source: trunk/yat

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Diff Rev Age Author Log Message
(edit) @2960   9 years Peter merge patch release 0.10.1 into trunk
(edit) @2949   9 years Peter comments describing defines from bam.h
(edit) @2943   9 years Peter merge release 0.10 into trunk
(edit) @2932   9 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2919   9 years Peter update copyright years
(edit) @2912   9 years Peter docs typo
(edit) @2911   9 years Peter accidently included in r2910
(edit) @2910   9 years Peter improve docs. closes #729
(edit) @2909   9 years Peter avoid creating a MatrixLookupWeighted? from a Matrix as it involves …
(edit) @2908   9 years Peter copy tests from http://dev.thep.lu.se/svndigest code. refs #717
(edit) @2907   9 years Peter extend intererface with mode_t as in C api and improve docs. refs #717
(edit) @2906   9 years Peter New functions chdir, chmod, copy_file, fnmatch, remove, rename, and …
(edit) @2905   9 years Peter remove superfluous 'using'
(edit) @2904   9 years Peter boost concept check. refs #729
(edit) @2903   9 years Peter refs #729. document bam_pair_analyse
(edit) @2902   9 years Peter test for bam_pair_analyse. refs #729
(edit) @2901   9 years Peter make random generators to model adaptable Generators
(edit) @2900   9 years Peter remove trailing WS
(edit) @2899   9 years Peter function bam_pair_analyse
(edit) @2898   9 years Peter dox typo
(edit) @2897   9 years Peter prefer throwing yat::utility::runtime_error. refs #729
(edit) @2896   9 years Peter improve doc and remove private classes from docs
(edit) @2895   9 years Peter add two tests for bam functionality
(edit) @2892   9 years Peter add functions mkdir, mkdir_p, basename, dirname. refs #717
(edit) @2891   9 years Peter check for samtools in configure; create bam file in 'make check' if we …
(edit) @2890   9 years Peter prefer calling base class constructor explicitly
(edit) @2889   9 years Peter Binomial distribution. fixes #730
(edit) @2887   9 years Peter docs typo
(edit) @2886   9 years Peter fast swap for BamRead?
(edit) @2884   9 years Peter add missing since tags. refs #729
(edit) @2883   9 years Peter New classes to wrap around functionality provided by samtools. refs #729
(edit) @2881   9 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2879   9 years Peter split function that splits on several chars
(edit) @2874   9 years Peter remove namespace bam. bam stuff will be put in omic namespace instead. …
(edit) @2867   9 years Peter A log2 function similar to std::log10.
(edit) @2864   9 years Peter file structure and empty automake file for new bam namespace. refs #729
(edit) @2863   9 years Peter prefer boost::shared_ptr. refs #712
(edit) @2862   9 years Peter prefer boost::shared_ptr. refs #712
(edit) @2861   9 years Peter avoid using SmartPtr?; prefer using boost::shared_ptr. refs #712
(edit) @2858   9 years Peter closes #725
(edit) @2857   9 years Peter closes #726
(edit) @2853   9 years Peter merge patch release 0.9.1 into trunk
(edit) @2842   9 years Peter remove todo doxygen tags
(edit) @2838   9 years Peter merge release 0.9 into trunk
(edit) @2837   9 years Peter avoid ancient inclusion guards around '#include <config.h>'
(edit) @2824   9 years Peter remove intermediate libraries. Makefiles in corresponding …
(edit) @2820   9 years Peter update copyright years
(edit) @2819   9 years Jari Häkkinen Migrating fix from http://dev.thep.lu.se/svndigest/changeset/1503. …
(edit) @2818   9 years Peter prefer 'if (b)' over 'if (a && b)' when 'b' is a subset of 'a'.
(edit) @2817   9 years Peter update copyright years
(edit) @2816   9 years Peter change name of function cigar => alignment
(edit) @2815   9 years Peter closes #706. Implement a generalization of SmithWaternan? and …
(edit) @2814   9 years Peter fixed docs typo
(edit) @2810   9 years Peter add missing files in r2809. refs #705
(edit) @2809   9 years Peter closes #705. Create a common interface class for average classes …
(edit) @2808   9 years Peter fixed grammar typo in docs
(edit) @2804   9 years Peter RNG::set_state: prefer throw on error.
(edit) @2803   9 years Peter fixed spurious test failures as well as a bug in operator+=. refs #705
(edit) @2802   9 years Peter adding documentation and tests. Remove private member count_ (not …
(edit) @2800   9 years Peter adding variables seed_ and count_ to make random numbers different in …
(edit) @2799   9 years Peter first version of class Averager4. refs #705
(edit) @2798   9 years Peter merge release 0.8.2 into trunk
(edit) @2792   9 years Peter introduced parameter mismatch in ssearch
(edit) @2790   9 years Peter remove useless forward declaration
(edit) @2789   9 years Peter adding a comment. refs #568
(edit) @2788   9 years Peter correct documentation
(edit) @2787   9 years Peter update coyright years
(edit) @2778   9 years Peter mark SmartPtr? as internal and point to boost::shared_ptr
(edit) @2773   9 years Peter declare HEADERs with srcdir so doxygen understands where to find them …
(edit) @2770   9 years Peter change back to RNG being a singleton, which now stores gsl_rng* in a …
(edit) @2768   9 years Peter First version of redesigned RNG that provides one instance per thread …
(edit) @2766   9 years Peter improve docs. closes #494
(edit) @2763   9 years Peter avoid race with static variable
(edit) @2761   9 years Peter refs #494. fix approx p-value with ties
(edit) @2760   9 years Peter allow copy and assignment. refs #494
(edit) @2758   9 years Peter test for approx p-value with ties refs #494
(edit) @2757   9 years Peter change definition of tau in presence of ties. refs #494
(edit) @2749   9 years Peter add small convenience Makefiles in subdirs. closes #703
(edit) @2748   9 years Peter avoid extra if statement
(edit) @2747   9 years Peter doc typo
(edit) @2743   9 years Peter correct doc typo
(edit) @2742   9 years Peter minor speedup in DNA::complement
(edit) @2741   9 years Peter prefer vector and string as internals in omic::DNA
(edit) @2739   9 years Peter refs #703 using a non-recursive Makefile. Old Makefile.am are kept but …
(edit) @2738   9 years Peter SmithWaterman? improve docs
(edit) @2736   9 years Peter fixes #702
(edit) @2735   9 years Peter fix matrix test and add new function trace
(edit) @2732   9 years Peter fix comment typo
(edit) @2731   9 years Peter avoid obscure code example
(edit) @2730   9 years Peter docs: clarification and code example for Dereferencer
(edit) @2723   10 years Peter avoid < with string::npos
(edit) @2722   10 years Peter fix implementation of ROC::remove. refs #211
(edit) @2721   10 years Peter add a remove function in KolmogorovSmirnov?
(edit) @2720   10 years Peter ROC: remove a data value. closes #688
(edit) @2719   10 years Peter improve branching
(edit) @2718   10 years Peter implement ROC p-value handling weights and ties. closes #211
(edit) @2717   10 years Peter remove trailing WS
(edit) @2716   10 years Peter fixed docs so doxygen can parse
(edit) @2715   10 years Peter fix latex quirky in doc
(edit) @2710   10 years Peter prefer using unsigned int rather than double
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