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Diff Rev Age Author Log Message
(edit) @3162   8 years Peter refs #778. samwrite returns -1 if file is closed, so correct code to …
(edit) @3161   8 years Peter fix docs so doxygen can parse correctly
(edit) @3160   8 years Peter closes #775
(edit) @3159   8 years Peter fixed docs typo
(edit) @3158   8 years Peter improve docs for BamHeader?
(edit) @3157   8 years Peter NEWS: record that GetlineIterator? constructor is declared explicit …
(edit) @3156   8 years Peter update copyright years
(edit) @3155   8 years Peter fixes #777. Make doxygen ignore internal stuff
(edit) @3154   8 years Peter Happy New 2014
(edit) @3153   8 years Peter document OstreamIterator? closes #770
(edit) @3152   8 years Peter add missing source file. refs #770
(edit) @3151   8 years Peter implement OstreamIterator? refs #770
(edit) @3150   8 years Peter test that BamWriteIterator? fulfills requirements defined in …
(edit) @3149   8 years Peter change test_output_iterator: there is requirement that output …
(edit) @3148   8 years Peter remove white-space
(edit) @3147   8 years Peter add missing public
(edit) @3146   8 years Peter fixed docs
(edit) @3145   8 years Peter bumping version to 0.11.2pre
(edit) @3144   8 years Peter merge patch release 0.11.1 into trunk
(edit) @3143   8 years Peter tagging version 0.11.1
(edit) @3142   8 years Peter prepare release
(edit) @3141   8 years Peter record bug #776 in NEWS
(edit) @3140   8 years Peter fixes #776 a bug in function BamHeader::tid
(edit) @3139   8 years Peter improve docs
(edit) @3138   8 years Peter change name of class and implement function llr(). closes #769
(edit) @3137   8 years Peter closes #772. new function that calculates mutual information
(edit) @3136   8 years Peter fix docs and remove WS
(edit) @3135   8 years Peter add function that calculates entropy from a range
(edit) @3134   8 years Peter refs #769 skeleton for new class LoglikelihoodRatioTestBinomial? (not …
(edit) @3133   8 years Peter yat-config: mention that YAT_CBLAS_LIB is overideable; doxygen docs: …
(edit) @3132   8 years Peter move ReleaseProcedure to file README.developer
(edit) @3131   8 years Peter bump version to 0.11.1pre
(edit) @3130   8 years Peter merge release 0.11 into trunk
(edit) @3129   8 years Peter tagging version 0.11
(edit) @3128   8 years Peter prepare 0.11 release
(edit) @3127   8 years Peter update copyright years
(edit) @3126   8 years Jari Häkkinen Relaxing requirement on autoconf, tests passes with 2.63
(edit) @3125   8 years Peter try <bam.h> before <bam/bam.h>
(edit) @3124   8 years Peter avoid using m4_map_args_w, which doesn't work with autoconf 2.63
(edit) @3123   8 years Peter turn off test that linking against a static lib when creating a …
(edit) @3122   8 years Peter define libdir directly rather than via prefix
(edit) @3121   8 years Peter always abort if command fails
(edit) @3120   8 years Jari Häkkinen Fixing disambiguity of -i option om mac (on mac a of another option …
(edit) @3119   8 years Jari Häkkinen Removing html code disrupting crosslink with doxygen 1.8.5 on my mac.
(edit) @3118   8 years Peter convenient targets for releaser
(edit) @3117   8 years Peter Bump version to 0.12pre
(edit) @3116   8 years Peter New stable branch for 0.11.x series
(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) @3097   8 years Peter bumping version to 0.10.4pre
(edit) @3096   8 years Peter tagging version 0.10.3
(edit) @3095   8 years Peter Prepare release 0.10.3
(edit) @3094   8 years Peter update copyright years
(edit) @3093   8 years Peter implement replace(3), which fixes #768
(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   8 years Peter add missing doxygen @since tags
(edit) @3065   8 years Peter improve docs
(edit) @3064   8 years Peter improve variable name for clearer doc
(edit) @3063   8 years Peter add another test for new class Queue
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