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Ticket Summary Owner Type Priority Milestone Component
#860 omic::DNA is not thread safe Peter defect trivial yat 0.14 omic
#864 change behaviour of yat-config so duplicated flag is kept Peter request major yat 0.14 build
#871 Distance base class Peter request major yat 0.14 statistics
#872 move test class weighted_iterator_archetype to namespace utility. Peter request minor yat 0.14 utility
#873 skip lvalue requirement in Distance concept Peter defect critical yat 0.14 utility
#876 RNG::instance is not thread safe Jari Häkkinen defect major yat 0.14 random
#884 VectorMutable += incorrect if lhs and rhs overlap Peter defect major yat 0.14.1 utility
#886 dna_reverse_complement_copy does not work Peter defect major yat 0.14.2 omic
#893 dirname("") triggers assertion Peter defect trivial yat 0.14.4 utility
#894 BamWriteIterator default constructor is declared but not implemented Peter defect major yat 0.14.4 omic
#895 InBamFile::n_mapped(int) throws when there are no reads in chromosome Peter defect major yat 0.14.4 omic
#474 create Vector from temporary VectorView fails Peter request major yat 0.15 utility
#821 union of a utility::Segment Peter request minor yat 0.15 utility
#828 try convert string to numeric type Peter request minor yat 0.15 utility
#834 make_segment for utility::Segment Peter request minor yat 0.15 utility
#836 allow operator*(const Matrix&, const Matrix&) Peter request major yat 0.15 utility
#851 includes are not stripped correctly (sometimes) Peter defect trivial yat 0.15 documentation
#861 detect failures in BamHeader::text(string) Peter request trivial yat 0.15 omic
#867 Negative Binomial Regression Peter request major yat 0.15 regression
#868 calculate inverse of (square) matrix Peter request minor yat 0.15 utility
#874 qQuantileNormalizer with unweighted source and weighted destination Peter request minor yat 0.15 normalizer
#875 speed up weighted qQuantileNormalizer::normalizer Peter enhancement minor yat 0.15 normalizer
#877 Use atomic in double checked locking pattern Peter enhancement major yat 0.15 random
#878 implement move semantics conditionally Peter discussion major yat 0.15 build
#879 document BamHeader::read_group_iterator Peter enhancement trivial yat 0.15 documentation
#880 transpose(A) in matrix expression Peter request major yat 0.15 utility
#882 Poissonian regression Peter request major yat 0.15 regression
#883 Base class for multivariate regression Peter request major yat 0.15 regression
#885 reuse blas_result in assignment from Matrix Expression Peter enhancement major yat 0.15 utility
#889 Parameter estimation of Gaussian mixture model Peter request major yat 0.15 statistics
#896 Scheduler job processing Peter discussion major yat 0.15 utility
#908 Fisher::p_value incorrect Peter defect major yat 0.15.1 statistics
#827 set unset and flip bits in BamRead::flag Peter discussion minor yat 0.16 omic
#848 class performing chi^2 test Peter request major yat 0.16 statistics
#866 Queue and PriorityQueue should be refactored with common base class Peter enhancement trivial yat 0.16 utility
#898 move assign element in Queue::pop Peter enhancement major yat 0.16 utility
#901 perceptron Markus Ringnér request major yat 0.16 classifier
#903 move function that works also in C++98 Peter discussion major yat 0.16 utility
#905 Support VCF (Variant Call Format) Peter request major yat 0.16 omic
#906 Constructor SVD(const Matrix&) is not declared explicit Peter defect major yat 0.16 utility
#907 RNG::seed_from_devurandom is not exception safe Peter defect trivial yat 0.16 random
#909 remove references to SGI Peter defect major yat 0.16 documentation
#924 race condition between Scheduler and Scheduler::JobHandler Peter defect major yat 0.16 utility
#927 PriorityQueue only stores unique elements Peter defect critical yat 0.16.1 utility
#928 GFF2 parser doesn't handle spaces correctly Peter defect major yat 0.16.2 omic
#929 Aligner::Cigar::begin(void) and ::end(void) are not implemented Peter defect major yat 0.16.2 utility
#931 Scheduler::jobs incorrect Peter defect major yat 0.16.3 utility
#904 cxx11 features - default behaviour Peter request major yat 0.17 utility
#910 add Scheduler API to modify size (number of threads) of the scheduler Peter request major yat 0.17 utility
#911 allow multiple arguments to yat-config Peter request minor yat 0.17 build
#914 Access number of threads in Scheduler Jari Häkkinen request trivial yat 0.17 utility
#916 recycle Scheduler after wait Peter request major yat 0.17 utility
#918 Pileup function for current read depth Peter request minor yat 0.17 omic
#919 implement Pileup::rbegin and :rend Peter request minor yat 0.17 omic
#921 wrapper around getcwd Peter request major yat 0.17 utility
#922 configure: gsl check doesn't use detected blas Peter defect major yat 0.17 build
#925 document parameter number in VCF::add* functions Peter enhancement trivial yat 0.17 documentation
#926 yat_lt_link_ifelse_test.sh and yat_m4_with_bam_test.sh fail because they use the wrong compiler Jari Häkkinen defect minor yat 0.17 test
#930 cyclic references in Scheduler::Job Peter defect critical yat 0.17 utility
#934 configure doesn't find libhts 1.10 Jari Häkkinen defect critical yat 0.17 build
#935 Percentiler requires ForwardIterator Peter defect major yat 0.17 test
#936 Scheduler skips jobs (sometimes) Jari Häkkinen defect critical yat 0.17 utility
#937 GFF2 crashes when attribute list ends with ';' Peter defect major yat 0.17 omic
#942 DiscreteUniform::result_type is ambiguous Peter defect minor yat 0.17.1 random
#947 getvector(vector<double>&) Peter defect major yat 0.17.1 utility
#950 spurious failures in yat_pc_test.sh Peter request minor yat 0.17.2 test
#952 Libraries are declared private in yat.pc incorrectly Peter defect minor yat 0.17.2 build
#954 Documentation doesn't work with doxygen 1.8.19 Peter defect major yat 0.17.2 documentation
#955 incorrect Kendall's tau p-value Peter defect major yat 0.17.2 statistics
#956 Vector::resize(0) crash Peter defect major yat 0.17.2 utility
#845 handle GSL errors gracefully in test suite Peter enhancement trivial yat 0.18 test
#869 class for random number from negative binomial distribution Peter request major yat 0.18 random
#881 expression class for dgemv Peter discussion major yat 0.18 utility
#890 normalize to unity Peter request minor yat 0.18 normalizer
#892 expression class for dgemm Peter request major yat 0.18 utility
#913 BamPairIterator sorted wrt first read Peter request major yat 0.18 omic
#915 read and write numbers in binary format Peter request major yat 0.18 utility
#932 squared norm of Vector Peter request major yat 0.18 utility
#933 function to remove entry in VcfHeader Peter request major yat 0.18 omic
#938 BamPairIterator does not pass test::Suite::input_iterator_test Jari Häkkinen defect trivial yat 0.18 test
#939 remove support for libbam Peter request critical yat 0.18 build
#940 add failure check in Fasta::fetch Peter request trivial yat 0.18 omic
#941 BamRead::sequence(2) speedup Peter enhancement minor 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
#948 handle missing values (.) in VCF files Peter request major yat 0.18 omic
#949 require c++11 compiler Peter request blocker yat 0.18 build
#953 replace boost::thread with std::thread Peter request major yat 0.18 utility
#957 regression::NegativeBinomial should inherit from regression::Multivariate Peter defect trivial yat 0.18 regression
#960 warnings from new autoconf Jari Häkkinen discussion minor yat 0.18 build
#970 SegmentTree compare functions do not compile Jari Häkkinen defect major yat 0.18.1 utility
#798 output sorted bam buffer Peter request major yat 0.19 omic
#958 Read - process - write MT pattern Peter request major yat 0.19 utility
#961 more informative exception from VCF::Data and VCF::Info Peter enhancement major yat 0.19 omic
#962 Aligner::Cigar(string) constructor Jari Häkkinen request major yat 0.19 utility
#963 Confidence interval for median (& other percentiles) Peter request major yat 0.19 statistics
#964 move constructor and assignment for DiscreteGeneral Peter request major yat 0.19 random
#965 default constructor for DiscreteGeneral Peter request major yat 0.19 random
#966 prefer std::shared_ptr in BamReadIterator Peter enhancement minor yat 0.19 omic
#968 rvalue insert in SegmentTree Peter request minor yat 0.19 utility
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