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Diff Rev Age Author Log Message
(edit) @3417   8 years Peter updating copyright statements
(edit) @3416   8 years Peter prepare 0.13-stable branch
(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) @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) @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) @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) @3392   8 years Peter refs #803. sort_index
(edit) @3391   8 years Peter document requirements in SmithWaterman?. refs #803
(edit) @3390   8 years Peter extend comment
(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) @3383   8 years Peter avoid tab in the middle of line
(edit) @3382   8 years Peter add link to yat home page in 'yat-config --help' output
(edit) @3381   8 years Peter we require Autoconf 2.64; remove workaround for older Autoconf.
(edit) @3380   8 years Peter document how to access size of CIGAR array.
(edit) @3379   8 years Peter avoid using weighted_iterator_archetype with …
(edit) @3378   8 years Peter Use latest version from git repo (patch was approved by archive managers)
(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) @3370   8 years Peter fix docs typo
(edit) @3369   8 years Peter make test compile in --without-samtools mode
(edit) @3368   8 years Peter add missing includes
(edit) @3367   8 years Peter update to autoconf-archive-2015-02-04. Note that m4/ax_append_flag.m4 …
(edit) @3366   8 years Peter prefer private variables in yat.pc. closes #808
(edit) @3365   8 years Peter Use pc from zlib and htslib when linking against those packages. …
(edit) @3364   8 years Peter describe htslib support in NEWS and README. refs #794
(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) @3356   8 years Peter refs #794. make test/pileup.cc compile with htslib
(edit) @3355   8 years Peter refs #794. implement BamRead::end() and BamRead::sequence() correctly …
(edit) @3354   8 years Peter refs #794. fix configure test so it works with htslib.
(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) @3331   8 years Peter update to autoconf-archive 2014.10.15
(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) @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
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