source: trunk/yat

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Diff Rev Age Author Log Message
(edit) @3068   9 years Peter Fixes #766 Replace #defines HAVE_BAM_H (and friends) in …
(edit) @3066   9 years Peter add missing doxygen @since tags
(edit) @3065   9 years Peter improve docs
(edit) @3064   9 years Peter improve variable name for clearer doc
(edit) @3062   9 years Peter implement copy and assignment (compiler generated does not compile …
(edit) @3061   9 years Peter mention that copy and assignment are not thread safe
(edit) @3060   9 years Peter add typedefs value_type and size_type to converge towards STL containers.
(edit) @3058   9 years Peter fix docs typo
(edit) @3057   9 years Peter New class: multithread safe queue
(edit) @3056   9 years Peter fixes #764: throw if region in BamReadIterator? is invalid
(edit) @3055   9 years Peter closes #746. New function BamRead::name(1)
(edit) @3052   9 years Peter remove empty line
(edit) @3048   9 years Peter avoid cassert in header file
(edit) @3047   9 years Peter add missing Id tag
(edit) @3046   9 years Peter include boost_exception_ptr.h in copyright update
(edit) @3045   9 years Peter fixes #762. workaround for broken boost header (in v1.41)
(edit) @3044   9 years Peter unpatched boost header file. refs #762
(edit) @3032   9 years Peter refs #746. Simplify cigar function using logic similar to sequence(2). …
(edit) @3031   9 years Peter new function BamRead::sequence(2). refs #746
(edit) @3030   9 years Peter refs #746. avoid false positive throws
(edit) @3029   9 years Peter refs #746. Add docs and throw in aux_del if tag is absent (rather than …
(edit) @3028   9 years Peter functions to access, append, and remove aux field. refs #746
(edit) @3027   9 years Peter don't mention cigar in docs when function is called alignment
(edit) @3026   9 years Peter add function to modify a base quality (BamRead?). refs #746
(edit) @3025   9 years Peter implement tTest::p_right(). closes #689
(edit) @3024   9 years Peter fixes #755
(edit) @3023   9 years Peter closes #754. ROC::area() is now const
(edit) @3018   9 years Peter merge patch release 0.10.2 into trunk
(edit) @3007   9 years Peter actually deprecate ROC::p_value_one_sided(). refs #689
(edit) @3006   9 years Peter deprecate ROC::p_value, first versions of p_left and p_right (refs …
(edit) @3005   9 years Peter refs #689. Deprecate PearsonCorrelation::p_value_one_sided. Replace it …
(edit) @3004   9 years Peter refs #689. Deprecate Fisher::one_sided_p; implement Fisher::left_p and …
(edit) @3002   9 years Peter closes #686
(edit) @3001   9 years Peter simplify docs
(edit) @2999   9 years Peter closes #739. Two new functions in BamHeader?: tid(string) and parse_region.
(edit) @2998   9 years Peter New class KolmogorovSmirnovOneSample?. closes #686
(edit) @2995   9 years Peter closes #741. New class MergeIterator?
(edit) @2994   9 years Peter new class BamReadFilter?. closes #738
(edit) @2993   9 years Peter conform GPL header to same style as in other yat files
(edit) @2992   9 years Peter set svndigest:ignore proprty to reflect when files were initially …
(edit) @2990   9 years Peter always install bam headers, but #error out noisily if included when …
(edit) @2989   9 years Peter speedup BamRead::cigar for case when size is not modified.
(edit) @2988   9 years Peter bam1_seq_seti was not defined in samtools 0.1.18. This workarounds …
(edit) @2986   9 years Peter merge 0.10-stable branch into trunk
(edit) @2985   9 years Peter refs #746. added function to modify one element in sequence
(edit) @2983   9 years Peter fixes #751. throw if OutBamFile::write fails
(edit) @2980   9 years Peter add syntax-check rule (included in maintainer-check), add two missing …
(edit) @2978   9 years Peter fix docs typos
(edit) @2966   9 years Jari Häkkinen Includes needed in openSUSE 12.2
(edit) @2964   9 years Peter prefer quoting like 'this' and not like `this'
(edit) @2963   9 years Peter closes #472. Defaut constructors in compose functors.
(edit) @2960   9 years Peter merge patch release 0.10.1 into trunk
(edit) @2949   9 years Peter comments describing defines from bam.h
(edit) @2943   9 years Peter merge release 0.10 into trunk
(edit) @2932   9 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2919   9 years Peter update copyright years
(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) @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) @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) @2881   10 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2879   10 years Peter split function that splits on several chars
(edit) @2874   10 years Peter remove namespace bam. bam stuff will be put in omic namespace instead. …
(edit) @2867   10 years Peter A log2 function similar to std::log10.
(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) @2858   10 years Peter closes #725
(edit) @2857   10 years Peter closes #726
(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) @2824   10 years Peter remove intermediate libraries. Makefiles in corresponding …
(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'.
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