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Diff Rev Age Author Log Message
(edit) @2928   9 years Peter Support different styles of including bam header files: <bam.h>, …
(edit) @2927   9 years Peter remove old core dumps in test prologue (to avoid accumulation of …
(edit) @2926   9 years Jari Häkkinen Added missing include
(edit) @2925   9 years Peter let bam files depend on Makefile to 1) regenerate bam files when rules …
(edit) @2924   9 years Peter cater for older samtools without support for '-o' switch
(edit) @2923   9 years Jari Häkkinen Adding missing include
(edit) @2922   9 years Peter mention samtools and zlib in README.
(edit) @2921   9 years Peter bump version to 0.11pre
(edit) @2920   9 years Peter New stable branch for 0.10.x
(edit) @2919   9 years Peter update copyright years
(edit) @2918   9 years Peter prepare new stable release 0.10
(edit) @2917   9 years Peter bump version to 0.9.3pre
(edit) @2916   9 years Peter merge patch release 0.9.2 into trunk. Ignore changes in …
(edit) @2915   9 years Peter tagging version 0.9.2
(edit) @2914   9 years Peter setting release date
(edit) @2913   9 years Peter Preparing release 0.9.2
(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) @2885   9 years Peter fixes #728
(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) @2860   9 years Peter mention configure options '--with-boost-thread' and …
(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) @2855   9 years Peter revert r2829 for m4 boost macros because it depends on tool tac, which …
(edit) @2854   9 years Peter bump version to 0.9.2pre
(edit) @2853   9 years Peter merge patch release 0.9.1 into trunk
(edit) @2852   9 years Peter tagging version 0.9.1
(edit) @2851   9 years Peter ensure that we build docs within mc_installcheck as installcheck now …
(edit) @2850   9 years Peter mention current version in list of libtool numbers
(edit) @2849   9 years Peter update copyright years
(edit) @2848   9 years Peter Preparing release 0.9.1
(edit) @2847   9 years Peter Fixes #724. Adding another test for NeedlemanWunsch?. Fix bug in NW …
(edit) @2846   9 years Peter Merged r2845 into 0.9.x branch and marked alignment.test as XFAIL. …
(edit) @2845   9 years Peter Extend test for NeedlemanWunsch? and check alignment score between …
(edit) @2844   9 years Peter add test for #723 and implement a fix. Fixes #723
(edit) @2843   9 years Peter fixes #722
(edit) @2842   9 years Peter remove todo doxygen tags
(edit) @2841   9 years Peter fixes #721. fix install-html-local rule and add a install-check rule …
(edit) @2840   9 years Peter bump version to 0.9.1pre
(edit) @2839   9 years Peter add missing '.' as we want version number A.B.C rather than A.BC
(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) @2836   9 years Peter tagging version 0.9
(edit) @2835   9 years Peter spell out 0.9 rather than intruction template A.B
(edit) @2834   9 years Peter update release date
(edit) @2833   9 years Peter fixes #720
(edit) @2832   9 years Peter Preparing release 0.9
(edit) @2831   9 years Peter remove debug code
(edit) @2830   9 years Peter add link tests with boost. closes #719
(edit) @2829   9 years Peter upgrade to latest AX version. backport r2825
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