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Diff Rev Age Author Log Message
(edit) @2952   9 years Peter look for openblas. closes #716
(edit) @2951   9 years Peter add deps for lazycheck
(edit) @2950   9 years Peter test for yat.pc. closes #734
(edit) @2949   9 years Peter comments describing defines from bam.h
(edit) @2948   9 years Peter prefer AC_SEARCH_LIBS over AC_CHECK_LIB
(edit) @2946   9 years Peter avoid duplication
(edit) @2945   9 years Peter avoid warning from Automake
(edit) @2943   10 years Peter merge release 0.10 into trunk
(edit) @2932   10 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2927   10 years Peter remove old core dumps in test prologue (to avoid accumulation of …
(edit) @2921   10 years Peter bump version to 0.11pre
(edit) @2919   10 years Peter update copyright years
(edit) @2918   10 years Peter prepare new stable release 0.10
(edit) @2916   10 years Peter merge patch release 0.9.2 into trunk. Ignore changes in …
(edit) @2912   10 years Peter docs typo
(edit) @2911   10 years Peter accidently included in r2910
(edit) @2910   10 years Peter improve docs. closes #729
(edit) @2909   10 years Peter avoid creating a MatrixLookupWeighted? from a Matrix as it involves …
(edit) @2908   10 years Peter copy tests from http://dev.thep.lu.se/svndigest code. refs #717
(edit) @2907   10 years Peter extend intererface with mode_t as in C api and improve docs. refs #717
(edit) @2906   10 years Peter New functions chdir, chmod, copy_file, fnmatch, remove, rename, and …
(edit) @2905   10 years Peter remove superfluous 'using'
(edit) @2904   10 years Peter boost concept check. refs #729
(edit) @2903   10 years Peter refs #729. document bam_pair_analyse
(edit) @2902   10 years Peter test for bam_pair_analyse. refs #729
(edit) @2901   10 years Peter make random generators to model adaptable Generators
(edit) @2900   10 years Peter remove trailing WS
(edit) @2899   10 years Peter function bam_pair_analyse
(edit) @2898   10 years Peter dox typo
(edit) @2897   10 years Peter prefer throwing yat::utility::runtime_error. refs #729
(edit) @2896   10 years Peter improve doc and remove private classes from docs
(edit) @2895   10 years Peter add two tests for bam functionality
(edit) @2894   10 years Peter fix VPATH build issues
(edit) @2893   10 years Peter run (also C++) tests in specific test dir so test can create temporary …
(edit) @2892   10 years Peter add functions mkdir, mkdir_p, basename, dirname. refs #717
(edit) @2891   10 years Peter check for samtools in configure; create bam file in 'make check' if we …
(edit) @2890   10 years Peter prefer calling base class constructor explicitly
(edit) @2889   10 years Peter Binomial distribution. fixes #730
(edit) @2888   10 years Peter add example SAM file. refs #729
(edit) @2887   10 years Peter docs typo
(edit) @2886   10 years Peter fast swap for BamRead?
(edit) @2884   10 years Peter add missing since tags. refs #729
(edit) @2883   10 years Peter New classes to wrap around functionality provided by samtools. refs #729
(edit) @2882   10 years Peter add --enable-assert option (in configure)
(edit) @2881   10 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2880   10 years Peter update to autoconf macro archive 2012.11.14 (just serial # updated)
(edit) @2879   10 years Peter split function that splits on several chars
(edit) @2878   10 years Peter typo
(edit) @2877   10 years Peter prepend LIBS to achieve recommended -lgsl -lcblas -lm
(edit) @2876   10 years Peter avoid word enable for something that is turned off with '--without'
(edit) @2875   10 years Peter delete leftover comments
(edit) @2874   10 years Peter remove namespace bam. bam stuff will be put in omic namespace instead. …
(edit) @2873   10 years Peter prefer using YAT_MSG_ERROR and simplify computation of …
(edit) @2872   10 years Peter prefer YAT_MSG_ERROR. using it in inf test
(edit) @2871   10 years Peter prefer YAT_MSG_ERROR. using it in quiet_NAN test
(edit) @2870   10 years Peter mention samtools and zlib requirements in README
(edit) @2869   10 years Peter improve error messages. emove debug code. refs #729
(edit) @2868   10 years Peter refs #729. Add configure tests for samtools
(edit) @2867   10 years Peter A log2 function similar to std::log10.
(edit) @2866   10 years Peter remove -Werror option for automake
(edit) @2865   10 years Peter rename record file because file named 'conftest*' are deleted inside …
(edit) @2864   10 years Peter file structure and empty automake file for new bam namespace. refs #729
(edit) @2863   10 years Peter prefer boost::shared_ptr. refs #712
(edit) @2862   10 years Peter prefer boost::shared_ptr. refs #712
(edit) @2861   10 years Peter avoid using SmartPtr?; prefer using boost::shared_ptr. refs #712
(edit) @2859   10 years Peter fix boost macros to remove usage of tool 'tac' and change file pattern …
(edit) @2858   10 years Peter closes #725
(edit) @2857   10 years Peter closes #726
(edit) @2856   10 years Peter if test fails, skip downstream tests
(edit) @2853   10 years Peter merge patch release 0.9.1 into trunk
(edit) @2842   10 years Peter remove todo doxygen tags
(edit) @2838   10 years Peter merge release 0.9 into trunk
(edit) @2837   10 years Peter avoid ancient inclusion guards around '#include <config.h>'
(edit) @2828   10 years Peter fix identation
(edit) @2827   10 years Peter Remove -Itop_srcdir from CPPFLAGS. Automake already adds -Isrcdir to …
(edit) @2825   10 years Peter upgrade to autoconf macro archive 2012.09.08
(edit) @2824   10 years Peter remove intermediate libraries. Makefiles in corresponding …
(edit) @2823   10 years Peter bumping version to 0.10pre
(edit) @2821   10 years Peter preparing new stable branch 0.9
(edit) @2820   10 years Peter update copyright years
(edit) @2819   10 years Jari Häkkinen Migrating fix from http://dev.thep.lu.se/svndigest/changeset/1503. …
(edit) @2818   10 years Peter prefer 'if (b)' over 'if (a && b)' when 'b' is a subset of 'a'.
(edit) @2817   10 years Peter update copyright years
(edit) @2816   10 years Peter change name of function cigar => alignment
(edit) @2815   10 years Peter closes #706. Implement a generalization of SmithWaternan? and …
(edit) @2814   10 years Peter fixed docs typo
(edit) @2810   10 years Peter add missing files in r2809. refs #705
(edit) @2809   10 years Peter closes #705. Create a common interface class for average classes …
(edit) @2808   10 years Peter fixed grammar typo in docs
(edit) @2807   10 years Peter allow enable/disable silent-rules
(edit) @2806   10 years Peter avoid spurious error on OSX Tiger on which 'rm foo/.*' tries to remove …
(edit) @2805   10 years Peter avoid autoconf warnings in tests and do not delete testdir in test …
(edit) @2804   10 years Peter RNG::set_state: prefer throw on error.
(edit) @2803   10 years Peter fixed spurious test failures as well as a bug in operator+=. refs #705
(edit) @2802   10 years Peter adding documentation and tests. Remove private member count_ (not …
(edit) @2801   10 years Peter add new alias for gsl doc url
(edit) @2800   10 years Peter adding variables seed_ and count_ to make random numbers different in …
(edit) @2799   10 years Peter first version of class Averager4. refs #705
(edit) @2798   10 years Peter merge release 0.8.2 into trunk
(edit) @2793   10 years Peter mention r2792 in NEWS
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