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Diff Rev Age Author Log Message
(edit) @2919   9 years Peter update copyright years
(edit) @2918   9 years Peter prepare new stable release 0.10
(edit) @2916   9 years Peter merge patch release 0.9.2 into trunk. Ignore changes in …
(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) @2894   9 years Peter fix VPATH build issues
(edit) @2893   9 years Peter run (also C++) tests in specific test dir so test can create temporary …
(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) @2888   9 years Peter add example SAM file. refs #729
(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) @2882   9 years Peter add --enable-assert option (in configure)
(edit) @2881   9 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2880   9 years Peter update to autoconf macro archive 2012.11.14 (just serial # updated)
(edit) @2879   9 years Peter split function that splits on several chars
(edit) @2878   9 years Peter typo
(edit) @2877   9 years Peter prepend LIBS to achieve recommended -lgsl -lcblas -lm
(edit) @2876   9 years Peter avoid word enable for something that is turned off with '--without'
(edit) @2875   9 years Peter delete leftover comments
(edit) @2874   9 years Peter remove namespace bam. bam stuff will be put in omic namespace instead. …
(edit) @2873   9 years Peter prefer using YAT_MSG_ERROR and simplify computation of …
(edit) @2872   9 years Peter prefer YAT_MSG_ERROR. using it in inf test
(edit) @2871   9 years Peter prefer YAT_MSG_ERROR. using it in quiet_NAN test
(edit) @2870   9 years Peter mention samtools and zlib requirements in README
(edit) @2869   9 years Peter improve error messages. emove debug code. refs #729
(edit) @2868   9 years Peter refs #729. Add configure tests for samtools
(edit) @2867   9 years Peter A log2 function similar to std::log10.
(edit) @2866   9 years Peter remove -Werror option for automake
(edit) @2865   9 years Peter rename record file because file named 'conftest*' are deleted inside …
(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) @2859   9 years Peter fix boost macros to remove usage of tool 'tac' and change file pattern …
(edit) @2858   9 years Peter closes #725
(edit) @2857   9 years Peter closes #726
(edit) @2856   9 years Peter if test fails, skip downstream tests
(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) @2828   9 years Peter fix identation
(edit) @2827   9 years Peter Remove -Itop_srcdir from CPPFLAGS. Automake already adds -Isrcdir to …
(edit) @2825   9 years Peter upgrade to autoconf macro archive 2012.09.08
(edit) @2824   9 years Peter remove intermediate libraries. Makefiles in corresponding …
(edit) @2823   9 years Peter bumping version to 0.10pre
(edit) @2821   9 years Peter preparing new stable branch 0.9
(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) @2807   9 years Peter allow enable/disable silent-rules
(edit) @2806   9 years Peter avoid spurious error on OSX Tiger on which 'rm foo/.*' tries to remove …
(edit) @2805   9 years Peter avoid autoconf warnings in tests and do not delete testdir in test …
(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) @2801   9 years Peter add new alias for gsl doc url
(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) @2793   9 years Peter mention r2792 in NEWS
(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) @2786   9 years Peter update README. mention boost libraries rather than specific Thread Library.
(edit) @2785   9 years Peter skip boost link tests if --without-boost was provided
(edit) @2784   9 years Jari Häkkinen Resolving precision issues on my macbook pro.
(edit) @2783   9 years Jari Häkkinen Addresses #714. Adding note on additional dependency on boost system.
(edit) @2782   9 years Jari Häkkinen Addresses #714. Added check for boost system libraries. Need to link …
(edit) @2781   9 years Peter fix spurious errors in long long test. First, remove -pthread before …
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