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Diff Rev Age Author Log Message
(edit) @4027   3 years Peter refs #968; fix implementation of SegmentSet::insert_merge and add some …
(edit) @4026   3 years Peter add rvalue insert to SegmentSet?; closes #968.
(edit) @4025   3 years Peter add move constructor for BamPair?
(edit) @4024   3 years Peter refs #968; SegmentTree::insert taking rvalue
(edit) @4023   3 years Peter refs #968; Segment constrctor taking rvalues
(edit) @4022   3 years Peter prefer std::shared_ptr over boost
(edit) @4021   3 years Peter closes #961. Improve message in thrown exceptions.
(edit) @4019   3 years Peter merge 0.18 into trunk
(edit) @4011   3 years Peter Use std smart pointers instead of boost. Prefer initialisation of …
(edit) @4010   3 years Peter Implement move constructo and move-assignment operator for …
(edit) @4009   3 years Peter closes #965; Default constructor for DiscreteGeneral?
(edit) @4005   3 years Peter int8_t needs <cstdint> when sam.h isn't included
(edit) @4004   3 years Peter add \since tag for new exception class invalid_argument
(edit) @4003   3 years Peter Add a constructor Aligner::Cigar(string) (closes #962) Add a function …
(edit) @4001   3 years Peter Bumping version to 0.19pre
(edit) @3999   3 years Peter update copyright years
(edit) @3998   3 years Peter Prepare 0.18-stable branch
(edit) @3997   3 years Peter merge 0.17-stable branch into trunk
(edit) @3996   3 years Peter prefer std smart pointers
(edit) @3995   3 years Peter avoid using macros marked obsolete and instead use versions in LT_ …
(edit) @3994   3 years Peter simplify code
(edit) @3993   3 years Peter simplify code
(edit) @3992   3 years Peter recommend std rather than boost
(edit) @3991   3 years Peter new constructor in GenomicPosition?
(edit) @3990   3 years Peter prefer name with 'htslib' (instead of 'samtools')
(edit) @3987   3 years Peter merge release 0.17.2 into trunk
(edit) @3983   3 years Peter remove some text not relevant anymore, when we assume c++11 and htslib
(edit) @3982   3 years Peter improve docs
(edit) @3980   3 years Peter fixes #957. NegativeBinomial? now inherits from Multivariate
(edit) @3977   3 years Peter avoid accessing passed matrix (Ain) after it has been moved.
(edit) @3970   3 years Peter explain what position is when inside an insertion
(edit) @3969   3 years Peter docs typo
(edit) @3968   3 years Peter merge r3967 into trunk
(edit) @3966   3 years Peter merge changes in 0.17-stable branch (since 0.17.1) into trunk.
(edit) @3964   3 years Peter avoid warning with doxygen 1.8.19
(edit) @3963   3 years Peter new function supposed to be used by GSL error handler, resulting in a …
(edit) @3962   3 years Peter a4wide used to be the default value for PAPER_TYPE. but with modern …
(edit) @3961   3 years Peter fixes #845. Replace default GSL error handler in tests with one that …
(edit) @3960   3 years Peter closes #953. Since we are no longer using libboost_thread (or …
(edit) @3959   3 years Peter use std::mutex and friends instead of boost variants. refs #953
(edit) @3958   3 years Peter change to using std distributions instead of boost. Some distributions …
(edit) @3957   3 years Peter closes #890. Implement normalizer::UnityScaler?.
(edit) @3956   3 years Peter simplify code
(edit) @3955   3 years Peter use std::move and friend rather than internal macro (since we can …
(edit) @3954   3 years Peter bind2nd is deprecated in C++11 (and removed in c++17). Replace with …
(edit) @3953   3 years Peter refs #890. Implement RangeNormalizer?, a generalization of Centralizer …
(edit) @3949   3 years Peter use std::thread rather than boost::thread in test, refs #953
(edit) @3948   3 years Peter replace boost::thread with std::thread in Scheduler. refs #953
(edit) @3947   3 years Peter fix includes
(edit) @3946   3 years Peter use mutex and locks from std:: rather than boost::. refs #953
(edit) @3945   3 years Peter avoid hard-coding autotools in tests and instead set shell variables …
(edit) @3944   3 years Peter Since we require C++11 compiler (refs #949), no need to check if …
(edit) @3943   3 years Peter merge r3941 into trunk
(edit) @3939   3 years Peter update README to reflect that C++11 is not optional. closes #949
(edit) @3938   3 years Peter let configure fail if compiler is not a C++11 compiler. …
(edit) @3937   3 years Peter refs #949. New macro YAT_CXX11 that tests if compiler is CXX compliant …
(edit) @3936   3 years Peter merge changeset r3935 into trunk
(edit) @3934   3 years Peter using default rules in GNU make, libraries such as -lfoo should be …
(edit) @3933   3 years Peter package is called zlib
(edit) @3932   3 years Peter Config variable PERL_PATH is obsolete and causing a warning with …
(edit) @3930   3 years Peter merge release 0.17.1 into trunk
(edit) @3926   3 years Peter always include config.h in source files
(edit) @3925   3 years Peter avoid warnings in c++98
(edit) @3924   3 years Peter use move constructor when available. Sinve we can't access line after …
(edit) @3922   3 years Peter correct typo in NEWS. refs #945.
(edit) @3921   3 years Peter Remove comment that implementation might be problematic with reference …
(edit) @3920   3 years Peter to handle ALT being <ID> string access to VCFHeader is needed and …
(edit) @3919   3 years Peter alt=* is not an SNV
(edit) @3918   3 years Peter remove FIXME comment
(edit) @3917   3 years Peter allow user to define stop condition
(edit) @3916   3 years Peter avoid incrementing read if it's being removed on the next line. Get …
(edit) @3915   3 years Peter remove FIXME comment; refs #946
(edit) @3914   3 years Peter prefer do while loop rather than some home brewed version
(edit) @3913   3 years Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3912   3 years Peter boost random classes beta_distribution, hyperexponential_distribution …
(edit) @3911   3 years Peter fix typos
(edit) @3910   3 years Peter add missing file
(edit) @3909   3 years Peter add missing file from previous changeset
(edit) @3908   3 years Peter #closes #881 Lift out expression classes to their own files, so they …
(edit) @3907   3 years Peter remove checks for nullptr before calling gsl free function and require …
(edit) @3906   3 years Peter fix bug introduced in r3890; variable is now named have_htslib
(edit) @3905   3 years Peter docs: add missing since tag
(edit) @3904   3 years Peter Closes #892 Speed up matrix multiplications when they involve a …
(edit) @3903   3 years Peter correct docs
(edit) @3902   3 years Peter closes #915. New functions that read and write numbers in binary format.
(edit) @3901   3 years Peter prefer tests in alphabetical order
(edit) @3900   3 years Peter closes #944; add configure check whether class is availabale in boost …
(edit) @3899   3 years Peter avoid doxygen warnings with v1.8.5
(edit) @3898   3 years Peter closes #858 and #869
(edit) @3897   3 years Peter refs #869 and #858
(edit) @3896   3 years Peter fixes #943, avoid compiler warning about deprecated boost header
(edit) @3895   3 years Peter miss missing source file for test; refs #869
(edit) @3894   3 years Peter extend DiscreteUniform? so it fulfills the requirements for …
(edit) @3893   3 years Peter merge latest revision from stable-0.17 branch into trunk
(edit) @3891   3 years Peter fixes #933
(edit) @3890   3 years Peter Both HAVE_HTSLIB and have_htslib we AC_SUBST'd with different output, …
(edit) @3889   3 years Peter closes #941
(edit) @3888   3 years Peter fix compilation errors in --with-htslib mode introduced in r3883, refs #939
(edit) @3887   3 years Peter detect error from faidx_fetch_seq in ::fetch rather thasn in function …
(edit) @3886   3 years Peter add missing macros in intstall target; sort files alphabetically
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