source: trunk/yat

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Diff Rev Age Author Log Message
(edit) @4117   3 months Peter add assert
(edit) @4115   3 months Peter always include config.h in source files
(edit) @4114   3 months Peter new class for one-way ANOVA test
(edit) @4113   4 months Peter fix docs typo
(edit) @4110   4 months Peter merge release 0.19 into trunk
(edit) @4106   4 months Peter docs: c++11 is required
(edit) @4105   4 months Peter implement +=, -=, and *= operators for DiagonalMatrix?; prefer using …
(edit) @4104   4 months Peter make doxygen happy
(edit) @4102   4 months Peter add wrapper function that calls std::string::contains, ::starts_with, …
(edit) @4098   4 months Peter minor docs change
(edit) @4097   4 months Peter use boost when functionality is available; prefer passing const& …
(edit) @4096   4 months Peter simplify code and alter private interface to reflect what's going on inside
(edit) @4095   4 months Peter docs
(edit) @4089   4 months Peter updating copyright years
(edit) @4087   5 months Peter extend docs; closes #710
(edit) @4086   5 months Peter handle header and source files in their own 'Makefile.am' in line with …
(edit) @4085   5 months Peter fix include so it works in a vpath build
(edit) @4083   5 months Peter merge kendall-score branch into trunk. refs #710
(edit) @4078   5 months Peter remove trailing ws
(edit) @4076   5 months Peter fixed docs typo
(edit) @4060   8 months Peter prefer throw_with_nested, when info in the caught expression makes …
(edit) @4059   9 months Peter new function: round, which is rounding elements in a range with the …
(edit) @4057   10 months Peter closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.
(edit) @4056   10 months Peter docs: fix typo and add clarification
(edit) @4055   10 months Peter remove unneeded includes
(edit) @4053   10 months Peter add some test for correlation(Matrix); speed up, particuarly when …
(edit) @4052   10 months Peter add description on what is optimised during the training.
(edit) @4051   11 months Peter make Target::classifier() const; closes #972
(edit) @4050   11 months Peter remove white-space
(edit) @4049   11 months Peter do not allow implicit conversion
(edit) @4048   11 months Peter add parameter allowing scaling to other than unity variance.
(edit) @4047   11 months Peter corrected includes
(edit) @4046   11 months Peter docs typo
(edit) @4044   11 months Peter new function multiprocess; closes #958
(edit) @4043   11 months Peter Add capacity to Queue and PriorityQueue?, which is a feature to limit …
(edit) @4041   11 months Peter avoid constructing temporary substring just for comparison
(edit) @4040   11 months Peter speed-up; prefer move instead of copy
(edit) @4039   11 months Peter Using me::value_type propagated to compilation errors and created …
(edit) @4036   12 months Peter closes #963. New class PercentileConfidenceInterval?
(edit) @4035   12 months Peter skeleton for PercentileConfidenceInterval?; refs #963
(edit) @4032   12 months Peter merge release 0.18.1 into trunk
(edit) @4027   12 months Peter refs #968; fix implementation of SegmentSet::insert_merge and add some …
(edit) @4026   12 months Peter add rvalue insert to SegmentSet?; closes #968.
(edit) @4025   12 months Peter add move constructor for BamPair?
(edit) @4024   13 months Peter refs #968; SegmentTree::insert taking rvalue
(edit) @4023   13 months Peter refs #968; Segment constrctor taking rvalues
(edit) @4022   13 months Peter prefer std::shared_ptr over boost
(edit) @4021   14 months Peter closes #961. Improve message in thrown exceptions.
(edit) @4019   15 months Peter merge 0.18 into trunk
(edit) @4011   15 months Peter Use std smart pointers instead of boost. Prefer initialisation of …
(edit) @4010   15 months Peter Implement move constructo and move-assignment operator for …
(edit) @4009   15 months Peter closes #965; Default constructor for DiscreteGeneral?
(edit) @4005   15 months Peter int8_t needs <cstdint> when sam.h isn't included
(edit) @4004   15 months Peter add \since tag for new exception class invalid_argument
(edit) @4003   15 months Peter Add a constructor Aligner::Cigar(string) (closes #962) Add a function …
(edit) @3999   15 months Peter update copyright years
(edit) @3996   16 months Peter prefer std smart pointers
(edit) @3994   16 months Peter simplify code
(edit) @3993   16 months Peter simplify code
(edit) @3992   16 months Peter recommend std rather than boost
(edit) @3991   17 months Peter new constructor in GenomicPosition?
(edit) @3987   17 months Peter merge release 0.17.2 into trunk
(edit) @3982   17 months Peter improve docs
(edit) @3980   17 months Peter fixes #957. NegativeBinomial? now inherits from Multivariate
(edit) @3977   17 months Peter avoid accessing passed matrix (Ain) after it has been moved.
(edit) @3970   17 months Peter explain what position is when inside an insertion
(edit) @3969   17 months Peter docs typo
(edit) @3963   18 months Peter new function supposed to be used by GSL error handler, resulting in a …
(edit) @3959   18 months Peter use std::mutex and friends instead of boost variants. refs #953
(edit) @3958   18 months Peter change to using std distributions instead of boost. Some distributions …
(edit) @3957   18 months Peter closes #890. Implement normalizer::UnityScaler?.
(edit) @3956   18 months Peter simplify code
(edit) @3955   18 months Peter use std::move and friend rather than internal macro (since we can …
(edit) @3954   18 months Peter bind2nd is deprecated in C++11 (and removed in c++17). Replace with …
(edit) @3953   18 months Peter refs #890. Implement RangeNormalizer?, a generalization of Centralizer …
(edit) @3948   18 months Peter replace boost::thread with std::thread in Scheduler. refs #953
(edit) @3947   18 months Peter fix includes
(edit) @3946   18 months Peter use mutex and locks from std:: rather than boost::. refs #953
(edit) @3938   18 months Peter let configure fail if compiler is not a C++11 compiler. …
(edit) @3930   19 months Peter merge release 0.17.1 into trunk
(edit) @3926   19 months Peter always include config.h in source files
(edit) @3925   19 months Peter avoid warnings in c++98
(edit) @3924   19 months Peter use move constructor when available. Sinve we can't access line after …
(edit) @3921   20 months Peter Remove comment that implementation might be problematic with reference …
(edit) @3920   20 months Peter to handle ALT being <ID> string access to VCFHeader is needed and …
(edit) @3919   20 months Peter alt=* is not an SNV
(edit) @3918   20 months Peter remove FIXME comment
(edit) @3917   20 months Peter allow user to define stop condition
(edit) @3916   20 months Peter avoid incrementing read if it's being removed on the next line. Get …
(edit) @3915   20 months Peter remove FIXME comment; refs #946
(edit) @3914   20 months Peter prefer do while loop rather than some home brewed version
(edit) @3913   20 months Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3912   20 months Peter boost random classes beta_distribution, hyperexponential_distribution …
(edit) @3909   20 months Peter add missing file from previous changeset
(edit) @3908   20 months Peter #closes #881 Lift out expression classes to their own files, so they …
(edit) @3907   21 months Peter remove checks for nullptr before calling gsl free function and require …
(edit) @3905   21 months Peter docs: add missing since tag
(edit) @3904   21 months Peter Closes #892 Speed up matrix multiplications when they involve a …
(edit) @3903   21 months Peter correct docs
(edit) @3902   21 months Peter closes #915. New functions that read and write numbers in binary format.
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