source: trunk

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Diff Rev Age Author Log Message
(edit) @3115   8 years Peter Prepare 0.11-stable branch
(edit) @3114   8 years Peter update copyright years
(edit) @3113   8 years Peter change YAT_USE_LIBTOOL_[PUSH|POP] so it only affects the linking tests …
(edit) @3112   8 years Peter In tests issue configure with --disable-shared/--disable-static if yat …
(edit) @3111   8 years Peter refs #737 configure.ac: Define new variables YAT_LIBS, …
(edit) @3110   8 years Peter Fix test of YAT_LT_LINK_IFELSE. The macro/linking worked also against …
(edit) @3109   8 years Peter correct dependency
(edit) @3108   8 years Peter Fix spurious test failure in yat_m4_with_bam_test.sh. Previously the …
(edit) @3107   8 years Peter avoid default make rule in test because it might be problamtic with …
(edit) @3106   8 years Peter fix typo in comment
(edit) @3105   8 years Peter upgrade to autoconf-archive-2013-11-01
(edit) @3104   8 years Peter allow construction of view into zero-sized Vector.
(edit) @3103   8 years Peter avoid compiler warning (-Wall) with gcc 4.8
(edit) @3102   8 years Peter avoid code duplication
(edit) @3101   8 years Peter remove forward declaration not needed (class matrix was renamed almost …
(edit) @3100   8 years Peter SKIP test when shared or static libs is not available
(edit) @3099   8 years Peter make rule for bams silent when in silent mode
(edit) @3098   8 years Peter merge release 0.10.3 into trunk
(edit) @3092   8 years Peter correct docs
(edit) @3091   8 years Peter add test for libz and libbam. refs #737
(edit) @3090   8 years Peter prefer using autoconf macro to create source file as it will include …
(edit) @3089   8 years Peter quote $2 in case expansion contains spaces
(edit) @3088   8 years Peter avoid repetetive code and add tests for boost libs. refs #737
(edit) @3087   8 years Peter refs #737. check if -lgsl is suitable for libtool archive
(edit) @3086   8 years Peter add a new variable YAT_STATIC_LIBS; perform test if LIBM is suitable …
(edit) @3085   8 years Peter fix problem that YAT_CBLAS_LIB were not subtracted from …
(edit) @3084   8 years Peter improve docs
(edit) @3083   8 years Peter avoid extra newlines
(edit) @3082   8 years Peter new compose functor: compose_f_gx_hx
(edit) @3081   8 years Peter make BamReadFilter? an adaptable functor by inheriting from …
(edit) @3080   8 years Peter improve erro message
(edit) @3079   8 years Peter throw if creating bam_header fails, e.g. if file is not a bam. fixes #767
(edit) @3078   8 years Peter quote filename in exception message
(edit) @3077   8 years Peter improve docs
(edit) @3076   8 years Peter remove todo doxygen tag
(edit) @3075   8 years Peter avoid full path in header
(edit) @3074   8 years Peter improve exception message; and prefer initialize ostringstream as …
(edit) @3073   8 years Peter improve docs and send clean up message to log (rather than stdout).
(edit) @3072   8 years Peter prefer aborting directly when error is detected rather than in the …
(edit) @3071   8 years Peter prefer operator = rather than ==
(edit) @3070   8 years Peter improve docs and clean up output files. closes #759
(edit) @3069   8 years Peter New macro YAT_LT_LINK_LA_IFELSE that tests if we can use code and LIBS …
(edit) @3068   8 years Peter Fixes #766 Replace #defines HAVE_BAM_H (and friends) in …
(edit) @3067   8 years Peter prefer sending people to mailinglist rather than trac as the latter …
(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) @3063   9 years Peter add another test for new class Queue
(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) @3059   9 years Peter add test that we can modify data() and weight() elements via …
(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) @3054   9 years Peter fetch flags directly from yat-config as variables YAT_* might be …
(edit) @3053   9 years Peter refs #757. new macro linking against bam stuff in libyat
(edit) @3052   9 years Peter remove empty line
(edit) @3051   9 years Peter simplify code
(edit) @3050   9 years Peter prefer including as <config.h> rather than "config.h"
(edit) @3049   9 years Peter fix typo in error message in sc_config_h rule
(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) @3043   9 years Peter avoid using deprecated functions in test
(edit) @3042   9 years Peter make rules for samtools more silent-rules friendly
(edit) @3041   9 years Peter fix distcheck issues
(edit) @3040   9 years Peter create build rule for test shared lib. closes #761
(edit) @3039   9 years Peter avoid building static when static is disabled which might indicate …
(edit) @3038   9 years Peter refs #761. added make rule to create static library
(edit) @3037   9 years Peter make shell tests work in VPATH build
(edit) @3036   9 years Peter common_defs does two things: 1) init test scripts 2) defines some …
(edit) @3035   9 years Peter allow test to require 'shared' in shell tests
(edit) @3034   9 years Peter fix bug that libtool tags were not expanded correctly
(edit) @3033   9 years Peter remove trailing white-space
(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
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