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Diff Rev Age Author Log Message
(edit) @4186   4 days Peter use QuantileNormalizer2 in QuantileNormalizer?, deprecate …
(edit) @4185   4 days Peter add a new class for Quantile Normalization that be used in a train set …
(edit) @4184   7 days Peter class to model mixture model of NegativeBinomials?, refs #979
(edit) @4183   7 days Peter prefer passing by const& not by value
(edit) @4182   3 weeks Peter avoid long lines
(edit) @4181   3 weeks Peter add brackets to help latex parsing; change log to ln to clarify that …
(edit) @4180   4 weeks Peter refs #979. Add class for inference of Poissonian mixture models.
(edit) @4179   5 weeks Peter don't include what message from caught exception when throw_with_nested
(edit) @4178   5 weeks Peter avoid limit interface to Matrix when not needed. refs #202
(edit) @4177   5 weeks Peter remove leftover
(edit) @4176   5 weeks Peter add missing files from prev changeset (refs #978)
(edit) @4175   5 weeks Peter add wrapper classes around GSL's multimin algos using derivative. …
(edit) @4174   7 weeks Peter Fix major memory leak introduced during the refactoring of the Matrix …
(edit) @4173   8 weeks Peter refs #978. Add missing file.
(edit) @4172   8 weeks Peter refs #978. Wrapper classes around gsl_multimin_fminimizer.
(edit) @4171   2 months Peter docs: add since tag for new function
(edit) @4170   2 months Peter New function VCF::Data::set(2)
(edit) @4169   3 months Peter docs: don't mention libbam (since we require htslib)
(edit) @4168   4 months Peter mention r4167 in NEWS
(edit) @4167   4 months Peter When a second exception was thrown, the JobHandler? would handle it …
(edit) @4166   4 months Peter remove trailing WS
(edit) @4165   4 months Peter Bumping version to 0.19.2pre
(edit) @4164   4 months Peter Merge release 0.19.1 into trunk
(edit) @4163   4 months Peter tagging version 0.19.1
(edit) @4162   4 months Peter add line for 0.19.1
(edit) @4161   4 months Peter update copyright years
(edit) @4160   4 months Peter Preparing release 0.19.1
(edit) @4159   4 months Peter mention #980, #981 and #982 in NEWS. (refs #980, #981 and #982)
(edit) @4158   4 months Peter fixes #982
(edit) @4157   4 months Peter fixes #981
(edit) @4156   4 months Peter refs #980. Test was inci=omplete in r4155. Fixed here.
(edit) @4155   4 months Peter fixes #980
(edit) @4154   4 months Peter fix spurious error
(edit) @4153   4 months Peter New class OptionVersion?. closes #824.
(edit) @4152   4 months Peter help.test was never meant as a test in itself but only as a program to …
(edit) @4151   4 months Peter fix bug UnityScaler? used std::accumulate but did not include <numeric>.
(edit) @4150   4 months Peter add a fit function that allows providing the starting values of model …
(edit) @4149   4 months Peter docs: fix typo
(edit) @4148   4 months Peter fix docs
(edit) @4147   4 months Peter add class for random number generator from negative binomial distribution.
(edit) @4146   4 months Peter assuming that VCF::Info operator<< is used more often that ::str(), …
(edit) @4145   4 months Peter implement subset functions and constructor taking #samples (refs …
(edit) @4144   4 months Peter Add interface to construct a VCF with n samples and to select a subset …
(edit) @4143   5 months Peter upgrade to autoconf-archive 2022.02.11
(edit) @4142   5 months Peter prefer https when uploading to sourceforge
(edit) @4141   5 months Peter closes #977. Implement view into gsl_vector, gsl_matrix, and arrays.
(edit) @4140   5 months Peter allow MatrixBase? as input in inverse_svd (refs #202). In Perceptron, …
(edit) @4139   5 months Peter the same bug reported in ticket #897 for vectors is also the case for …
(edit) @4138   5 months Peter allow matrix views in nan function
(edit) @4137   6 months Peter add proxy class to allow returnning a MatrixView? from a function (same …
(edit) @4136   6 months Peter closes #975 and refs #202; use Container2DIterator as …
(edit) @4135   6 months Peter refs #975; allow conversion from Container2DIterator<C1> to …
(edit) @4134   6 months Peter avoid duplicated typedefs for mutable iterators in MatrixBase? and …
(edit) @4133   6 months Peter refs #202 and #975; fix issue with column_iterators in matrix view …
(edit) @4132   6 months Peter fixes #976 concept for Container2D now works with abstract class
(edit) @4131   6 months Peter tests for Matrix View iterators; refs #975 and #202.
(edit) @4130   6 months Peter Add function fit2 taking new class MatrixBase?. Keep the old interface …
(edit) @4129   6 months Peter refs #202. Adding classes for Matrix View (and corresponding const version)
(edit) @4128   6 months Peter fix typo. Doesn't matter what the condition is named, but let's call …
(edit) @4127   6 months Peter add needed include
(edit) @4126   6 months Peter avoid including cassert in header files.
(edit) @4125   6 months Peter when possible change public interface 'const Matrix&' and 'Matrix&' to …
(edit) @4124   6 months Peter refs #202. Rearrange structure of matrix classes. After trying a few …
(edit) @4123   6 months Peter remove old debug printout
(edit) @4122   7 months Peter extend test with call to VCF::Info::count(1)
(edit) @4121   8 months Peter prefer * over /
(edit) @4120   8 months Peter make the message in thrown exception more informative
(edit) @4119   8 months Peter split Matrix interface into three classes: MatrixBase?, MatrixMutable?
(edit) @4118   9 months Peter document operations that invalidate references, views, iterators, etc. …
(edit) @4117   9 months Peter add assert
(edit) @4116   9 months Peter correct typo
(edit) @4115   9 months Peter always include config.h in source files
(edit) @4114   9 months Peter new class for one-way ANOVA test
(edit) @4113   9 months Peter fix docs typo
(edit) @4112   9 months Peter bump lt-version-info post-release, noy just before.
(edit) @4111   9 months Peter bumping version to 0.19.1pre
(edit) @4110   9 months Peter merge release 0.19 into trunk
(edit) @4109   9 months Peter tagging version 0.19
(edit) @4108   9 months Peter update copyright years
(edit) @4107   9 months Peter Preparing release 0.19
(edit) @4106   9 months Peter docs: c++11 is required
(edit) @4105   10 months Peter implement +=, -=, and *= operators for DiagonalMatrix?; prefer using …
(edit) @4104   10 months Peter make doxygen happy
(edit) @4103   10 months Peter closes #710
(edit) @4102   10 months Peter add wrapper function that calls std::string::contains, ::starts_with, …
(edit) @4101   10 months Peter AX_CXX_COMPILE_STDCXX_11 is just a one-line call to …
(edit) @4100   10 months Peter refs #710; activate tests and set XFAIL
(edit) @4099   10 months Peter avoid setting svn:keywords on 3rd-party files
(edit) @4098   10 months Peter minor docs change
(edit) @4097   10 months Peter use boost when functionality is available; prefer passing const& …
(edit) @4096   10 months Peter simplify code and alter private interface to reflect what's going on inside
(edit) @4095   10 months Peter docs
(edit) @4094   10 months Peter handle spaces in argument to --htmldir
(edit) @4093   10 months Peter update RP to match changes on the wiki
(edit) @4092   10 months Peter prefer https when referring to ~jari/documents pages; mention function …
(edit) @4091   10 months Peter bumping version to 0.20pre
(edit) @4090   10 months Peter New stable branch 0.19
(edit) @4089   10 months Peter updating copyright years
(edit) @4088   10 months Peter Prepare 0.19-stable branch
(edit) @4087   10 months Peter extend docs; closes #710
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