source: trunk/yat

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Diff Rev Age Author Log Message
(edit) @3417   8 years Peter updating copyright statements
(edit) @3415   8 years Peter refs #794 Change logic in configure test looking for libhts/samtools …
(edit) @3414   8 years Peter fix docs typo
(edit) @3412   8 years Peter throw exception rather than returnining empty string when ID or KEY is …
(edit) @3411   8 years Peter remove confusing reference to samtools API
(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) @3407   8 years Peter typo in comment
(edit) @3406   8 years Peter docs. refs #800
(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) @3398   8 years Peter refs #794 Global arrays bam_nt16_stable and bam_nt16_rev_table in …
(edit) @3397   8 years Peter fix regression introduced in r3287 (0.13pre).
(edit) @3396   8 years Peter include CigarIterator?.h in dist
(edit) @3395   8 years Peter closes #830. New function that calculates alignment_score of a bam …
(edit) @3393   8 years Peter refs #803 The std::random_access_iterator promises that iterator …
(edit) @3392   8 years Peter refs #803. sort_index
(edit) @3391   8 years Peter document requirements in SmithWaterman?. refs #803
(edit) @3389   8 years Peter docs
(edit) @3388   8 years Peter document requirements in MergeIterator?. refs #803
(edit) @3387   8 years Peter refs #803. MergeIterator?
(edit) @3386   8 years Peter remove trailing spaces
(edit) @3385   8 years Peter refs #803
(edit) @3384   8 years Peter closes #826
(edit) @3380   8 years Peter document how to access size of CIGAR array.
(edit) @3372   8 years Peter Fix bug in CigarIterator? that assumed BASE could be constructed from …
(edit) @3370   8 years Peter fix docs typo
(edit) @3368   8 years Peter add missing includes
(edit) @3363   8 years Peter improve docs. refs #794
(edit) @3362   8 years Peter avoid temp variable. refs #794
(edit) @3361   8 years Peter remove superfluous namespace
(edit) @3360   8 years Peter update copyright years
(edit) @3359   8 years Peter fix issues in OutBamFile::write. refs #794
(edit) @3358   8 years Peter fix how to read from a hts_itr_t. refs #794
(edit) @3357   8 years Peter refs #794. implement open and close functions
(edit) @3355   8 years Peter refs #794. implement BamRead::end() and BamRead::sequence() correctly …
(edit) @3353   8 years Peter refs #794. First version that compiles against htslib. Alibi …
(edit) @3352   8 years Peter implement BamHeader? against htslib, except parse region which requires …
(edit) @3351   8 years Peter make BamRead? compile with htslib. refs #794
(edit) @3350   8 years Peter Make configure htslib aware. Header detection changed to look for …
(edit) @3349   8 years Peter avoid having a std::set just to count number of jobs. refs #800
(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) @3337   8 years Peter use better hint; remove ws
(edit) @3336   8 years Peter closes #816
(edit) @3335   8 years Peter closes #806
(edit) @3334   8 years Peter Avoid stopping at position one passed a pile, instead fast forward to …
(edit) @3333   8 years Peter correct docs. refs #806
(edit) @3332   8 years Peter In Pileup store reads in a std::list (rather than std::deque) to allow …
(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) @3328   8 years Peter avoid temporary variables; prefer initialization. refs #806
(edit) @3327   8 years Peter redefine Pileup::const_iterator so it avoids reads that do not overlap …
(edit) @3326   8 years Peter use same variable name (p) in docs as in argument list
(edit) @3325   8 years Peter new functions phred and phred_inv that calculate phred scaled …
(edit) @3324   8 years Peter grammar in comment
(edit) @3323   8 years Peter prefer strcmp over generic std::equal
(edit) @3322   8 years Peter change name of test function to more descriptive …
(edit) @3320   8 years Peter speedup. assume Distance is symmetric. closes #814
(edit) @3319   8 years Peter avoid long line
(edit) @3318   8 years Peter closes #813
(edit) @3317   8 years Peter refs #806 add test for Pileup class
(edit) @3316   8 years Peter remove trailing ws
(edit) @3310   8 years Peter a first version of new class Pileup. refs #806
(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) @3297   8 years Peter fix mess up caused in latest merge (r3295).
(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) @3288   9 years Peter add doxygen since tag
(edit) @3287   9 years Peter new function sum_weight
(edit) @3286   9 years Peter fixed docs typo
(edit) @3285   9 years Peter refs #803. Use boost concepts in sort_index. Make requirements more …
(edit) @3282   9 years Peter avoid extra tabs
(edit) @3281   9 years Peter Using boost concepts to define requirments in Centralizer. …
(edit) @3279   9 years Peter use boost_concepts requirements in random namespace. refs #803
(edit) @3278   9 years Peter use boost concept requirements in random namespace. refs #803
(edit) @3276   9 years Peter ref #803. revert part of r3273 for the same reason as explained in r3275
(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) @3258   9 years Peter correct docs of YAT_DEV_BUILD
(edit) @3257   9 years Peter added missing deprecated attribute
(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) @3252   9 years Peter avoid split in Codon
(edit) @3249   9 years Peter mention Deleter in SmartPtr? doc
(edit) @3247   9 years Peter docs: fixed typo in example code
(edit) @3245   9 years Peter avoid sorting entire range; instead let Percentiler be clever
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