|
|
|
@2932
|
10 years |
Peter |
remove misleading comment as these files are no longer direct input to …
|
|
|
|
@2927
|
10 years |
Peter |
remove old core dumps in test prologue (to avoid accumulation of …
|
|
|
|
@2921
|
10 years |
Peter |
bump version to 0.11pre
|
|
|
|
@2919
|
10 years |
Peter |
update copyright years
|
|
|
|
@2918
|
10 years |
Peter |
prepare new stable release 0.10
|
|
|
|
@2916
|
10 years |
Peter |
merge patch release 0.9.2 into trunk. Ignore changes in …
|
|
|
|
@2912
|
10 years |
Peter |
docs typo
|
|
|
|
@2911
|
10 years |
Peter |
accidently included in r2910
|
|
|
|
@2910
|
10 years |
Peter |
improve docs. closes #729
|
|
|
|
@2909
|
10 years |
Peter |
avoid creating a MatrixLookupWeighted? from a Matrix as it involves …
|
|
|
|
@2908
|
10 years |
Peter |
copy tests from http://dev.thep.lu.se/svndigest code. refs #717
|
|
|
|
@2907
|
10 years |
Peter |
extend intererface with mode_t as in C api and improve docs. refs #717
|
|
|
|
@2906
|
10 years |
Peter |
New functions chdir, chmod, copy_file, fnmatch, remove, rename, and …
|
|
|
|
@2905
|
10 years |
Peter |
remove superfluous 'using'
|
|
|
|
@2904
|
10 years |
Peter |
boost concept check. refs #729
|
|
|
|
@2903
|
10 years |
Peter |
refs #729. document bam_pair_analyse
|
|
|
|
@2902
|
10 years |
Peter |
test for bam_pair_analyse. refs #729
|
|
|
|
@2901
|
10 years |
Peter |
make random generators to model adaptable Generators
|
|
|
|
@2900
|
10 years |
Peter |
remove trailing WS
|
|
|
|
@2899
|
10 years |
Peter |
function bam_pair_analyse
|
|
|
|
@2898
|
10 years |
Peter |
dox typo
|
|
|
|
@2897
|
10 years |
Peter |
prefer throwing yat::utility::runtime_error. refs #729
|
|
|
|
@2896
|
10 years |
Peter |
improve doc and remove private classes from docs
|
|
|
|
@2895
|
10 years |
Peter |
add two tests for bam functionality
|
|
|
|
@2894
|
10 years |
Peter |
fix VPATH build issues
|
|
|
|
@2893
|
10 years |
Peter |
run (also C++) tests in specific test dir so test can create temporary …
|
|
|
|
@2892
|
10 years |
Peter |
add functions mkdir, mkdir_p, basename, dirname. refs #717
|
|
|
|
@2891
|
10 years |
Peter |
check for samtools in configure; create bam file in 'make check' if we …
|
|
|
|
@2890
|
11 years |
Peter |
prefer calling base class constructor explicitly
|
|
|
|
@2889
|
11 years |
Peter |
Binomial distribution. fixes #730
|
|
|
|
@2888
|
11 years |
Peter |
add example SAM file. refs #729
|
|
|
|
@2887
|
11 years |
Peter |
docs typo
|
|
|
|
@2886
|
11 years |
Peter |
fast swap for BamRead?
|
|
|
|
@2884
|
11 years |
Peter |
add missing since tags. refs #729
|
|
|
|
@2883
|
11 years |
Peter |
New classes to wrap around functionality provided by samtools. refs #729
|
|
|
|
@2882
|
11 years |
Peter |
add --enable-assert option (in configure)
|
|
|
|
@2881
|
11 years |
Peter |
Define PP variables in config.h rather than in CPPFLAGS. Include …
|
|
|
|
@2880
|
11 years |
Peter |
update to autoconf macro archive 2012.11.14 (just serial # updated)
|
|
|
|
@2879
|
11 years |
Peter |
split function that splits on several chars
|
|
|
|
@2878
|
11 years |
Peter |
typo
|
|
|
|
@2877
|
11 years |
Peter |
prepend LIBS to achieve recommended -lgsl -lcblas -lm
|
|
|
|
@2876
|
11 years |
Peter |
avoid word enable for something that is turned off with '--without'
|
|
|
|
@2875
|
11 years |
Peter |
delete leftover comments
|
|
|
|
@2874
|
11 years |
Peter |
remove namespace bam. bam stuff will be put in omic namespace instead. …
|
|
|
|
@2873
|
11 years |
Peter |
prefer using YAT_MSG_ERROR and simplify computation of …
|
|
|
|
@2872
|
11 years |
Peter |
prefer YAT_MSG_ERROR. using it in inf test
|
|
|
|
@2871
|
11 years |
Peter |
prefer YAT_MSG_ERROR. using it in quiet_NAN test
|
|
|
|
@2870
|
11 years |
Peter |
mention samtools and zlib requirements in README
|
|
|
|
@2869
|
11 years |
Peter |
improve error messages. emove debug code. refs #729
|
|
|
|
@2868
|
11 years |
Peter |
refs #729. Add configure tests for samtools
|
|
|
|
@2867
|
11 years |
Peter |
A log2 function similar to std::log10.
|
|
|
|
@2866
|
11 years |
Peter |
remove -Werror option for automake
|
|
|
|
@2865
|
11 years |
Peter |
rename record file because file named 'conftest*' are deleted inside …
|
|
|
|
@2864
|
11 years |
Peter |
file structure and empty automake file for new bam namespace. refs #729
|
|
|
|
@2863
|
11 years |
Peter |
prefer boost::shared_ptr. refs #712
|
|
|
|
@2862
|
11 years |
Peter |
prefer boost::shared_ptr. refs #712
|
|
|
|
@2861
|
11 years |
Peter |
avoid using SmartPtr?; prefer using boost::shared_ptr. refs #712
|
|
|
|
@2859
|
11 years |
Peter |
fix boost macros to remove usage of tool 'tac' and change file pattern …
|
|
|
|
@2858
|
11 years |
Peter |
closes #725
|
|
|
|
@2857
|
11 years |
Peter |
closes #726
|
|
|
|
@2856
|
11 years |
Peter |
if test fails, skip downstream tests
|
|
|
|
@2853
|
11 years |
Peter |
merge patch release 0.9.1 into trunk
|
|
|
|
@2842
|
11 years |
Peter |
remove todo doxygen tags
|
|
|
|
@2838
|
11 years |
Peter |
merge release 0.9 into trunk
|
|
|
|
@2837
|
11 years |
Peter |
avoid ancient inclusion guards around '#include <config.h>'
|
|
|
|
@2828
|
11 years |
Peter |
fix identation
|
|
|
|
@2827
|
11 years |
Peter |
Remove -Itop_srcdir from CPPFLAGS. Automake already adds -Isrcdir to …
|
|
|
|
@2825
|
11 years |
Peter |
upgrade to autoconf macro archive 2012.09.08
|
|
|
|
@2824
|
11 years |
Peter |
remove intermediate libraries. Makefiles in corresponding …
|
|
|
|
@2823
|
11 years |
Peter |
bumping version to 0.10pre
|
|
|
|
@2821
|
11 years |
Peter |
preparing new stable branch 0.9
|
|
|
|
@2820
|
11 years |
Peter |
update copyright years
|
|
|
|
@2819
|
11 years |
Jari Häkkinen |
Migrating fix from http://dev.thep.lu.se/svndigest/changeset/1503. …
|
|
|
|
@2818
|
11 years |
Peter |
prefer 'if (b)' over 'if (a && b)' when 'b' is a subset of 'a'.
|
|
|
|
@2817
|
11 years |
Peter |
update copyright years
|
|
|
|
@2816
|
11 years |
Peter |
change name of function cigar => alignment
|
|
|
|
@2815
|
11 years |
Peter |
closes #706. Implement a generalization of SmithWaternan? and …
|
|
|
|
@2814
|
11 years |
Peter |
fixed docs typo
|
|
|
|
@2810
|
11 years |
Peter |
add missing files in r2809. refs #705
|
|
|
|
@2809
|
11 years |
Peter |
closes #705. Create a common interface class for average classes …
|
|
|
|
@2808
|
11 years |
Peter |
fixed grammar typo in docs
|
|
|
|
@2807
|
11 years |
Peter |
allow enable/disable silent-rules
|
|
|
|
@2806
|
11 years |
Peter |
avoid spurious error on OSX Tiger on which 'rm foo/.*' tries to remove …
|
|
|
|
@2805
|
11 years |
Peter |
avoid autoconf warnings in tests and do not delete testdir in test …
|
|
|
|
@2804
|
11 years |
Peter |
RNG::set_state: prefer throw on error.
|
|
|
|
@2803
|
11 years |
Peter |
fixed spurious test failures as well as a bug in operator+=. refs #705
|
|
|
|
@2802
|
11 years |
Peter |
adding documentation and tests. Remove private member count_ (not …
|
|
|
|
@2801
|
11 years |
Peter |
add new alias for gsl doc url
|
|
|
|
@2800
|
11 years |
Peter |
adding variables seed_ and count_ to make random numbers different in …
|
|
|
|
@2799
|
11 years |
Peter |
first version of class Averager4. refs #705
|
|
|
|
@2798
|
11 years |
Peter |
merge release 0.8.2 into trunk
|
|
|
|
@2793
|
11 years |
Peter |
mention r2792 in NEWS
|
|
|
|
@2792
|
11 years |
Peter |
introduced parameter mismatch in ssearch
|
|
|
|
@2790
|
11 years |
Peter |
remove useless forward declaration
|
|
|
|
@2789
|
11 years |
Peter |
adding a comment. refs #568
|
|
|
|
@2788
|
11 years |
Peter |
correct documentation
|
|
|
|
@2787
|
11 years |
Peter |
update coyright years
|
|
|
|
@2786
|
11 years |
Peter |
update README. mention boost libraries rather than specific Thread Library.
|
|
|
|
@2785
|
11 years |
Peter |
skip boost link tests if --without-boost was provided
|
|
|
|
@2784
|
11 years |
Jari Häkkinen |
Resolving precision issues on my macbook pro.
|
|
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|
