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Diff Rev Age Author Log Message
(edit) @4334   6 months Peter new class NeedlemanWunsch?.
(edit) @4333   7 months Peter variables that are checked with AC_CHECK_PROG, also call AC_ARG_VAR.
(edit) @4332   7 months Peter don't depend on removed files
(edit) @4331   7 months Peter commited wrong version in latest changeset; fixed here.
(edit) @4330   7 months Peter remove files no longer used
(edit) @4329   7 months Peter check if date program supports --date= or -r options and choose make …
(edit) @4328   7 months Peter update autoconf-archive macros
(edit) @4327   7 months Peter avoid Makefile input prefixed with spaces
(edit) @4326   7 months Peter We had two macros with very similar behaviour: YAT_AC_APPEND in …
(edit) @4325   7 months Peter correct PP guard to reflect namespace
(edit) @4324   7 months Peter the docs described the standard as it was in C++03; update.
(edit) @4323   7 months Peter the rules for timestamp require the revision files to be present, so …
(edit) @4322   7 months Peter make the test case work in a svn wc as well (although the test does …
(edit) @4321   7 months Peter YAT_SVN_TIMESTAMP uses make variable SVN; AC_REQUIRE new macro …
(edit) @4320   7 months Peter add docs; fix dist-hook issue in test and improve diagnosis in configure.
(edit) @4319   7 months Peter add macro YAT_SVN_TIMESTAMP, which creates automake blurb with rules …
(edit) @4318   8 months Peter make test compile on CentOS.
(edit) @4317   8 months Peter bumping version to 0.20.3pre
(edit) @4316   8 months Peter Merged release 0.20.2 into trunk
(edit) @4315   8 months Peter tagging version 0.20.2
(edit) @4314   8 months Peter update copyright years
(edit) @4313   8 months Peter Preparing release 0.20.2
(edit) @4312   8 months Peter when tests create write-protected files the removal in 'init.sh' would …
(edit) @4311   8 months Peter fixes #995. If key is present, clear the value before appending the …
(edit) @4310   8 months Peter refs #995. Add tests for the case.
(edit) @4309   8 months Peter bump version to 0.20.2pre
(edit) @4308   8 months Peter merge release 0.20.1 into trunk.
(edit) @4307   8 months Peter tagging version 0.20.1
(edit) @4306   8 months Peter update copyright years
(edit) @4305   8 months Peter Preparing release 0.20.1
(edit) @4304   8 months Peter mention #994 in NEWS
(edit) @4303   8 months Peter fixes #994
(edit) @4302   8 months Peter add test for bug in VcfHeader? (refs #994).
(edit) @4301   8 months Peter docs: fix typo
(edit) @4300   8 months Peter Fixed a bug in NeedlemanWunsch? functions caused by an unsigned integer …
(edit) @4299   8 months Peter include config.h in all source files
(edit) @4298   8 months Peter fix typo in output variable causing empty output
(edit) @4297   8 months Peter simplifiy code, avoid home-brewed looping, and use blas.
(edit) @4296   8 months Peter get rid of superfluous temporary matrices U and V; avoid allocating …
(edit) @4295   8 months Peter avoid loops when functionality exists (which likely is faster).
(edit) @4294   8 months Peter simplify code
(edit) @4293   8 months Peter minor style changes
(edit) @4292   8 months Peter prefer BLAS multiplication
(edit) @4291   8 months Peter prefer blast rather than home brewed looping although the latter used …
(edit) @4290   8 months Peter add same interface for program_group as for read_group in class BamHeader?.
(edit) @4289   8 months Peter add a class Likelihood; closes #988
(edit) @4288   8 months Peter fix #include (so it compiles in VPATH build)
(edit) @4287   8 months Peter add class for KalmanFilter?
(edit) @4286   8 months Peter provide the SVD inverse function as a member function so the …
(edit) @4285   8 months Peter simplify code with test code recently added to.
(edit) @4284   8 months Peter merge test from 0.20.x branch
(edit) @4283   8 months Peter fix spurious test failure due to numerical problems when taking …
(edit) @4282   8 months Peter refs #992; add test for bug.
(edit) @4281   8 months Peter Random generator from a Multivariate Gaussian Distribution. closes #983
(edit) @4280   8 months Peter wrapper class around gsl_linalg_cholesky_decomp.
(edit) @4279   8 months Peter require GSL 2.2. refs #983.
(edit) @4278   8 months Peter closes #990. Backport some functions when building against buggy …
(edit) @4277   8 months Peter Check if wanted_version is empty at configure time (not autoconf time) …
(edit) @4276   8 months Peter require htslib v1.10; closes #991
(edit) @4275   8 months Peter htslib 1.10 is missing includes; #include here instead.
(edit) @4274   8 months Peter reimplement the other constructors using the new constructor taking a …
(edit) @4273   8 months Peter provide interface with hts_pos_t rather than int32_t (to allow large …
(edit) @4272   8 months Peter closes #774. Create multi-region iterator.
(edit) @4271   9 months Peter cater for older htslib version in which HTS_VERSION is not #defined
(edit) @4270   9 months Peter add htslib versions
(edit) @4269   9 months Peter add test code (refs #987)
(edit) @4268   9 months Peter remove leftover comment
(edit) @4267   9 months Peter remove debug code
(edit) @4266   9 months Peter if bam_copy1 fails it's not guaranteed that passed bam_ is not …
(edit) @4265   9 months Peter detect when calls to htslib functions fail.
(edit) @4264   9 months Peter extend tests for copy and assignment of BamHeader?; refs #989.
(edit) @4263   9 months Peter refs #989; remove inaccurate comment.
(edit) @4262   9 months Peter use std:: version when available
(edit) @4261   9 months Peter remove debug sleep(1)
(edit) @4260   10 months Peter improve docs
(edit) @4259   10 months Peter make scores function public
(edit) @4258   10 months Peter revert changeset r4257
(edit) @4257   10 months Peter new functions max_score and min_score
(edit) @4256   10 months Peter remove configure test that just made the code complex; prefer …
(edit) @4255   10 months Peter add class doing Kaplan-Meier estimations
(edit) @4254   10 months Peter closes #986
(edit) @4253   11 months Peter Bumping VERSION to 0.20.1pre
(edit) @4252   11 months Peter merge 0.20 release into trunk
(edit) @4251   11 months Peter tagging version 0.20
(edit) @4250   11 months Peter updating copyright years
(edit) @4249   11 months Peter Preparing release 0.20
(edit) @4248   12 months Peter change API on MultiMinimizer? and MultiMinimizerDerivative? to same as …
(edit) @4247   12 months Peter change API of Minimizer to same as RootFinder?, using a polymorphic …
(edit) @4246   12 months Peter implement functor calculating the score (derivative of logL) and its …
(edit) @4245   13 months Peter GCC -Wdeprecated-copy complains when some but not all of copy ctor, …
(edit) @4244   13 months Peter fix distcheck
(edit) @4243   13 months Peter fix compilation with GCC 9
(edit) @4242   13 months Peter turn off deprecation warning in test.
(edit) @4241   13 months Peter turn on deprecation warning also with modern GCC.
(edit) @4240   13 months Peter refs #985. Use RootFinderDerivative? rather than boost::newton_raphson. …
(edit) @4239   13 months Peter fix typo. refs #985
(edit) @4238   13 months Peter Add wrapper classes around GSL One-Dimnesional Root-Finding algorithms …
(edit) @4237   13 months Peter Add wrapper classes around GSL One-Dimensional Root Bracketing …
(edit) @4236   13 months Peter avoid compiler warning and YAT_ASSERT with gcc 11
(edit) @4235   13 months Peter remove COLS_IN_ALPHA_INDEX to avoid warning from doxygen 1.9.1
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