|
|
|
@4346
|
5 months |
Peter |
prefer /* copyright (C) */ rather than Copyright (C)
|
|
|
|
@4345
|
6 months |
Peter |
new class BamReadSequenceIterator?
|
|
|
|
@4344
|
6 months |
Peter |
fix distcheck; include header files in dist and document classes. refs #782
|
|
|
|
@4343
|
6 months |
Peter |
removing operator== reduces too much senistivity in the tests, so …
|
|
|
|
@4342
|
6 months |
Peter |
test for random_access_iterator incorrectly assumed that value_type …
|
|
|
|
@4341
|
6 months |
Peter |
increase error margin to avoid spurious test failure. (reported by jari)
|
|
|
|
@4340
|
6 months |
Peter |
refs #782; first version of less-hungry Aligner.
|
|
|
|
@4339
|
6 months |
Peter |
fixes #998
|
|
|
|
@4338
|
6 months |
Peter |
get rid of yat::utility:: when in namespace yat::utility
|
|
|
|
@4337
|
6 months |
Peter |
avoid a couple of multiplications
|
|
|
|
@4336
|
6 months |
Peter |
a set of new functions calculating logarithm of pdf for various …
|
|
|
|
@4335
|
6 months |
Peter |
add division operator
|
|
|
|
@4334
|
6 months |
Peter |
new class NeedlemanWunsch?.
|
|
|
|
@4333
|
7 months |
Peter |
variables that are checked with AC_CHECK_PROG, also call AC_ARG_VAR.
|
|
|
|
@4332
|
7 months |
Peter |
don't depend on removed files
|
|
|
|
@4331
|
7 months |
Peter |
commited wrong version in latest changeset; fixed here.
|
|
|
|
@4330
|
7 months |
Peter |
remove files no longer used
|
|
|
|
@4329
|
7 months |
Peter |
check if date program supports --date= or -r options and choose make …
|
|
|
|
@4328
|
7 months |
Peter |
update autoconf-archive macros
|
|
|
|
@4327
|
7 months |
Peter |
avoid Makefile input prefixed with spaces
|
|
|
|
@4326
|
7 months |
Peter |
We had two macros with very similar behaviour: YAT_AC_APPEND in …
|
|
|
|
@4325
|
7 months |
Peter |
correct PP guard to reflect namespace
|
|
|
|
@4324
|
7 months |
Peter |
the docs described the standard as it was in C++03; update.
|
|
|
|
@4323
|
7 months |
Peter |
the rules for timestamp require the revision files to be present, so …
|
|
|
|
@4322
|
7 months |
Peter |
make the test case work in a svn wc as well (although the test does …
|
|
|
|
@4321
|
7 months |
Peter |
YAT_SVN_TIMESTAMP uses make variable SVN; AC_REQUIRE new macro …
|
|
|
|
@4320
|
7 months |
Peter |
add docs; fix dist-hook issue in test and improve diagnosis in configure.
|
|
|
|
@4319
|
7 months |
Peter |
add macro YAT_SVN_TIMESTAMP, which creates automake blurb with rules …
|
|
|
|
@4316
|
8 months |
Peter |
Merged release 0.20.2 into trunk
|
|
|
|
@4312
|
8 months |
Peter |
when tests create write-protected files the removal in 'init.sh' would …
|
|
|
|
@4308
|
8 months |
Peter |
merge release 0.20.1 into trunk.
|
|
|
|
@4299
|
8 months |
Peter |
include config.h in all source files
|
|
|
|
@4298
|
8 months |
Peter |
fix typo in output variable causing empty output
|
|
|
|
@4297
|
8 months |
Peter |
simplifiy code, avoid home-brewed looping, and use blas.
|
|
|
|
@4296
|
8 months |
Peter |
get rid of superfluous temporary matrices U and V; avoid allocating …
|
|
|
|
@4295
|
8 months |
Peter |
avoid loops when functionality exists (which likely is faster).
|
|
|
|
@4294
|
8 months |
Peter |
simplify code
|
|
|
|
@4293
|
8 months |
Peter |
minor style changes
|
|
|
|
@4292
|
8 months |
Peter |
prefer BLAS multiplication
|
|
|
|
@4291
|
8 months |
Peter |
prefer blast rather than home brewed looping although the latter used …
|
|
|
|
@4290
|
8 months |
Peter |
add same interface for program_group as for read_group in class BamHeader?.
|
|
|
|
@4289
|
8 months |
Peter |
add a class Likelihood; closes #988
|
|
|
|
@4288
|
8 months |
Peter |
fix #include (so it compiles in VPATH build)
|
|
|
|
@4287
|
8 months |
Peter |
add class for KalmanFilter?
|
|
|
|
@4286
|
8 months |
Peter |
provide the SVD inverse function as a member function so the …
|
|
|
|
@4285
|
8 months |
Peter |
simplify code with test code recently added to.
|
|
|
|
@4284
|
8 months |
Peter |
merge test from 0.20.x branch
|
|
|
|
@4281
|
8 months |
Peter |
Random generator from a Multivariate Gaussian Distribution. closes #983
|
|
|
|
@4280
|
8 months |
Peter |
wrapper class around gsl_linalg_cholesky_decomp.
|
|
|
|
@4279
|
8 months |
Peter |
require GSL 2.2. refs #983.
|
|
|
|
@4278
|
8 months |
Peter |
closes #990. Backport some functions when building against buggy …
|
|
|
|
@4277
|
8 months |
Peter |
Check if wanted_version is empty at configure time (not autoconf time) …
|
|
|
|
@4276
|
8 months |
Peter |
require htslib v1.10; closes #991
|
|
|
|
@4275
|
8 months |
Peter |
htslib 1.10 is missing includes; #include here instead.
|
|
|
|
@4274
|
8 months |
Peter |
reimplement the other constructors using the new constructor taking a …
|
|
|
|
@4273
|
8 months |
Peter |
provide interface with hts_pos_t rather than int32_t (to allow large …
|
|
|
|
@4272
|
8 months |
Peter |
closes #774. Create multi-region iterator.
|
|
|
|
@4271
|
9 months |
Peter |
cater for older htslib version in which HTS_VERSION is not #defined
|
|
|
|
@4270
|
9 months |
Peter |
add htslib versions
|
|
|
|
@4269
|
9 months |
Peter |
add test code (refs #987)
|
|
|
|
@4268
|
9 months |
Peter |
remove leftover comment
|
|
|
|
@4267
|
9 months |
Peter |
remove debug code
|
|
|
|
@4266
|
9 months |
Peter |
if bam_copy1 fails it's not guaranteed that passed bam_ is not …
|
|
|
|
@4265
|
9 months |
Peter |
detect when calls to htslib functions fail.
|
|
|
|
@4264
|
9 months |
Peter |
extend tests for copy and assignment of BamHeader?; refs #989.
|
|
|
|
@4263
|
9 months |
Peter |
refs #989; remove inaccurate comment.
|
|
|
|
@4262
|
9 months |
Peter |
use std:: version when available
|
|
|
|
@4261
|
9 months |
Peter |
remove debug sleep(1)
|
|
|
|
@4260
|
10 months |
Peter |
improve docs
|
|
|
|
@4259
|
10 months |
Peter |
make scores function public
|
|
|
|
@4258
|
10 months |
Peter |
revert changeset r4257
|
|
|
|
@4257
|
10 months |
Peter |
new functions max_score and min_score
|
|
|
|
@4256
|
10 months |
Peter |
remove configure test that just made the code complex; prefer …
|
|
|
|
@4255
|
10 months |
Peter |
add class doing Kaplan-Meier estimations
|
|
|
|
@4254
|
10 months |
Peter |
closes #986
|
|
|
|
@4252
|
11 months |
Peter |
merge 0.20 release into trunk
|
|
|
|
@4245
|
13 months |
Peter |
GCC -Wdeprecated-copy complains when some but not all of copy ctor, …
|
|
|
|
@4216
|
13 months |
Peter |
update to autoconf-archive-2022.09.03
|
|
|
|
@4209
|
13 months |
Peter |
Bumping VERSION to 0.21pre
|
|
|
|
@4207
|
13 months |
Peter |
update copyright statements
|
|
|
|
@4206
|
13 months |
Peter |
Prepare 0.20-stable branch
|
|
|
|
@4204
|
13 months |
Peter |
merge release 0.19.2 into trunk
|
|
|
|
@4200
|
14 months |
Peter |
removing trailing whitespace and empty lines at bottom of files.
|
|
|
|
@4199
|
14 months |
Peter |
fix warning
|
|
|
|
@4198
|
14 months |
Peter |
add classes doing Cox regression
|
|
|
|
@4197
|
14 months |
Peter |
move_iterator defined in <iterator>
|
|
|
|
@4196
|
14 months |
Peter |
fix regression introduced in r4193. yat::split adds elements at back …
|
|
|
|
@4195
|
14 months |
Peter |
avoid copying in getvector. closes #887
|
|
|
|
@4194
|
14 months |
Peter |
simplify code; possible optimisation
|
|
|
|
@4193
|
14 months |
Peter |
use boost
|
|
|
|
@4192
|
14 months |
Peter |
New class NegativeBinomialExtendedMixture?, a variant of Negative …
|
|
|
|
@4191
|
15 months |
Peter |
improve docs
|
|
|
|
@4190
|
15 months |
Peter |
fix docs
|
|
|
|
@4189
|
15 months |
Peter |
recycle interpolator rather than rebuilding it every time.
|
|
|
|
@4188
|
15 months |
Peter |
allow different size in template and data
|
|
|
|
@4187
|
15 months |
Peter |
GSLInterpolation contained two 'new double[size]' but the arrays were …
|
|
|
|
@4186
|
15 months |
Peter |
use QuantileNormalizer2 in QuantileNormalizer?, deprecate …
|
|
|
|
@4185
|
15 months |
Peter |
add a new class for Quantile Normalization that be used in a train set …
|
|
|
|
@4184
|
15 months |
Peter |
class to model mixture model of NegativeBinomials?, refs #979
|
|
|
|
@4183
|
15 months |
Peter |
prefer passing by const& not by value
|
|
|
|
