source: trunk/yat/utility

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Diff Rev Age Author Log Message
(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) @4089   5 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) @4076   5 months Peter fixed docs typo
(edit) @4060   9 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) @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) @4039   12 months Peter Using me::value_type propagated to compilation errors and created …
(edit) @4032   12 months Peter merge release 0.18.1 into trunk
(edit) @4027   13 months Peter refs #968; fix implementation of SegmentSet::insert_merge and add some …
(edit) @4026   13 months Peter add rvalue insert to SegmentSet?; closes #968.
(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) @4005   16 months Peter int8_t needs <cstdint> when sam.h isn't included
(edit) @4004   16 months Peter add \since tag for new exception class invalid_argument
(edit) @4003   16 months Peter Add a constructor Aligner::Cigar(string) (closes #962) Add a function …
(edit) @3999   16 months Peter update copyright years
(edit) @3994   16 months Peter simplify code
(edit) @3993   16 months Peter simplify code
(edit) @3992   17 months Peter recommend std rather than boost
(edit) @3987   17 months Peter merge release 0.17.2 into trunk
(edit) @3977   17 months Peter avoid accessing passed matrix (Ain) after it has been moved.
(edit) @3963   18 months Peter new function supposed to be used by GSL error handler, resulting in a …
(edit) @3958   18 months Peter change to using std distributions instead of boost. Some distributions …
(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) @3948   19 months Peter replace boost::thread with std::thread in Scheduler. refs #953
(edit) @3947   19 months Peter fix includes
(edit) @3946   19 months Peter use mutex and locks from std:: rather than boost::. refs #953
(edit) @3938   19 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) @3924   20 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) @3918   20 months Peter remove FIXME comment
(edit) @3913   21 months Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3912   21 months Peter boost random classes beta_distribution, hyperexponential_distribution …
(edit) @3909   21 months Peter add missing file from previous changeset
(edit) @3908   21 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) @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.
(edit) @3900   21 months Peter closes #944; add configure check whether class is availabale in boost …
(edit) @3899   22 months Peter avoid doxygen warnings with v1.8.5
(edit) @3898   22 months Peter closes #858 and #869
(edit) @3888   22 months Peter fix compilation errors in --with-htslib mode introduced in r3883, refs #939
(edit) @3883   23 months Peter remove support for building against libbam (which allows us to remove …
(edit) @3871   2 years Peter closes #932
(edit) @3870   2 years Peter merge changes from 0.17-stable branch
(edit) @3855   2 years Peter updating copyright statements
(edit) @3853   2 years Peter fixes #930. Remove obervers_ variable in Job and instead keep that …
(edit) @3848   2 years Peter add functionality to alter number of threads used by Scheduler. closes #910
(edit) @3847   2 years Peter improve docs
(edit) @3845   2 years Peter remove exception specifications, which are deprecated in C++11, …
(edit) @3840   2 years Peter merge release yat-0.16.2 into trunk
(edit) @3832   2 years Peter merge release 0.16.1 intro trunk
(edit) @3828   3 years Peter Make the Scheduler recyclable i.e. allow jobs to be submitted also …
(edit) @3826   3 years Peter function to access number of threads in Scheduler. closes #914
(edit) @3823   3 years Peter Merge release 0.16 into trunk
(edit) @3816   3 years Peter revert r3815 as it didn't fix the problem; instead skip doxygen test …
(edit) @3815   3 years Peter avoid warning from doxygen 1.8.15
(edit) @3813   3 years Jari Häkkinen Typos
(edit) @3806   3 years Peter add missing include
(edit) @3804   3 years Peter closes #904; turn on cxx11 features by default
(edit) @3803   3 years Peter implement wrapper function around getcwd. closes #921.
(edit) @3792   3 years Peter update copyright years
(edit) @3788   3 years Peter avoid compiler warnings with GCC v6.4.0
(edit) @3787   3 years Peter std::auto_ptr is deprecated in cxx11, so to avoid compiler warnings we …
(edit) @3781   3 years Peter simplify code (using std and yat features) and remove some trailing spaces
(edit) @3780   3 years Peter simplify code (slightly)
(edit) @3779   3 years Peter docs
(edit) @3778   3 years Peter declare variable 'element' within the loop and thus avoid using the …
(edit) @3777   3 years Peter speedup in function load; avoid copying when std::move is available.
(edit) @3775   3 years Peter avoid dead links to STL docs at CGI. fixes #909
(edit) @3751   3 years Peter adjust license text to be same as in other files
(edit) @3749   3 years Peter docs: convert: add pointer to std::to_string
(edit) @3748   3 years Peter declare SVD constructor explicit; fixes #906
(edit) @3746   3 years Peter new wrapper function around posix function 'symlink'
(edit) @3743   4 years Peter merge release 0.15.1 into trunk
(edit) @3738   4 years Peter leftover from r3736
(edit) @3736   4 years Peter - add move constructor in SVD and PCA - remove some unneeded …
(edit) @3735   4 years Peter mention std::swap in docs
(edit) @3730   4 years Peter new function print_what() to print error message from std::nested_exception
(edit) @3729   4 years Peter optimisation; insert with hint
(edit) @3722   4 years Peter closes #898 and #903
(edit) @3721   4 years Peter Make assignment thread safe by locking both lhs and rhs. Avoid locking …
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