --libs-without-cblas
     48grep lgsl stdout || exit_fail
     49
    4450exit_success

  • trunk/yat/omic/BamHeader.h

    r2999 r3188  
    55
    66/*
    7   Copyright (C) 2012, 2013 Peter Johansson
     7  Copyright (C) 2012, 2013, 2014 Peter Johansson
    88
    99  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3434
    3535  /**
    36      Wrapper around bam_header_t struct.
     36     \brief Wrapper around bam_header_t struct.
    3737
    38      Class is typically created within InBamFile
     38     Class is typically created via InBamFile::header().
     39
     40     It is possible to copy and assign a BamHeader, but note that a
     41     BamHeader does not own underlying data. The underlying data is
     42     owned by the InBamFile and the BamHeader is thus invalid after
     43     the corresponding InBamFile has been destroyed.
    3944
    4045     \since New in yat 0.10
    … …  
    5257       values in variables \a tid, \a begin and \a end. \a reg is
    5358       1-based and \a begin and \a end are 0-based, i.e.,
    54        "chr2:100,000-200,000" will set \a begin = 99000 and \a end =
     59       "chr2:100,000-200,000" will set \a begin = 99999 and \a end =
    5560       200000.
    5661
    … …  
    7782       \brief inverse of target_name(size_t)
    7883
    79        \note If \a name does not exist, behaviour is unexpected.
     84       \note If \a name does not exist, behaviour is undefined.
    8085
    8186       \since new in yat 0.11

  • trunk/yat/regression/KernelBox.h

    r2119 r3188  
    99  Copyright (C) 2006 Jari Häkkinen
    1010  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
     11  Copyright (C) 2014 Peter Johansson
    1112
    1213  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3738  class KernelBox : public Kernel
    3839  {
    39    
    4040  public:
    4141    ///
    … …  
    4444    KernelBox(void);
    4545
    46     ///
    47     /// Function calculating kernel value as \f$ w(x)=1\f$ if \f$|x|\le 1
    48     /// \f$, \f$ w(x)=0 \f$ otherwise.
    49     ///
     46    /**
     47      Function calculating kernel value as \f$ w(x)=1\f$ if \f$|x|\le 1
     48      \f$, \f$ w(x)=0 \f$ otherwise.
     49    */
    5050    double operator()(const double) const;
    51  
     51
    5252  private:
    5353  };

  • trunk/yat/utility/CommandLine.h

    r3114 r3188  
    66/*
    77  Copyright (C) 2007, 2008, 2009 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2010, 2011, 2012, 2013 Peter Johansson
     8  Copyright (C) 2010, 2011, 2012, 2013, 2014 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    209209
    210210    // use cond to make doxygen ignore this privat class
    211     /// \cond yat_ignore_this
     211    /// \cond IGNORE_DOXYGEN
    212212    struct OptionCompare
    213213    {

  • trunk/yat/utility/Queue.h

    r3062 r3188  
    6666
    6767    /**
    68        \brief Create a Queue with no elements
     68       \brief Copy constructor
    6969
    7070       \note is not thread safe

  • trunk/yat/utility/iterator_traits.h

    r2472 r3188  
    77  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
    88  Copyright (C) 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
    9   Copyright (C) 2010, 2011 Peter Johansson
     9  Copyright (C) 2010, 2011, 2014 Peter Johansson
    1010
    1111  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    5555
    5656
     57/// \cond IGNORE_DOXYGEN
     58
    5759namespace detail {
    5860  /**
    … …  
    8385
    8486} // namespace detail
     87
     88/// \endcond
    8589
    8690
    … …  
    106110
    107111
     112/// \cond IGNORE_DOXYGEN
    108113namespace detail {
    109114  /**
    … …  
    136141  };
    137142} // namespace detail
     143
     144/// \endcond
     145
    138146
    139147  /**
    … …  
    165173  };
    166174
     175  /// \cond IGNORE_DOXYGEN
    167176  namespace detail {
    168177    /**
    … …  
    174183    check_iterator_is_unweighted(utility::unweighted_iterator_tag x){}
    175184  } // namespace detail
     185
     186  /// \endcond
    176187
    177188  /**
    … …  
    187198
    188199
     200/// \cond IGNORE_DOXYGEN
    189201namespace detail {
    190202
    … …  
    380392} // namespace detail
    381393
     394/// \endcond
     395
     396
    382397  /**
    383398     The purpose of this class is to allow polymorphism between

  • trunk/yat/utility/utility.h

    r3177 r3188  
    88  Copyright (C) 2006 Jari Häkkinen
    99  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    10   Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
     10  Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014 Peter Johansson
    1111
    1212  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    274274  T log2(T x) { return std::log(x)/M_LN2; }
    275275
     276/// \cond IGNORE_DOXYGEN
     277
    276278// private namespace
    277279namespace detail {
    278280
    279281  /**
     282     \internal
     283
    280284     \brief convert s to t
    281285
    … …  
    328332
    329333} // end of namespace detail
     334
     335/// \endcond
    330336
    331337
    … …  
    478484  }
    479485
     486/// \cond IGNORE_DOXYGEN
    480487namespace detail {
    481488  template<typename T>
    … …  
    518525} // of namespace detail
    519526
     527/// \endcond
     528
    520529}}} // of namespace utility, yat, and theplu
    521530

  • trunk/yat/utility/yat_assert.h

    r3114 r3188  
    55/*
    66  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    7   Copyright (C) 2009, 2010, 2013 Peter Johansson
     7  Copyright (C) 2009, 2010, 2013, 2014 Peter Johansson
    88
    99  This file is part of the yat library, http://dev.thep.lu.se/yat
    … …  
    3333namespace utility {
    3434
     35  /// \cond IGNORE_DOXYGEN
     36
    3537  /**
    3638     \internal
    … …  
    4749  { }
    4850#endif
     51
     52  /// \endcond
    4953
    5054}}}
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