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Diff Rev Age Author Log Message
(edit) @2940   10 years Peter update copyright years
(edit) @2939   10 years Peter Prepare 0.10 release
(edit) @2938   10 years Peter unset some make variables in tests. fixes #731
(edit) @2937   10 years Peter improve doc
(edit) @2936   10 years Peter avoid repeating code
(edit) @2935   10 years Peter avoid multiple calls to join_all (and underlying join) which might be …
(edit) @2934   10 years Peter check that compiled and linked versions are the same
(edit) @2933   10 years Peter avoid transfer exception between threads. Print as early as possible. …
(edit) @2932   10 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2931   10 years Peter add test that configure --without-samtools within maintainer-check
(edit) @2930   10 years Peter fix typo and ensure directory exists bfore creating file in it.
(edit) @2929   10 years Peter add EXIT_SKIP macro. make test compile also --without-samtools
(edit) @2928   10 years Peter Support different styles of including bam header files: <bam.h>, …
(edit) @2927   10 years Peter remove old core dumps in test prologue (to avoid accumulation of …
(edit) @2926   10 years Jari Häkkinen Added missing include
(edit) @2925   10 years Peter let bam files depend on Makefile to 1) regenerate bam files when rules …
(edit) @2924   10 years Peter cater for older samtools without support for '-o' switch
(edit) @2923   10 years Jari Häkkinen Adding missing include
(edit) @2922   10 years Peter mention samtools and zlib in README.
(edit) @2921   10 years Peter bump version to 0.11pre
(edit) @2920   10 years Peter New stable branch for 0.10.x
(edit) @2919   10 years Peter update copyright years
(edit) @2918   10 years Peter prepare new stable release 0.10
(edit) @2917   10 years Peter bump version to 0.9.3pre
(edit) @2916   10 years Peter merge patch release 0.9.2 into trunk. Ignore changes in …
(edit) @2915   10 years Peter tagging version 0.9.2
(edit) @2914   10 years Peter setting release date
(edit) @2913   10 years Peter Preparing release 0.9.2
(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   11 years Peter add example SAM file. refs #729
(edit) @2887   11 years Peter docs typo
(edit) @2886   11 years Peter fast swap for BamRead?
(edit) @2885   11 years Peter fixes #728
(edit) @2884   11 years Peter add missing since tags. refs #729
(edit) @2883   11 years Peter New classes to wrap around functionality provided by samtools. refs #729
(edit) @2882   11 years Peter add --enable-assert option (in configure)
(edit) @2881   11 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2880   11 years Peter update to autoconf macro archive 2012.11.14 (just serial # updated)
(edit) @2879   11 years Peter split function that splits on several chars
(edit) @2878   11 years Peter typo
(edit) @2877   11 years Peter prepend LIBS to achieve recommended -lgsl -lcblas -lm
(edit) @2876   11 years Peter avoid word enable for something that is turned off with '--without'
(edit) @2875   11 years Peter delete leftover comments
(edit) @2874   11 years Peter remove namespace bam. bam stuff will be put in omic namespace instead. …
(edit) @2873   11 years Peter prefer using YAT_MSG_ERROR and simplify computation of …
(edit) @2872   11 years Peter prefer YAT_MSG_ERROR. using it in inf test
(edit) @2871   11 years Peter prefer YAT_MSG_ERROR. using it in quiet_NAN test
(edit) @2870   11 years Peter mention samtools and zlib requirements in README
(edit) @2869   11 years Peter improve error messages. emove debug code. refs #729
(edit) @2868   11 years Peter refs #729. Add configure tests for samtools
(edit) @2867   11 years Peter A log2 function similar to std::log10.
(edit) @2866   11 years Peter remove -Werror option for automake
(edit) @2865   11 years Peter rename record file because file named 'conftest*' are deleted inside …
(edit) @2864   11 years Peter file structure and empty automake file for new bam namespace. refs #729
(edit) @2863   11 years Peter prefer boost::shared_ptr. refs #712
(edit) @2862   11 years Peter prefer boost::shared_ptr. refs #712
(edit) @2861   11 years Peter avoid using SmartPtr?; prefer using boost::shared_ptr. refs #712
(edit) @2860   11 years Peter mention configure options '--with-boost-thread' and …
(edit) @2859   11 years Peter fix boost macros to remove usage of tool 'tac' and change file pattern …
(edit) @2858   11 years Peter closes #725
(edit) @2857   11 years Peter closes #726
(edit) @2856   11 years Peter if test fails, skip downstream tests
(edit) @2855   11 years Peter revert r2829 for m4 boost macros because it depends on tool tac, which …
(edit) @2854   11 years Peter bump version to 0.9.2pre
(edit) @2853   11 years Peter merge patch release 0.9.1 into trunk
(edit) @2852   11 years Peter tagging version 0.9.1
(edit) @2851   11 years Peter ensure that we build docs within mc_installcheck as installcheck now …
(edit) @2850   11 years Peter mention current version in list of libtool numbers
(edit) @2849   11 years Peter update copyright years
(edit) @2848   11 years Peter Preparing release 0.9.1
(edit) @2847   11 years Peter Fixes #724. Adding another test for NeedlemanWunsch?. Fix bug in NW …
(edit) @2846   11 years Peter Merged r2845 into 0.9.x branch and marked alignment.test as XFAIL. …
(edit) @2845   11 years Peter Extend test for NeedlemanWunsch? and check alignment score between …
(edit) @2844   11 years Peter add test for #723 and implement a fix. Fixes #723
(edit) @2843   11 years Peter fixes #722
(edit) @2842   11 years Peter remove todo doxygen tags
(edit) @2841   11 years Peter fixes #721. fix install-html-local rule and add a install-check rule …
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