#14 |
add reset function to SVM
|
Peter
|
enhancement
|
trivial
|
|
classifier
|
#15 |
Copy constructor for SVM
|
Peter
|
enhancement
|
trivial
|
|
classifier
|
#56 |
SVM convergence problem
|
Peter
|
request
|
trivial
|
yat 0.2
|
documentation
|
#87 |
replace cumulative hypergeometric with GSL implementation
|
Peter
|
request
|
trivial
|
yat 0.5
|
statistics
|
#97 |
copyright in test source
|
Jari Häkkinen
|
request
|
trivial
|
yat 0.3 (Public release)
|
documentation
|
#123 |
document SNR::score weighted version
|
Peter
|
enhancement
|
trivial
|
yat 0.2
|
documentation
|
#125 |
KerneFunction remove obsolete operator() taking FOUR arguments
|
Peter
|
defect
|
trivial
|
yat 0.3 (Public release)
|
classifier
|
#130 |
KernelLookups and MatrixLookups not in inheritance structure but template
|
Peter
|
discussion
|
trivial
|
yat 0.4
|
classifier
|
#140 |
Don't keep SVM and Index in same file
|
Peter
|
request
|
trivial
|
yat 0.3 (Public release)
|
documentation
|
#157 |
make Commandline::print_try_help(void) public
|
Peter
|
enhancement
|
trivial
|
yat 0.4
|
utility
|
#213 |
should we remove minmax_index
|
Jari Häkkinen
|
request
|
trivial
|
yat 0.3 (Public release)
|
utility
|
#239 |
to_lower and to_upper should return reference to passed string
|
Peter
|
enhancement
|
trivial
|
yat 0.4
|
utility
|
#282 |
check for 'd' in FileUtil::permission
|
Jari Häkkinen
|
enhancement
|
trivial
|
yat 0.4
|
utility
|
#329 |
rename struct weighted_type to weighted_tag
|
Peter
|
enhancement
|
trivial
|
yat 0.4
|
utility
|
#334 |
return Derived* from make_classifier not SupervisedClassifier
|
Markus Ringnér
|
enhancement
|
trivial
|
yat 0.4
|
classifier
|
#338 |
configure warning about missing latex could be improved when Doxygen already is missing
|
Jari Häkkinen
|
enhancement
|
trivial
|
yat 0.4
|
build
|
#352 |
modify FLAGS when configure option --with-gsl-prefix
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#354 |
automake and COPYING
|
Jari Häkkinen
|
request
|
trivial
|
yat 0.5
|
build
|
#371 |
remove ax_prefix_config_h.m4
|
Peter
|
request
|
trivial
|
yat 0.5
|
build
|
#383 |
why both operator() and operator[] in Target?
|
Markus Ringnér
|
discussion
|
trivial
|
yat 0.5
|
classifier
|
#386 |
AX_PATH_GSL doesn't check for GSL header files
|
Peter
|
defect
|
trivial
|
yat 0.6
|
build
|
#388 |
use fifth argument [action-if-cross-compiling] in AC_RUN_IF_ELSE
|
Jari Häkkinen
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#390 |
libyat is linked together with C-linker
|
Peter
|
defect
|
trivial
|
yat 0.5
|
build
|
#392 |
doxygen, tests, and His ol' Grandma
|
Jari Häkkinen
|
discussion
|
trivial
|
yat 0.8
|
build
|
#408 |
Using gnuify-changelog.pl ... or re-think how ChangeLog should be maintained.
|
Jari Häkkinen
|
discussion
|
trivial
|
yat 0.5
|
build
|
#410 |
/bin/sh: line 1: *.h: command not found
|
Peter
|
defect
|
trivial
|
yat 0.5
|
build
|
#411 |
pkg-config doesn't work because missing file boost.pc
|
Peter
|
defect
|
trivial
|
yat 0.5
|
build
|
#412 |
Doxygen - Build redundancy
|
Peter
|
defect
|
trivial
|
yat 0.6
|
build
|
#420 |
typedef iterator_type in Range
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
utility
|
#438 |
make doc will not regenerate docs when a file has been removed
|
Peter
|
defect
|
trivial
|
yat 0.6
|
build
|
#446 |
skip documentation test rather that run it conditionally
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#454 |
Matrix(0, 42) or its transpose Matrix(42, 0) is not allowed
|
Peter
|
discussion
|
trivial
|
yat 0.6
|
utility
|
#455 |
take care of ties in KolmogorovSmirnov
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
statistics
|
#456 |
avoid using namespace LT_
|
Peter
|
defect
|
trivial
|
yat 0.5
|
build
|
#468 |
propagate configure arguments to DISTCHECK_CONFIGURE_FLAGS
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#469 |
add doxygen tag "\since New in yat 0.5" in new interpolation classes
|
Jari Häkkinen
|
request
|
trivial
|
yat 0.5
|
documentation
|
#471 |
check for svn wc relies on svnversion
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#479 |
Ranger normalizers should return void
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
normalizer
|
#481 |
calling functions in Option before Commandline has been parsed should throw
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
utility
|
#482 |
$(ECHO) is not defined using libtool 2
|
Jari Häkkinen
|
defect
|
trivial
|
yat 0.5
|
build
|
#483 |
install yat_add_flag.m4
|
Peter
|
request
|
trivial
|
yat 0.5
|
build
|
#486 |
yat_m4_test.sh does not honor --prefix and friend set at make time
|
Peter
|
defect
|
trivial
|
yat 0.5
|
build
|
#487 |
output from yat.m4 is ugly
|
Peter
|
enhancement
|
trivial
|
yat 0.5
|
build
|
#499 |
percentile occurs twice in doxygen output
|
Peter
|
defect
|
trivial
|
yat 0.5.2
|
documentation
|
#519 |
ostream.precision should be restored in output operators
|
Peter
|
enhancement
|
trivial
|
yat 0.6
|
utility
|
#521 |
deprecate OptionInFile and OptionOutFile
|
Peter
|
request
|
trivial
|
yat 0.6
|
utility
|
#530 |
add version output of doxygen in documentation_test.sh
|
Peter
|
request
|
trivial
|
yat 0.6
|
test
|
#534 |
"./configure --without-boost" returns "old boost found"
|
Jari Häkkinen
|
defect
|
trivial
|
yat 0.6
|
build
|
#539 |
including uninstalled <yat/utility/deprecate.h> fails in VPATH build
|
Peter
|
defect
|
trivial
|
yat 0.5.4
|
utility
|
#544 |
allow --without-boost, --without-gsl and --without-blas
|
Peter
|
request
|
trivial
|
yat 0.6
|
build
|
#546 |
configure finds gsl-config but not gsl header
|
Peter
|
defect
|
trivial
|
yat 0.6
|
build
|
#547 |
configure suntax error when adding /opt/local/include to CPPFLAGS
|
Peter
|
defect
|
trivial
|
yat 0.6
|
build
|
#557 |
support env var VERBOSE in tests and deprecate YAT_TEST_VERBOSE
|
Peter
|
request
|
trivial
|
yat 0.6
|
test
|
#559 |
OptionFile says permission denied when file does not exist
|
Peter
|
enhancement
|
trivial
|
yat 0.6
|
utility
|
#574 |
avoid conflict in NEWS when merging patch release into trunk
|
Peter
|
enhancement
|
trivial
|
yat 0.6
|
build
|
#576 |
improve docs of utility::is_equal
|
Peter
|
enhancement
|
trivial
|
yat 0.6
|
documentation
|
#622 |
no table in Container2D concept page
|
Peter
|
defect
|
trivial
|
yat 0.7
|
documentation
|
#630 |
HAVE_YAT is defined to /**/
|
Peter
|
enhancement
|
trivial
|
yat 0.7
|
m4
|
#636 |
"make distclean; ./configure; make clean;" fails
|
Peter
|
defect
|
trivial
|
yat 0.7
|
build
|
#645 |
cmd_error with 'prog: : invalid argument'
|
Peter
|
enhancement
|
trivial
|
yat 0.7
|
utility
|
#646 |
change name of tests from *_test to *.test
|
Peter
|
enhancement
|
trivial
|
yat 0.7
|
test
|
#652 |
mention provided funtors that work with Centralizer
|
Peter
|
enhancement
|
trivial
|
yat 0.8
|
normalizer
|
#657 |
make srcdir and builddir siblings in maintainer-check
|
Peter
|
enhancement
|
trivial
|
yat 0.8
|
m4
|
#658 |
doxygen warns: 'Found \endcond command without matching \cond'
|
Peter
|
defect
|
trivial
|
yat 0.7.2
|
documentation
|
#662 |
create test/environment.h with AC_CONFIG_HEADERS
|
Peter
|
enhancement
|
trivial
|
yat 0.8
|
build
|
#683 |
configure says no doxygen found when old doxygen is found
|
Peter
|
defect
|
trivial
|
yat 0.9
|
build
|
#696 |
cache results in yat.m4
|
Peter
|
enhancement
|
trivial
|
yat 0.9
|
m4
|
#698 |
SegmentTree docs has traces from SegmentSet
|
Peter
|
enhancement
|
trivial
|
yat 0.8.1
|
documentation
|
#713 |
gcc 4.0.1 complains about -pthread
|
Peter
|
defect
|
trivial
|
yat 0.9
|
build
|
#715 |
distcheck fails
|
Peter
|
defect
|
trivial
|
yat 0.8.2
|
build
|
#728 |
documentation displays full absolute include path
|
Peter
|
defect
|
trivial
|
yat 0.9.2
|
documentation
|
#736 |
-lbam and -lz are not mentioned in yat.pc
|
Peter
|
defect
|
trivial
|
yat 0.10.1
|
build
|
#748 |
SKIP yat_pc_test.sh when --without-samtools
|
Peter
|
enhancement
|
trivial
|
yat 0.11
|
test
|
#750 |
update svndigest:ignore properties
|
Peter
|
request
|
trivial
|
yat 0.11
|
build
|
#756 |
yat-pc-check is not working in parallel build
|
Peter
|
defect
|
trivial
|
yat 0.10.3
|
build
|
#777 |
private namespace detail is included in doxygen output
|
Peter
|
defect
|
trivial
|
yat 0.11.2
|
documentation
|
#789 |
./configure CXXFLAGS="-g -O3"
|
Jari Häkkinen
|
discussion
|
trivial
|
yat 0.12
|
build
|
#808 |
prefer using .private variable (when possible) in yat.pc
|
Peter
|
enhancement
|
trivial
|
yat 0.13
|
build
|
#809 |
use zlib's pc file
|
Peter
|
enhancement
|
trivial
|
yat 0.13
|
build
|
#811 |
brokeln html link to trivial iterator
|
Peter
|
defect
|
trivial
|
yat 0.13
|
documentation
|
#813 |
add short description of IGP
|
Peter
|
enhancement
|
trivial
|
yat 0.13
|
documentation
|
#845 |
handle GSL errors gracefully in test suite
|
Peter
|
enhancement
|
trivial
|
yat 0.18
|
test
|
#851 |
includes are not stripped correctly (sometimes)
|
Peter
|
defect
|
trivial
|
yat 0.15
|
documentation
|
#860 |
omic::DNA is not thread safe
|
Peter
|
defect
|
trivial
|
yat 0.14
|
omic
|
#861 |
detect failures in BamHeader::text(string)
|
Peter
|
request
|
trivial
|
yat 0.15
|
omic
|
#866 |
Queue and PriorityQueue should be refactored with common base class
|
Peter
|
enhancement
|
trivial
|
yat 0.16
|
utility
|
#879 |
document BamHeader::read_group_iterator
|
Peter
|
enhancement
|
trivial
|
yat 0.15
|
documentation
|
#893 |
dirname("") triggers assertion
|
Peter
|
defect
|
trivial
|
yat 0.14.4
|
utility
|
#907 |
RNG::seed_from_devurandom is not exception safe
|
Peter
|
defect
|
trivial
|
yat 0.16
|
random
|
#914 |
Access number of threads in Scheduler
|
Jari Häkkinen
|
request
|
trivial
|
yat 0.17
|
utility
|
#925 |
document parameter number in VCF::add* functions
|
Peter
|
enhancement
|
trivial
|
yat 0.17
|
documentation
|
#938 |
BamPairIterator does not pass test::Suite::input_iterator_test
|
Jari Häkkinen
|
defect
|
trivial
|
yat 0.18
|
test
|
#940 |
add failure check in Fasta::fetch
|
Peter
|
request
|
trivial
|
yat 0.18
|
omic
|
#943 |
boost/random/negative_binomial_distribution.hpp in boost 1.69.0 includes deprecated files
|
Peter
|
defect
|
trivial
|
yat 0.18
|
random
|
#945 |
require GSL 1.13
|
Peter
|
request
|
trivial
|
yat 0.18
|
utility
|
#957 |
regression::NegativeBinomial should inherit from regression::Multivariate
|
Peter
|
defect
|
trivial
|
yat 0.18
|
regression
|
#19 |
Averager.n() return unsigned
|
Peter
|
enhancement
|
minor
|
yat 0.3 (Public release)
|
statistics
|
#20 |
implement WilcoxonFoldChange
|
Peter
|
enhancement
|
minor
|
yat 0.5
|
statistics
|
#22 |
Implement class AveragerPairWeighted
|
Peter
|
enhancement
|
minor
|
|
statistics
|
#23 |
redesign OnedimensionalWeighted
|
Peter
|
request
|
minor
|
yat 0.2
|
statistics
|