source: trunk/test

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Diff Rev Age Author Log Message
(edit) @3417   8 years Peter updating copyright statements
(edit) @3413   8 years Peter Prefer variable name HAVE_SAMTOOLS_EXECUTABLE instead of HAVE_SAMTOOLS …
(edit) @3412   8 years Peter throw exception rather than returnining empty string when ID or KEY is …
(edit) @3410   8 years Peter add two new functions read_group and program_group to access data in …
(edit) @3409   8 years Peter refs #817. Fix bug that struct was not updated in text(1) function (in …
(edit) @3408   8 years Peter Implement functions to get/set free text in BamHeader?. As setting the …
(edit) @3405   8 years Peter fixes #832
(edit) @3404   8 years Peter new function to reduce capacity in a vector
(edit) @3403   8 years Peter add constructor that takes compare functor
(edit) @3402   8 years Peter add interface to set priority of Scheduler::Job and make the order the …
(edit) @3401   8 years Peter refs #800 Avoid using parents and children terminologoy to describe …
(edit) @3400   8 years Peter refs #794 Deprecate configure option --without-samtools and add new …
(edit) @3399   8 years Peter closes #831; added new class PriorityQueue?.
(edit) @3395   8 years Peter closes #830. New function that calculates alignment_score of a bam …
(edit) @3394   8 years Peter remove static_test.sh. The test is identical with yat_m4_test.sh …
(edit) @3393   8 years Peter refs #803 The std::random_access_iterator promises that iterator …
(edit) @3390   8 years Peter extend comment
(edit) @3387   8 years Peter refs #803. MergeIterator?
(edit) @3384   8 years Peter closes #826
(edit) @3383   8 years Peter avoid tab in the middle of line
(edit) @3379   8 years Peter avoid using weighted_iterator_archetype with …
(edit) @3377   8 years Peter check that iterators are weighted
(edit) @3376   8 years Peter use weighted_iterator_traits in test for weighted_iterator_archetype
(edit) @3375   8 years Peter extend test
(edit) @3374   8 years Peter improve test diagnosis
(edit) @3373   8 years Peter remove empty lines
(edit) @3372   8 years Peter Fix bug in CigarIterator? that assumed BASE could be constructed from …
(edit) @3371   8 years Peter fix typo
(edit) @3369   8 years Peter make test compile in --without-samtools mode
(edit) @3365   8 years Peter Use pc from zlib and htslib when linking against those packages. …
(edit) @3360   8 years Peter update copyright years
(edit) @3359   8 years Peter fix issues in OutBamFile::write. refs #794
(edit) @3356   8 years Peter refs #794. make test/pileup.cc compile with htslib
(edit) @3348   8 years Peter Replace Scheduler::launch() with a function Scheduler::wait(). Before …
(edit) @3347   8 years Peter remove protected function Scheduler::Job::submit. refs #800.
(edit) @3346   8 years Peter first version of Scheduler class. refs #800.
(edit) @3345   8 years Peter new function SegmentSet::insert_merge(first, last). closes #818
(edit) @3344   8 years Peter new function SegmentSet::insert_merge with hint. refs #818
(edit) @3342   8 years Peter merge 0.12.2 into trunk
(edit) @3336   8 years Peter closes #816
(edit) @3330   8 years Peter update copyright years
(edit) @3329   8 years Peter new class CigarIterator? that can be used to (surprise) iterate over a …
(edit) @3327   8 years Peter redefine Pileup::const_iterator so it avoids reads that do not overlap …
(edit) @3325   8 years Peter new functions phred and phred_inv that calculate phred scaled …
(edit) @3322   8 years Peter change name of test function to more descriptive …
(edit) @3317   8 years Peter refs #806 add test for Pileup class
(edit) @3315   8 years Peter added inclusion of boost iterator_facade header. refs #803.
(edit) @3314   8 years Peter new test class: weighted_iterator_archetype. refs #803
(edit) @3313   8 years Peter Correct syntax so it works in VPATH build. Correct yat-hello source so …
(edit) @3312   8 years Peter correct lazycheck deps
(edit) @3306   8 years Peter merge ptach release 0.12.1 into trunk
(edit) @3298   8 years Peter Yates' correction in Fisher's exact test. fixes #807.
(edit) @3295   9 years Peter merge release 0.12 into trunk
(edit) @3290   9 years Peter refs #803. Correct docs and reflect that random access iterators are …
(edit) @3289   9 years Peter refs #803. use boost concepts in Spearman.
(edit) @3287   9 years Peter new function sum_weight
(edit) @3285   9 years Peter refs #803. Use boost concepts in sort_index. Make requirements more …
(edit) @3283   9 years Peter remove trailing WS
(edit) @3281   9 years Peter Using boost concepts to define requirments in Centralizer. …
(edit) @3280   9 years Peter avoid tabs on otherwise empty lines
(edit) @3273   9 years Peter refs #803. Extend iterator tests using boost concepts. For …
(edit) @3266   9 years Peter fixes #802
(edit) @3259   9 years Peter deprecated class Range. closes #786
(edit) @3255   9 years Peter removed repeat typedef
(edit) @3254   9 years Peter fixes #799
(edit) @3253   9 years Peter refs #799. get_error: don't use operator<< on Key just to create an …
(edit) @3251   9 years Peter remove WS
(edit) @3238   9 years Peter sort_index: add some compile tests, CONCEPT_ASSERTs, and add docs on …
(edit) @3236   9 years Peter BH correction on unsorted range. closes #796
(edit) @3228   9 years Peter test for YAT_HEADER_ASSERT
(edit) @3227   9 years Peter improve 'required' field. The tests use aclocal via the bootstrap …
(edit) @3213   9 years Peter three new cigar functions
(edit) @3210   9 years Peter update copyright years
(edit) @3209   9 years Peter add missing source file and fix compilation error --without-samtools
(edit) @3205   9 years Peter implement new class SmithWaterman?
(edit) @3201   9 years Peter add #define YAT_HAVE_LIBBAM to API and replace HAVE_LIBBAM accordingly.
(edit) @3200   9 years Peter implement first version of CIGAR (refs #785). Note, this revision does …
(edit) @3197   9 years Peter refs #790. workaround for old boost
(edit) @3196   9 years Peter avoid test code that won't compile with old boost.
(edit) @3194   9 years Peter add missing file. see r3173
(edit) @3190   9 years Peter new class KernelMatrix?. closes #381
(edit) @3188   9 years Peter merge patch release 0.11.2
(edit) @3177   9 years Peter Change behaviour if convert<T> and is<T> so they accept "-nan" (case …
(edit) @3175   9 years Peter new class BamPair?. refs #784
(edit) @3173   9 years Peter a first version of BamPairIterator?. refs #784
(edit) @3170   9 years Peter in yat-hello-check test that versions agree. refs #771.
(edit) @3162   9 years Peter refs #778. samwrite returns -1 if file is closed, so correct code to …
(edit) @3160   9 years Peter closes #775
(edit) @3152   9 years Peter add missing source file. refs #770
(edit) @3151   9 years Peter implement OstreamIterator? refs #770
(edit) @3150   9 years Peter test that BamWriteIterator? fulfills requirements defined in …
(edit) @3149   9 years Peter change test_output_iterator: there is requirement that output …
(edit) @3144   9 years Peter merge patch release 0.11.1 into trunk
(edit) @3138   9 years Peter change name of class and implement function llr(). closes #769
(edit) @3137   9 years Peter closes #772. new function that calculates mutual information
(edit) @3135   9 years Peter add function that calculates entropy from a range
(edit) @3134   9 years Peter refs #769 skeleton for new class LoglikelihoodRatioTestBinomial? (not …
(edit) @3130   9 years Peter merge release 0.11 into trunk
(edit) @3114   9 years Peter update copyright years
(edit) @3113   9 years Peter change YAT_USE_LIBTOOL_[PUSH|POP] so it only affects the linking tests …
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