source: trunk

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Diff Rev Age Author Log Message
(edit) @4059   6 months Peter new function: round, which is rounding elements in a range with the …
(edit) @4058   6 months Peter a not-so-random number generator that can be used to fill containers …
(edit) @4057   7 months Peter closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.
(edit) @4056   7 months Peter docs: fix typo and add clarification
(edit) @4055   7 months Peter remove unneeded includes
(edit) @4054   7 months Peter mention modified interface in previous commit
(edit) @4053   7 months Peter add some test for correlation(Matrix); speed up, particuarly when …
(edit) @4052   7 months Peter add description on what is optimised during the training.
(edit) @4051   8 months Peter make Target::classifier() const; closes #972
(edit) @4050   8 months Peter remove white-space
(edit) @4049   8 months Peter do not allow implicit conversion
(edit) @4048   8 months Peter add parameter allowing scaling to other than unity variance.
(edit) @4047   8 months Peter corrected includes
(edit) @4046   8 months Peter docs typo
(edit) @4045   8 months Peter add missing file
(edit) @4044   8 months Peter new function multiprocess; closes #958
(edit) @4043   8 months Peter Add capacity to Queue and PriorityQueue?, which is a feature to limit …
(edit) @4042   8 months Peter upgrade to autoconf-archive-2021.02.19
(edit) @4041   8 months Peter avoid constructing temporary substring just for comparison
(edit) @4040   8 months Peter speed-up; prefer move instead of copy
(edit) @4039   9 months Peter Using me::value_type propagated to compilation errors and created …
(edit) @4036   9 months Peter closes #963. New class PercentileConfidenceInterval?
(edit) @4035   9 months Peter skeleton for PercentileConfidenceInterval?; refs #963
(edit) @4034   9 months Peter Decouple variables for extra programs and test programs, to allow …
(edit) @4032   9 months Peter merge release 0.18.1 into trunk
(edit) @4027   9 months Peter refs #968; fix implementation of SegmentSet::insert_merge and add some …
(edit) @4026   9 months Peter add rvalue insert to SegmentSet?; closes #968.
(edit) @4025   10 months Peter add move constructor for BamPair?
(edit) @4024   10 months Peter refs #968; SegmentTree::insert taking rvalue
(edit) @4023   10 months Peter refs #968; Segment constrctor taking rvalues
(edit) @4022   10 months Peter prefer std::shared_ptr over boost
(edit) @4021   11 months Peter closes #961. Improve message in thrown exceptions.
(edit) @4019   12 months Peter merge 0.18 into trunk
(edit) @4011   12 months Peter Use std smart pointers instead of boost. Prefer initialisation of …
(edit) @4010   12 months Peter Implement move constructo and move-assignment operator for …
(edit) @4009   12 months Peter closes #965; Default constructor for DiscreteGeneral?
(edit) @4005   13 months Peter int8_t needs <cstdint> when sam.h isn't included
(edit) @4004   13 months Peter add \since tag for new exception class invalid_argument
(edit) @4003   13 months Peter Add a constructor Aligner::Cigar(string) (closes #962) Add a function …
(edit) @4001   13 months Peter Bumping version to 0.19pre
(edit) @3999   13 months Peter update copyright years
(edit) @3998   13 months Peter Prepare 0.18-stable branch
(edit) @3997   13 months Peter merge 0.17-stable branch into trunk
(edit) @3996   13 months Peter prefer std smart pointers
(edit) @3995   13 months Peter avoid using macros marked obsolete and instead use versions in LT_ …
(edit) @3994   13 months Peter simplify code
(edit) @3993   13 months Peter simplify code
(edit) @3992   13 months Peter recommend std rather than boost
(edit) @3991   14 months Peter new constructor in GenomicPosition?
(edit) @3990   14 months Peter prefer name with 'htslib' (instead of 'samtools')
(edit) @3987   14 months Peter merge release 0.17.2 into trunk
(edit) @3983   14 months Peter remove some text not relevant anymore, when we assume c++11 and htslib
(edit) @3982   14 months Peter improve docs
(edit) @3980   14 months Peter fixes #957. NegativeBinomial? now inherits from Multivariate
(edit) @3977   14 months Peter avoid accessing passed matrix (Ain) after it has been moved.
(edit) @3970   15 months Peter explain what position is when inside an insertion
(edit) @3969   15 months Peter docs typo
(edit) @3968   15 months Peter merge r3967 into trunk
(edit) @3966   15 months Peter merge changes in 0.17-stable branch (since 0.17.1) into trunk.
(edit) @3964   15 months Peter avoid warning with doxygen 1.8.19
(edit) @3963   15 months Peter new function supposed to be used by GSL error handler, resulting in a …
(edit) @3962   15 months Peter a4wide used to be the default value for PAPER_TYPE. but with modern …
(edit) @3961   15 months Peter fixes #845. Replace default GSL error handler in tests with one that …
(edit) @3960   15 months Peter closes #953. Since we are no longer using libboost_thread (or …
(edit) @3959   15 months Peter use std::mutex and friends instead of boost variants. refs #953
(edit) @3958   15 months Peter change to using std distributions instead of boost. Some distributions …
(edit) @3957   15 months Peter closes #890. Implement normalizer::UnityScaler?.
(edit) @3956   15 months Peter simplify code
(edit) @3955   15 months Peter use std::move and friend rather than internal macro (since we can …
(edit) @3954   15 months Peter bind2nd is deprecated in C++11 (and removed in c++17). Replace with …
(edit) @3953   15 months Peter refs #890. Implement RangeNormalizer?, a generalization of Centralizer …
(edit) @3949   15 months Peter use std::thread rather than boost::thread in test, refs #953
(edit) @3948   15 months Peter replace boost::thread with std::thread in Scheduler. refs #953
(edit) @3947   15 months Peter fix includes
(edit) @3946   15 months Peter use mutex and locks from std:: rather than boost::. refs #953
(edit) @3945   15 months Peter avoid hard-coding autotools in tests and instead set shell variables …
(edit) @3944   15 months Peter Since we require C++11 compiler (refs #949), no need to check if …
(edit) @3943   16 months Peter merge r3941 into trunk
(edit) @3939   16 months Peter update README to reflect that C++11 is not optional. closes #949
(edit) @3938   16 months Peter let configure fail if compiler is not a C++11 compiler. …
(edit) @3937   16 months Peter refs #949. New macro YAT_CXX11 that tests if compiler is CXX compliant …
(edit) @3936   16 months Peter merge changeset r3935 into trunk
(edit) @3934   16 months Peter using default rules in GNU make, libraries such as -lfoo should be …
(edit) @3933   16 months Peter package is called zlib
(edit) @3932   16 months Peter Config variable PERL_PATH is obsolete and causing a warning with …
(edit) @3930   16 months Peter merge release 0.17.1 into trunk
(edit) @3926   16 months Peter always include config.h in source files
(edit) @3925   16 months Peter avoid warnings in c++98
(edit) @3924   16 months Peter use move constructor when available. Sinve we can't access line after …
(edit) @3922   17 months Peter correct typo in NEWS. refs #945.
(edit) @3921   17 months Peter Remove comment that implementation might be problematic with reference …
(edit) @3920   17 months Peter to handle ALT being <ID> string access to VCFHeader is needed and …
(edit) @3919   17 months Peter alt=* is not an SNV
(edit) @3918   17 months Peter remove FIXME comment
(edit) @3917   17 months Peter allow user to define stop condition
(edit) @3916   17 months Peter avoid incrementing read if it's being removed on the next line. Get …
(edit) @3915   17 months Peter remove FIXME comment; refs #946
(edit) @3914   17 months Peter prefer do while loop rather than some home brewed version
(edit) @3913   18 months Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3912   18 months Peter boost random classes beta_distribution, hyperexponential_distribution …
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