#470 |
avoid using test::Suite::equal when comparing with value from file
|
Peter
|
defect
|
minor
|
yat 0.5
|
test
|
#473 |
disallow assignment of interpolation claases
|
Peter
|
request
|
minor
|
yat 0.5
|
regression
|
#475 |
upgrade to automake 1.11
|
Peter
|
request
|
minor
|
yat 0.7
|
build
|
#478 |
Generalize qQuantileNormalizer to work also on weighted data
|
Peter
|
discussion
|
minor
|
yat 0.5
|
normalizer
|
#480 |
missing operator- for DataIterator
|
Peter
|
defect
|
minor
|
yat 0.5
|
utility
|
#484 |
install-hook in build_support does not work on mac
|
Jari Häkkinen
|
defect
|
minor
|
yat 0.5
|
build
|
#485 |
yat-config --cppflags returns `-DGSL_RANGE_CHECK_OFF` and `-DNDEBUG`
|
Peter
|
defect
|
minor
|
yat 0.5
|
build
|
#502 |
clarify what KolmogorovSmirnov::signed_score returns
|
Peter
|
enhancement
|
minor
|
yat 0.5.2
|
documentation
|
#504 |
remove default value for second argument 'msg' in yat_assert
|
Peter
|
request
|
minor
|
yat 0.6
|
utility
|
#505 |
avoid polluting commandline with -I/usr/include and -L/usr/lib
|
Peter
|
enhancement
|
minor
|
yat 0.6
|
build
|
#506 |
change 'SVM::max_epochs' to be unsigned
|
Peter
|
defect
|
minor
|
yat 0.6
|
classifier
|
#508 |
Commandline throws exception without message
|
Peter
|
defect
|
minor
|
yat 0.5.2
|
utility
|
#514 |
concept: Weighted Iterator or unweighted with value type convertible to double.
|
Peter
|
request
|
minor
|
yat 0.6
|
documentation
|
#522 |
yat-config should honor environment variable YAT_CBLAS_LIB
|
Peter
|
request
|
minor
|
yat 0.6
|
build
|
#523 |
add support for option --libs-without-cblas in yat-config
|
Peter
|
request
|
minor
|
yat 0.6
|
build
|
#524 |
add configure option --with-cblas in yat's configure
|
Peter
|
request
|
minor
|
yat 0.6
|
build
|
#540 |
EnsembleBuilder::validate triggers assert when EB is built with one class having zero number of samples
|
Peter
|
defect
|
minor
|
yat 0.6
|
classifier
|
#545 |
doc claims median only works with unweighted iterators
|
Peter
|
defect
|
minor
|
yat 0.5.4
|
documentation
|
#551 |
alpha_var() and beta_var() in regression::Linear claims to return standard deviation
|
Peter
|
defect
|
minor
|
yat 0.6
|
documentation
|
#556 |
make Histogram output complete - allow construction of an object from the output
|
Peter
|
enhancement
|
minor
|
yat 0.7
|
statistics
|
#564 |
gcc complains about long long when compiling against Boost 1.40
|
Peter
|
defect
|
minor
|
yat 0.5.5
|
build
|
#572 |
GCC 4.3 complains about deprecated conversion from string constant to char*
|
Peter
|
defect
|
minor
|
yat 0.6
|
test
|
#580 |
test and document iterator type in Centralizer
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#581 |
test and document iterator type in ColumnNormalizer and RowNormalizer
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#582 |
test and document iterator type in Gauss
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#583 |
test and document iterator type in Spearman
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#584 |
test and document iterator type in qQuantileNormalizer
|
Peter
|
defect
|
minor
|
yat 0.6
|
test
|
#585 |
test and document iterator type in Average
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#586 |
test and document iterator type in Averager
|
Peter
|
defect
|
minor
|
yat 0.6
|
test
|
#587 |
test and document iterator type in AveragerWeighted
|
Peter
|
defect
|
minor
|
yat 0.6
|
test
|
#588 |
test and document iterator type in AveragerPair
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#589 |
test and document iterator type in AveragerPairWeighted
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#590 |
test and document iterator type in EuclideanDistance
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#591 |
test and document iterator type in PearsonDistance
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#592 |
test and document iterator type in Histogram
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#593 |
test and document iterator type in KolmogorovSmirnov
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#594 |
test and document iterator type in Smoother
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#595 |
test and document iterator types in functions in statistics/utility.h
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#596 |
test and document types in Container2DIterator
|
Peter
|
request
|
minor
|
yat 0.7
|
test
|
#597 |
test and document DataWeightProxy with trivial iterator
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#598 |
test and document iterator type in StrideIterator
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#600 |
test and document container type in merge
|
Peter
|
request
|
minor
|
yat 0.7
|
test
|
#601 |
test and document iterator type in sort_index
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#602 |
test and document iterator type in inverse
|
Peter
|
request
|
minor
|
yat 0.6
|
test
|
#617 |
FileUtil::permission bug when file (in root dir) does not exist
|
Peter
|
defect
|
minor
|
yat 0.6.1
|
utility
|
#619 |
static_test should be skipped when no static libyat is built
|
Peter
|
enhancement
|
minor
|
yat 0.7
|
test
|
#620 |
use AC_CONFIG_HEADER to genrate yat/utility/version.h
|
Jari Häkkinen
|
enhancement
|
minor
|
yat 0.8
|
build
|
#624 |
add concept check class for concept DataIterator
|
Peter
|
request
|
minor
|
yat 0.7
|
utility
|
#625 |
add concept check class for concept Distance
|
Peter
|
request
|
minor
|
yat 0.7
|
utility
|
#626 |
add concept check class for concept Mutable_Container2D
|
Peter
|
request
|
minor
|
yat 0.7
|
utility
|
#627 |
add concept check class for concept Neighbor Weighting Method
|
Peter
|
request
|
minor
|
yat 0.7
|
utility
|
#628 |
doxygen shows private class (in CommandLine)
|
Peter
|
defect
|
minor
|
yat 0.7
|
documentation
|
#629 |
yat::random classes should comply with STL's concept Random Number Generator
|
Peter
|
enhancement
|
minor
|
yat 0.7
|
random
|
#644 |
doxygen 1.7.2 complains about YAT_DEPRECATE
|
Peter
|
defect
|
minor
|
yat 0.7
|
documentation
|
#648 |
compiler warnings with gcc 4.4
|
Peter
|
defect
|
minor
|
yat 0.7.1
|
build
|
#654 |
allow silent-rules?
|
Peter
|
request
|
minor
|
yat 0.8
|
build
|
#655 |
avoid expanding variables in yat.pc
|
Peter
|
request
|
minor
|
yat 0.8
|
build
|
#656 |
convert numerical type to string
|
Peter
|
request
|
minor
|
yat 0.8
|
utility
|
#659 |
yat_am_macros (re)create files every time autoconf is run
|
Peter
|
enhancement
|
minor
|
yat 0.8
|
m4
|
#660 |
median crashes on empty range
|
Peter
|
defect
|
minor
|
yat 0.7.2
|
statistics
|
#667 |
documentation missing for namespace classifier
|
Peter
|
defect
|
minor
|
yat 0.7.3
|
documentation
|
#670 |
yat_am_macros tests fail
|
Peter
|
defect
|
minor
|
yat 0.8
|
test
|
#671 |
Increase accuracy in Averager
|
Peter
|
enhancement
|
minor
|
yat 0.8
|
statistics
|
#672 |
DNA assignment from char
|
Peter
|
request
|
minor
|
yat 0.8
|
omic
|
#675 |
document how to turn off deprecate warnings
|
Peter
|
enhancement
|
minor
|
yat 0.8
|
documentation
|
#677 |
When to use approximation for ROC p-value
|
Peter
|
defect
|
minor
|
yat 0.8
|
statistics
|
#681 |
Missing deprecated list
|
Peter
|
defect
|
minor
|
yat 0.8
|
documentation
|
#684 |
compiler icpc complains about -pedantic
|
Peter
|
defect
|
minor
|
yat 0.8
|
build
|
#693 |
use gsl_blas_ddot
|
Peter
|
request
|
minor
|
yat 0.9
|
utility
|
#694 |
use gsl_blas_dgemv
|
Peter
|
request
|
minor
|
yat 0.9
|
utility
|
#702 |
ROC::p_value crashes
|
Peter
|
defect
|
minor
|
yat 0.9
|
statistics
|
#716 |
look for openblas in configure
|
Peter
|
request
|
minor
|
yat 0.11
|
build
|
#718 |
remove convenience library
|
Peter
|
request
|
minor
|
yat 0.10
|
build
|
#720 |
rng-mt failure
|
Peter
|
defect
|
minor
|
yat 0.9
|
random
|
#723 |
CommandLine accepts passed '--no-foo'
|
Peter
|
defect
|
minor
|
yat 0.9.1
|
utility
|
#731 |
yat_revision_header fails with Automake 1.13
|
Peter
|
defect
|
minor
|
yat 0.10
|
test
|
#734 |
test yat.pc
|
Peter
|
request
|
minor
|
yat 0.11
|
test
|
#735 |
missing HAVE_SAMTOOLS_BAM_H in config_public.h.in
|
Peter
|
defect
|
minor
|
yat 0.10.1
|
build
|
#743 |
BamRead::mtid is not implemented
|
Peter
|
defect
|
minor
|
yat 0.10.2
|
omic
|
#749 |
asserts are turned on (default)
|
Peter
|
defect
|
minor
|
yat 0.10.2
|
build
|
#751 |
OutBamFile::write() ignores return value from samwrite
|
Peter
|
request
|
minor
|
yat 0.11
|
omic
|
#752 |
avoid installing header files conditionally
|
Peter
|
enhancement
|
minor
|
yat 0.11
|
omic
|
#757 |
m4 macro checking that -lyat has bam support
|
Peter
|
request
|
minor
|
yat 0.11
|
m4
|
#771 |
test version number of libyat in shell tests that link against libyat
|
Peter
|
enhancement
|
minor
|
yat 0.12
|
test
|
#772 |
calculate mutual information
|
Peter
|
request
|
minor
|
yat 0.12
|
statistics
|
#778 |
throw OutBamFile::error from OutBamFile::write(const BamRead& read)
|
Peter
|
request
|
minor
|
yat 0.12
|
omic
|
#780 |
Aligner vertical and horizon gap
|
Peter
|
enhancement
|
minor
|
yat 0.12
|
documentation
|
#790 |
workaround for BamPairIterator::operator->
|
Peter
|
request
|
minor
|
yat 0.12
|
omic
|
#795 |
write a test for macro YAT_HEADER_ASSERT
|
Peter
|
request
|
minor
|
yat 0.13
|
test
|
#802 |
AveragerWeighted::n(void) returns NaN for empty object
|
Peter
|
specification
|
minor
|
yat 0.13
|
statistics
|
#814 |
IGP: avoid calculating distance between every pair
|
Peter
|
enhancement
|
minor
|
yat 0.13
|
classifier
|
#818 |
SegmentSet::insert_merge(range)
|
Peter
|
request
|
minor
|
yat 0.13
|
utility
|
#819 |
SmithWaterman::operator()(4)
|
Peter
|
defect
|
minor
|
yat 0.12.2
|
documentation
|
#821 |
union of a utility::Segment
|
Peter
|
request
|
minor
|
yat 0.15
|
utility
|
#822 |
static_test.sh fails when htslib installed outside runtime linker path
|
Peter
|
defect
|
minor
|
yat 0.13
|
test
|
#824 |
OptionVersion class
|
Peter
|
request
|
minor
|
yat 0.20
|
utility
|
#826 |
function and/or functor to compare bam query name
|
Peter
|
request
|
minor
|
yat 0.13
|
omic
|
#827 |
set unset and flip bits in BamRead::flag
|
Peter
|
discussion
|
minor
|
yat 0.16
|
omic
|
#828 |
try convert string to numeric type
|
Peter
|
request
|
minor
|
yat 0.15
|
utility
|
#831 |
PriorityQueue
|
Peter
|
request
|
minor
|
yat 0.13
|
utility
|