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Ticket Summary Owner Type Priority Milestone Component
#788 yat-config --libs does not include -lgsl Peter defect major yat 0.11.2 build
#792 BamRead::flag is not implemented Peter defect major yat 0.12 omic
#796 benjamini hochberg on unsorted range Peter request major yat 0.13 statistics
#797 yat/omic/algorithm.h is missing include Peter defect major yat 0.12 omic
#799 allow conversion in get(map, key) Peter enhancement major yat 0.13 utility
#800 Scheduler Peter specification major yat 0.13 utility
#803 use new iterator concepts Peter request major yat 0.14 utility
#804 remove and rename are not implemented Peter defect major yat 0.12 utility
#806 bam pileup Peter request major yat 0.13 omic
#807 Yates' correction in Fisher Peter enhancement major yat 0.13 statistics
#810 Bam::end() doesn't work when cigar contains BAM_CEQUAL and BAM_CDIFF Peter defect major yat 0.12.1 omic
#815 QuantileNormalizer segfaults if input has more columns than rows Peter defect major yat 0.12.2 normalizer
#816 create CigarIterator from Aligner::Cigar Peter request major yat 0.13 utility
#817 access misc text in BamHeader Peter request major yat 0.13 omic
#820 Unexpected CIGAR Peter defect major yat 0.12.2 utility
#830 calculate BAM's alignment score from cigar and reference Peter request major yat 0.13 omic
#832 Scheduler causes pthread_mutex_lock assertion Peter defect major yat 0.13 utility
#836 allow operator*(const Matrix&, const Matrix&) Peter request major yat 0.15 utility
#837 Geometric Distribution Jari Häkkinen request major yat 0.14 random
#838 copy k elements out of N Peter request major yat 0.14 random
#840 assignment of VectorMutable does not compile Peter defect major yat 0.14 utility
#841 Fisher's exact two-sided p-value Peter request major yat 0.14 statistics
#846 ROC::p_value() returns value greater than 1 Peter defect major yat 0.13 statistics
#848 class performing chi^2 test Peter request major yat 0.16 statistics
#849 Segment equality Jari Häkkinen request major yat 0.14 utility
#852 function to access 'samtools idxstats' stats Peter request major yat 0.14 omic
#856 random number from hypergeometric distribution Peter request major yat 0.14 random
#857 RNG from negative hypergeometric distribution Peter request major yat 0.14 random
#859 wrapper class around faidx_t Peter request major yat 0.14 omic
#864 change behaviour of yat-config so duplicated flag is kept Peter request major yat 0.14 build
#867 Negative Binomial Regression Peter request major yat 0.15 regression
#869 class for random number from negative binomial distribution Peter request major yat 0.18 random
#871 Distance base class Peter request major yat 0.14 statistics
#876 RNG::instance is not thread safe Jari Häkkinen defect major yat 0.14 random
#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
#880 transpose(A) in matrix expression Peter request major yat 0.15 utility
#881 expression class for dgemv Peter discussion major yat 0.18 utility
#882 Poissonian regression Peter request major yat 0.15 regression
#883 Base class for multivariate regression Peter request major yat 0.15 regression
#884 VectorMutable += incorrect if lhs and rhs overlap Peter defect major yat 0.14.1 utility
#885 reuse blas_result in assignment from Matrix Expression Peter enhancement major yat 0.15 utility
#886 dna_reverse_complement_copy does not work Peter defect major yat 0.14.2 omic
#889 Parameter estimation of Gaussian mixture model Peter request major yat 0.15 statistics
#892 expression class for dgemm Peter request major yat 0.18 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
#896 Scheduler job processing Peter discussion major yat 0.15 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
#904 cxx11 features - default behaviour Peter request major yat 0.17 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
#908 Fisher::p_value incorrect Peter defect major yat 0.15.1 statistics
#909 remove references to SGI Peter defect major yat 0.16 documentation
#910 add Scheduler API to modify size (number of threads) of the scheduler Peter request major yat 0.17 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
#916 recycle Scheduler after wait Peter request major yat 0.17 utility
#917 undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3' Jari Häkkinen defect major build
#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
#924 race condition between Scheduler and Scheduler::JobHandler Peter defect major yat 0.16 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
#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
#935 Percentiler requires ForwardIterator Peter defect major yat 0.17 test
#937 GFF2 crashes when attribute list ends with ';' Peter defect major yat 0.17 omic
#944 missing boost header <boost/random/non_central_chi_squared_distribution.hpp> Jari Häkkinen defect major test
#947 getvector(vector<double>&) Peter defect major yat 0.17.1 utility
#953 replace boost::thread with std::thread Peter request major yat 0.18 utility
#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
#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
#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
#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
#25 approximative calculation of p-value in Fisher's exact test Peter enhancement minor yat 0.2 statistics
#26 throw exception in statistics::Fisher Peter request minor yat 0.2 statistics
#30 ConsensusInputRanker: move CrossSplitting Peter enhancement minor classifier
#33 reimplement ROC::score_weighted Peter enhancement minor yat 0.3 (Public release) statistics
#37 rewrite Weighted Statistics documentation Peter request minor documentation
#44 templates for median and percentile should not sort but rather require sorted objects. Peter defect minor yat 0.3 (Public release) statistics
#45 test median functions Peter request minor yat 0.3 (Public release) test
#46 median functions should be coherent Peter defect minor yat 0.3 (Public release) statistics
#49 ConsensusInputRanker.add(InputRanker) Peter enhancement minor yat 0.3 (Public release) classifier
#71 Test that output from classifier::DataLook1D can be read by gslapi::vector Markus Ringnér defect minor yat 0.3 (Public release) test
#72 Document Kernel class Peter defect minor yat 0.2 documentation
#90 rows, columns, and size functions are redundant in Kernel Peter enhancement minor yat 0.3 (Public release) classifier
#91 Parameter class Jari Häkkinen enhancement minor yat 0.3 (Public release) utility
#93 EnsembleBuilder crashes if validate() is called before build() Peter defect minor yat 0.4 classifier
#98 is_int("1.2") returns true Markus Ringnér defect minor yat 0.3 (Public release) utility
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