source: tags/0.14.3/NEWS

Last change on this file was 3633, checked in by peter, 9 months ago

Preparing release 0.14.3

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$Id: NEWS 3633 2017-03-22 03:15:09Z peter $

See the end of this file for copyrights and conditions.

yat 0.14.x series from http://dev.thep.lu.se/yat/svn/branches/0.14-stable

version 0.14.3 (released 22 March 2017)

  • Fixed code so it compiles against HTSlib 1.4 (see r3662)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.14.3

version 0.14.2 (released 8 March 2017)

  • Bug fixed in omic::dna_reverse_complement_copy (see bug #886)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.14.2

version 0.14.1 (released 8 February 2017)

  • Fixed bug in element-by-element operations in VectorMutable? such as operator+=, operator-=, ::mul(), and ::div(), when underlying data structures of lhs and rhs overlap such that elements in rhs are affected by the operation on lhs before they have been used on rhs (bug #884).

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.14.1

version 0.14 (released 16 January 2017)

  • The concept 'Distance' now requires that operator() works on iterator that are readable and forward traversal, i.e., the previously implicit requirement that iterator's reference type is lvalue is dropped (ticket #873)
  • libbam support is marked deprecated; use htslib.
  • A new (private) pure virtual function assign(const VectorBase?&) was added in VectorMutable?. (ticket #840)
  • WeightedIterator? is std::input_iterator_tag (ticket #803, r3459)
  • Fisher::p_value exact is modified and the summation now runs over i for which P(i)<=P(k). (#841)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.14

yat 0.13.x series from http://dev.thep.lu.se/yat/svn/branches/0.13-stable

version 0.13.1 (released 4 January 2017)

  • fixed bug in pkg-config file 'yat.pc' (bug #850)
  • improved detection of boost thread detection (bug #863)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.13

version 0.13 (released 20 November 2015)

  • added support for htslib (see ticket #794)
    • macro YAT_HAVE_LIBBAM is #defined if linking against either libbam or libhts. Use #if defined YAT_HAVE_LIBBAM && !defined (YAT_HAVE_HTSLIB) to check that building against libbam.
    • macro YAT_BAM_HEADER is only #defined when building against libbam
  • utility::get separates types in map and passed key (ticket #799)
  • utility::Range is deprecated (ticket #786)
  • AveragerWeighted::n(void) now return 0, when object is empty (ticket #802)
  • Container2DIterator is now tagged with boost::random_access_traversal_tag (see ticket #803, r3393)
  • StrideIterator? is now tagged with use_default (see ticket #803, r3393)
  • configure option --without-samtools is deprecated; use --without-htslib

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.13

yat 0.12.x series from http://dev.thep.lu.se/yat/svn/branches/0.12-stable

version 0.12.2 (released 6 November 2014)

  • Fixed bug in Aligner that internal data was not cleared between alignments resulting in incorrect CIGAR (see bug #820)
  • Fixed QuantileNormalizer? seqfault when input had more columns than rows (see bug #815)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.12.2

version 0.12.1 (released 21 August 2014)

  • bam_calend is buggy in older versions of samtools; configure script checks that bam_calend works as expected; if not use its own implementation (see bug #810)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.12.1

version 0.12 (released 25 July 2014)

  • BamRead::cigar(const std::vector<uint32_t>&) is deprecated
  • Aligner(double, double) is now explicit (see r3207)
  • GetlineIterator?(istream&, char) is now explicit (see r3148)
  • rename(2) and remove(1) are now implemented (bug #804)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.12

yat 0.11.x series from http://dev.thep.lu.se/yat/svn/branches/0.11-stable

version 0.11.2 (released 25 March 2014)

  • Fixed bug that error in OutBamFile::write was not detected (see r3163)
  • Fixed bug that -lgsl was not included in yat-config --libs (bug #788)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.11.2

version 0.11.1 (released 18 December 2013)

  • Fixed bug in BamHeader::tid(const std::string&) (see bug #776)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.11.1

version 0.11 (released 18 November 2013)

  • Fisher::one_sided_p(void) is now deprecated (ticket #689)
  • PearsonCorrelation::one_sided_p(void) is now deprecated (ticket #689)
  • PearsonCorrelation::one_sided_p(void) is now deprecated (ticket #689)
  • ROC::p_value_one_sided(void is now deprecated (ticket #689)
  • ROC::area(void) is now declared const (ticket #754)
  • tTest::score(void) is now declared const (ticket #755)
  • BamReadIterator?(4) will now throw if region is invalid (ticket #764)
  • #defines HAVE_BAM_H, HAVE_BAM_BAM_H, and HAVE_SAMTOOLS_BAM_H have been replaced with corresponding macros with prefix 'YAT_' (see ticket #766)
  • Bam interface is now more complete (see tickets #746 and #739)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.11

yat 0.10.x series from http://dev.thep.lu.se/yat/svn/branches/0.10-stable

version 0.10.3 (released 28 October 2013)

  • utility::replace(string&, string, string) is now implemented (bug #768)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10.3

version 0.10.2 (released 4 April 2013)

  • On OSX yat is built using flat_namespace (see bug #745)
  • BamRead::mtid(void) is now implemented (see bug #743)
  • Fixed bug in KolmogorovSmirnov::remove (see bug #753)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10.2

version 0.10.1 (released 17 January 2013)

  • libyat is no longer linked against -lbam (bug #733)
  • yat.pc now mentions -lbam and -lz (bug #736)
  • include style <samtools/bam.h> now supported (bug #735)
  • BamHeader::target_length(1) is now implemented (bug #740)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10.1

version 0.10 (released 4 January 2013)

  • samtools wrapper classes (ticket #729)
  • new utility functions (ticket #717)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10

yat 0.9.x series from http://dev.thep.lu.se/yat/svn/branches/0.9-stable

version 0.9.2 (released 19 December 2012)

  • fixed bug how inclusion path is displayed in documentation (bug #728)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.9.2

version 0.9.1 (released 23 September 2012)

  • bug in Aligner fixed (see bug #724)
  • Commandline::parse now throws when finding '--no-foo' (bug #723)
  • yat.pc now mentions Boost::System and Boost::Thread in Libs.private (#722)
  • documentations is now installed again (bug #721)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.9.1

version 0.9 (released 16 September 2012)

  • utility::SmithWaterman? is deprecated (ticket #706)
  • yat now depends on boost thread and system library (ticket #568 and #714)
  • utility::SmartPtr? was marked internal (see r2778)
  • ssearch now takes parameter setting mismatch (r2792)
  • RNG class is now multithread safe (ticket #568)
  • The build system now uses a non-recursive Makefile (ticket #703)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.9

yat 0.8.x series from http://dev.thep.lu.se/yat/svn/branches/0.8-stable

version 0.8.2 (released 27 July 2012)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.8.2

version 0.8.1 (released 12 March 2012)

  • Fixed bug that GFF::attribute was only loaded first time (see bug #697)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.8.1

version 0.8 (released 2 December 2011)

  • Rule for when to use approximation in ROC::p_value modified (ticket #677)
  • Discrete::seed, Continuous::seed, Discrete::seed_from_devurandom, and Continuous::seed_from_devurandom are deprecated (issue #674)
  • configure supports --enable-silent-rules (#654)
  • Macros YAT_CPP_ADD_FLAG, YAT_CXX_ADD_FLAG and YAT_LD_ADD_FLAG now require macros provided in ax_check*flag.m4 and ax_append*flags.m4(r2524)
  • Exception classes inherit from yat::utility::runtime_error (r2459)
  • deprecated configure option --with-gsl-prefix is removed
  • deprecated configure option --with-gsl-exec-prefix is removed
  • changed behavior of configure option --htmldir (r2487)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.8

yat 0.7.x series from http://dev.thep.lu.se/yat/svn/branches/0.7-stable

version 0.7.3 (released 30 October 2011)

  • ROC::area no longer crashes when no data have been added (bug #669)
  • namespace classifier is no included in doxygen input again (bug #667)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.7.3

version 0.7.2 (released 12 April 2011)

  • omic::Codon("ATG").amino_acid() now return 'M' (bug #664)
  • median now works on empty ranges (bug #660)
  • fixed bug percentiler sometimes zero weight elements (r2466)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.7.2

version 0.7.1 (released 13 January 2011)

  • Fixed compiler (gcc 3) error in Histogram.cc (issue #649)
  • Fixed compiler warning in concept_check.h (issue #648)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.7.1

version 0.7 (released 8 January 2011)

  • new namespace theplu::yat::omic
  • Constructors *Lookup(Matrix, Index, bool) are deprecated (#543)
  • dvi, ps and pdf docs are no longer generated
  • utility::load functions now work with std::string as well.

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.7

yat 0.6.x series from http://dev.thep.lu.se/yat/svn/branches/0.6-stable

Version 0.6.3 (released 21 December 2010)

  • fixed overflow in statistics::Fisher (#638)
  • fixed bug that double was hard-coded in function load<T>(6) (r2271)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6.3

Version 0.6.2 (released 18 May 2010)

  • fixed bug with merge when result is weighted (r2251)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6.2

Version 0.6.1 (released 14 March 2010)

  • fixed bug with yat-config --ldflags (#615)
  • fixed bug in FileUtil::permission when file does not exist (#617)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6.1

Version 0.6 (released 21 February 2010)

  • Boost 1.35 is now required (#603)
  • new configure option --with-gsl (#544)
  • configure option --with-gsl-prefix is deprecated (#544)
  • configure option --with-gsl-exec-prefix is deprecated (#544)
  • Behavior of operator==(DataWeightProxy?, DataWeightProxy?) is modified (#578)
  • several constructors in namespace random are now declared explicit (#571)
  • pair_first_iterator and pair_second_iterator now work with const_iterator (ticket:562)
  • Passing by const& in KolmogorovSmirnov::Element::operator< (r2064)
  • classes OptionInFile? and OptionOutFile? are deprecated (ticket:521)
  • DataWeight? comparison operators were changed in case of NaN (ticket:536)
  • new option --libs-without-cblas in yat-config (ticket:523)
  • blas is no longer hard-coded into libyat.so and libyat.la (ticket:518)
  • using unsigned long int (rather than signed) in SVN::max_epoch (ticket:506)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6

Version 0.5.6 (released 24 December 2009)

  • Fixed bugs in EnsembleBuilder::predict (bugs #567 and #579)
  • Corrected dependency libs in libyat.la (bug #573)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.6

Version 0.5.5 (released 5 November 2009)

  • SVM::predict is calculated as geometric distance (issue #542)
  • detection of GSL is improved (issue #558)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.5

Version 0.5.4 (released 12 June 2009)

  • Disable dvi ps and pdf documentation in case of doxygen 1.5.8 (issue #548)
  • improved uninstalled yat-config so it works in VPATH build (issue #539)
  • improved documentation

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.4

Version 0.5.3 (released 7 May 2009)

  • fixed serious bug in qQuantileNormalization related to sorting with NaNs? in vectors (issue #535). VectorMutable? and Percentiler classes were affected with the same issue.
  • fixed problem with running configure on 64-bit CentOS (issue #527)
  • make check works again (issue #528)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.3

Version 0.5.2 (released 17 March 2009)

  • fixed compilation error in IGP (issue #503)
  • fixed incorrect error message from CommandLine? (issue #508)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.2

Version 0.5.1 (released 26 February 2009)

  • libtool version number was corrected (see r1833)

Version 0.5 (released 24 February 2009)

  • Upgraded to GLPv3
  • yat now requires GSL 1.8 or later
  • yat now requires Boost 1.33 or later
  • Imlicit conversion between Vector and its Views disabled (ticket:467)
  • Averager::add and AveragerPair::add take a _signed_ long (ticket:361)
  • IteratorPolicy? removed (ticket:398)
  • MatrixLookupWeighted?(const MatrixLookup?&) modified (ticket:396)
  • Option::parse and OptionArg::do_parse takes references (ticket:418)
  • is_int now depends on numerical_limits for inf and NaN treatment
  • Similar for is_float. See revision [1312] for details.
  • config.h is no longer installed
  • Copy and assignment are now allowed for KolmogorovSmirnov?
  • is_int(1), is_float(1), is_float(1) are deprecated use is<T>
  • percentile(3) is deprecated, use percentile2(3)
  • Target::operator[] is deprecated, use Target::operator()

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5

Version 0.4.3 (released 23 January 2009)

  • Fisher::p_value is now correct (bug #461)
  • Fisher::oddsratio is now correct (bug #460)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.4.3

Version 0.4.2 (released 25 August 2008)

  • FileUtil? can now handle large files (#378)
  • x variable is trained in regression::Local::fit() (#423)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.4.2

Version 0.4.1 (released 14 May 2008)

  • Files needed for build of documentation is included in distribution (#365)

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.4.1

Version 0.4 (released 11 April 2008)

  • Class vector was split into Vector, VectorView? and VectorConstView?
  • Class matrix was renamed to Matrix
  • Containers, e.g. Vector, now have iterators.
  • EnsembleBuilder? and SubSetGenerator? were refactored and are now templates
  • SupervisedClassifier? is now a pure interface class
  • SVM is not inherited from SupervisedClassifier?
  • NCC was refactored and is now a template
  • Distance interfaces against iterators
  • interface of median, percentile, and mad functions are modified. They now take iterators rather than containers.
  • is_double(), is_int(), and is_float() return true also when string is a nan or inf.
  • add_values function in Averagers replaced by iterator interface

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.4

Version 0.3.1 (released 28 April 2007)

  • Bugfix release

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.3.1

Version 0.3 (released 9 April 2007)

  • First public release

A complete list of closed tickets can be found here
http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.3+%28Public+release%29


Copyright (C) 2003, 2006 Jari Häkkinen
Copyright (C) 2007, 2008, 2009 Jari Häkkinen, Peter Johansson
Copyright (C) 2010, 2011 Peter Johansson
Copyright (C) 2012 Jari Häkkinen, Peter Johansson
Copyright (C) 2013, 2014, 2015, 2016, 2017 Peter Johansson
This file is part of yat library, http://dev.thep.lu.se/yat
The yat library is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 3 of the
License, or (at your option) any later version.
The yat library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with yat. If not, see <http://www.gnu.org/licenses/>.

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