source: trunk/yat

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Diff Rev Age Author Log Message
(edit) @4059   3 weeks Peter new function: round, which is rounding elements in a range with the …
(edit) @4057   6 weeks Peter closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.
(edit) @4056   6 weeks Peter docs: fix typo and add clarification
(edit) @4055   7 weeks Peter remove unneeded includes
(edit) @4053   7 weeks Peter add some test for correlation(Matrix); speed up, particuarly when …
(edit) @4052   7 weeks Peter add description on what is optimised during the training.
(edit) @4051   2 months Peter make Target::classifier() const; closes #972
(edit) @4050   2 months Peter remove white-space
(edit) @4049   2 months Peter do not allow implicit conversion
(edit) @4048   2 months Peter add parameter allowing scaling to other than unity variance.
(edit) @4047   2 months Peter corrected includes
(edit) @4046   2 months Peter docs typo
(edit) @4044   2 months Peter new function multiprocess; closes #958
(edit) @4043   2 months Peter Add capacity to Queue and PriorityQueue?, which is a feature to limit …
(edit) @4041   3 months Peter avoid constructing temporary substring just for comparison
(edit) @4040   3 months Peter speed-up; prefer move instead of copy
(edit) @4039   3 months Peter Using me::value_type propagated to compilation errors and created …
(edit) @4036   4 months Peter closes #963. New class PercentileConfidenceInterval?
(edit) @4035   4 months Peter skeleton for PercentileConfidenceInterval?; refs #963
(edit) @4032   4 months Peter merge release 0.18.1 into trunk
(edit) @4027   4 months Peter refs #968; fix implementation of SegmentSet::insert_merge and add some …
(edit) @4026   4 months Peter add rvalue insert to SegmentSet?; closes #968.
(edit) @4025   4 months Peter add move constructor for BamPair?
(edit) @4024   4 months Peter refs #968; SegmentTree::insert taking rvalue
(edit) @4023   4 months Peter refs #968; Segment constrctor taking rvalues
(edit) @4022   4 months Peter prefer std::shared_ptr over boost
(edit) @4021   6 months Peter closes #961. Improve message in thrown exceptions.
(edit) @4019   6 months Peter merge 0.18 into trunk
(edit) @4011   7 months Peter Use std smart pointers instead of boost. Prefer initialisation of …
(edit) @4010   7 months Peter Implement move constructo and move-assignment operator for …
(edit) @4009   7 months Peter closes #965; Default constructor for DiscreteGeneral?
(edit) @4005   7 months Peter int8_t needs <cstdint> when sam.h isn't included
(edit) @4004   7 months Peter add \since tag for new exception class invalid_argument
(edit) @4003   7 months Peter Add a constructor Aligner::Cigar(string) (closes #962) Add a function …
(edit) @3999   7 months Peter update copyright years
(edit) @3996   7 months Peter prefer std smart pointers
(edit) @3994   8 months Peter simplify code
(edit) @3993   8 months Peter simplify code
(edit) @3992   8 months Peter recommend std rather than boost
(edit) @3991   8 months Peter new constructor in GenomicPosition?
(edit) @3987   9 months Peter merge release 0.17.2 into trunk
(edit) @3982   9 months Peter improve docs
(edit) @3980   9 months Peter fixes #957. NegativeBinomial? now inherits from Multivariate
(edit) @3977   9 months Peter avoid accessing passed matrix (Ain) after it has been moved.
(edit) @3970   9 months Peter explain what position is when inside an insertion
(edit) @3969   9 months Peter docs typo
(edit) @3963   9 months Peter new function supposed to be used by GSL error handler, resulting in a …
(edit) @3959   10 months Peter use std::mutex and friends instead of boost variants. refs #953
(edit) @3958   10 months Peter change to using std distributions instead of boost. Some distributions …
(edit) @3957   10 months Peter closes #890. Implement normalizer::UnityScaler?.
(edit) @3956   10 months Peter simplify code
(edit) @3955   10 months Peter use std::move and friend rather than internal macro (since we can …
(edit) @3954   10 months Peter bind2nd is deprecated in C++11 (and removed in c++17). Replace with …
(edit) @3953   10 months Peter refs #890. Implement RangeNormalizer?, a generalization of Centralizer …
(edit) @3948   10 months Peter replace boost::thread with std::thread in Scheduler. refs #953
(edit) @3947   10 months Peter fix includes
(edit) @3946   10 months Peter use mutex and locks from std:: rather than boost::. refs #953
(edit) @3938   10 months Peter let configure fail if compiler is not a C++11 compiler. …
(edit) @3930   10 months Peter merge release 0.17.1 into trunk
(edit) @3926   10 months Peter always include config.h in source files
(edit) @3925   10 months Peter avoid warnings in c++98
(edit) @3924   11 months Peter use move constructor when available. Sinve we can't access line after …
(edit) @3921   12 months Peter Remove comment that implementation might be problematic with reference …
(edit) @3920   12 months Peter to handle ALT being <ID> string access to VCFHeader is needed and …
(edit) @3919   12 months Peter alt=* is not an SNV
(edit) @3918   12 months Peter remove FIXME comment
(edit) @3917   12 months Peter allow user to define stop condition
(edit) @3916   12 months Peter avoid incrementing read if it's being removed on the next line. Get …
(edit) @3915   12 months Peter remove FIXME comment; refs #946
(edit) @3914   12 months Peter prefer do while loop rather than some home brewed version
(edit) @3913   12 months Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3912   12 months Peter boost random classes beta_distribution, hyperexponential_distribution …
(edit) @3909   12 months Peter add missing file from previous changeset
(edit) @3908   12 months Peter #closes #881 Lift out expression classes to their own files, so they …
(edit) @3907   12 months Peter remove checks for nullptr before calling gsl free function and require …
(edit) @3905   12 months Peter docs: add missing since tag
(edit) @3904   12 months Peter Closes #892 Speed up matrix multiplications when they involve a …
(edit) @3903   12 months Peter correct docs
(edit) @3902   12 months Peter closes #915. New functions that read and write numbers in binary format.
(edit) @3900   13 months Peter closes #944; add configure check whether class is availabale in boost …
(edit) @3899   14 months Peter avoid doxygen warnings with v1.8.5
(edit) @3898   14 months Peter closes #858 and #869
(edit) @3894   14 months Peter extend DiscreteUniform? so it fulfills the requirements for …
(edit) @3893   14 months Peter merge latest revision from stable-0.17 branch into trunk
(edit) @3891   14 months Peter fixes #933
(edit) @3889   14 months Peter closes #941
(edit) @3888   14 months Peter fix compilation errors in --with-htslib mode introduced in r3883, refs #939
(edit) @3887   14 months Peter detect error from faidx_fetch_seq in ::fetch rather thasn in function …
(edit) @3883   14 months Peter remove support for building against libbam (which allows us to remove …
(edit) @3881   14 months Peter correct PP guard names
(edit) @3880   14 months Peter In c++11 std::multiset<T>::erase(1) takes an ::iterator, whereas in …
(edit) @3878   14 months Peter New class BamPairIterator2 that takes a sort range of bam reads as …
(edit) @3875   15 months Peter merge release 0.17 into trunk
(edit) @3871   15 months Peter closes #932
(edit) @3870   15 months Peter merge changes from 0.17-stable branch
(edit) @3855   17 months Peter updating copyright statements
(edit) @3853   17 months Peter fixes #930. Remove obervers_ variable in Job and instead keep that …
(edit) @3848   20 months Peter add functionality to alter number of threads used by Scheduler. closes #910
(edit) @3847   20 months Peter improve docs
(edit) @3845   20 months Peter remove exception specifications, which are deprecated in C++11, …
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