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Diff Rev Age Author Log Message
(edit) @2960   9 years Peter merge patch release 0.10.1 into trunk
(edit) @2959   9 years Peter tagging version 0.10.1
(edit) @2958   9 years Peter prepare release 0.10.1
(edit) @2957   9 years Peter update copyright years
(edit) @2956   9 years Peter update NEWS
(edit) @2955   9 years Peter refs #736. Fix creation of yat.pc
(edit) @2954   9 years Peter fixes #733 and #736. Do not link -lbam into libyat.la, but do mention …
(edit) @2953   9 years Peter implement BamHeader::target_length(). fixes #740
(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) @2947   9 years Peter #define/#undef HAVE_SAMTOOL_BAM_H in config_public.h.in and remove …
(edit) @2946   9 years Peter avoid duplication
(edit) @2945   9 years Peter avoid warning from Automake
(edit) @2944   9 years Peter bumping version to 0.10.1pre
(edit) @2943   9 years Peter merge release 0.10 into trunk
(edit) @2942   9 years Peter tagging version 0.10
(edit) @2941   9 years Peter correct typo
(edit) @2940   9 years Peter update copyright years
(edit) @2939   9 years Peter Prepare 0.10 release
(edit) @2938   9 years Peter unset some make variables in tests. fixes #731
(edit) @2937   9 years Peter improve doc
(edit) @2936   9 years Peter avoid repeating code
(edit) @2935   9 years Peter avoid multiple calls to join_all (and underlying join) which might be …
(edit) @2934   9 years Peter check that compiled and linked versions are the same
(edit) @2933   9 years Peter avoid transfer exception between threads. Print as early as possible. …
(edit) @2932   9 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2931   9 years Peter add test that configure --without-samtools within maintainer-check
(edit) @2930   9 years Peter fix typo and ensure directory exists bfore creating file in it.
(edit) @2929   9 years Peter add EXIT_SKIP macro. make test compile also --without-samtools
(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
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