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Ticket Summary Owner Type Priority Milestone Component
#750 update svndigest:ignore properties Peter request trivial yat 0.11 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
#754 Why is ROC::area not const? Peter request major yat 0.11 statistics
#755 tTest::score should be const Peter request major yat 0.11 statistics
#757 m4 macro checking that -lyat has bam support Peter request minor yat 0.11 m4
#759 Create a macro that can test whether shared library is available Peter request major yat 0.11 m4
#761 Create libs that can be used in tests for m4 macros Peter request major yat 0.11 test
#762 <boost/exception_ptr.hpp> in boost 1.41 problematic Peter request major yat 0.11 build
#764 BamReadIterator with invalid region Peter request major yat 0.11 omic
#766 PP #DEFINEs in global namespace Jari Häkkinen defect major yat 0.11 utility
#767 InBamFile::open should throw [not assert] when input is a wrong format Peter defect major yat 0.11 omic
#776 BamHeader::tid incorrect at first call Peter defect major yat 0.11.1 omic
#777 private namespace detail is included in doxygen output Peter defect trivial yat 0.11.2 documentation
#788 yat-config --libs does not include -lgsl Peter defect major yat 0.11.2 build
#381 Generalize Kernel_MEV Peter request major yat 0.12 utility
#769 class calculating likelihood ratio test for binomial models Peter request major yat 0.12 statistics
#770 ostream_iterator with no separator after last element Peter request major yat 0.12 utility
#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
#775 uncompressed OutBamFile Peter request major yat 0.12 omic
#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
#783 convert<double>("-nan") fails Peter discussion major yat 0.12 utility
#784 BamPairIterator Peter request major yat 0.12 omic
#785 CIGAR functionality Peter request major yat 0.12 omic
#789 ./configure CXXFLAGS="-g -O3" Jari Häkkinen discussion trivial yat 0.12 build
#790 workaround for BamPairIterator::operator-> Peter request minor yat 0.12 omic
#792 BamRead::flag is not implemented Peter defect major yat 0.12 omic
#797 yat/omic/algorithm.h is missing include Peter defect major yat 0.12 omic
#804 remove and rename are not implemented Peter defect major yat 0.12 utility
#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
#819 SmithWaterman::operator()(4) Peter defect minor yat 0.12.2 documentation
#820 Unexpected CIGAR Peter defect major yat 0.12.2 utility
#786 deprecate utility::Range Jari Häkkinen request major yat 0.13 utility
#794 support for htslib Peter request critical yat 0.13 build
#795 write a test for macro YAT_HEADER_ASSERT Peter request minor yat 0.13 test
#796 benjamini hochberg on unsorted range Peter request major yat 0.13 statistics
#799 allow conversion in get(map, key) Peter enhancement major yat 0.13 utility
#800 Scheduler Peter specification major yat 0.13 utility
#802 AveragerWeighted::n(void) returns NaN for empty object Peter specification minor yat 0.13 statistics
#806 bam pileup Peter request major yat 0.13 omic
#807 Yates' correction in Fisher Peter enhancement major yat 0.13 statistics
#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
#814 IGP: avoid calculating distance between every pair Peter enhancement minor yat 0.13 classifier
#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
#818 SegmentSet::insert_merge(range) Peter request minor yat 0.13 utility
#822 static_test.sh fails when htslib installed outside runtime linker path Peter defect minor yat 0.13 test
#826 function and/or functor to compare bam query name Peter request minor yat 0.13 omic
#830 calculate BAM's alignment score from cigar and reference Peter request major yat 0.13 omic
#831 PriorityQueue Peter request minor yat 0.13 utility
#832 Scheduler causes pthread_mutex_lock assertion Peter defect major yat 0.13 utility
#846 ROC::p_value() returns value greater than 1 Peter defect major yat 0.13 statistics
#847 ROC p_value; when is exact method used Peter defect minor yat 0.13 documentation
#850 yat.pc should use htslib.pc Jari Häkkinen defect minor yat 0.13.1 build
#862 samtools sort fails with samtools 1.2 and older Jari Häkkinen defect minor yat 0.13.1 test
#863 boost thread not detected Peter defect critical yat 0.13.1 build
#803 use new iterator concepts Peter request major yat 0.14 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
#839 Cannot find atlas on CentOS7 Peter defect minor yat 0.14 build
#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
#842 functor to compare pairs wrt to first only (ignore second) Peter request minor yat 0.14 utility
#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
#855 OutBamFile constructor segfaults if header is a NULL header Peter enhancement minor 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
#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
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