source: trunk

Revision Log Mode:


Legend:

Added
Modified
Copied or renamed
Diff Rev Age Author Log Message
(edit) @3555   5 years Peter fix indentation and avoid long lines
(edit) @3554   5 years Peter remove ws
(edit) @3553   5 years Peter reactivate concept assert
(edit) @3552   5 years Peter remove ws
(edit) @3551   5 years Peter improve docs
(edit) @3550   5 years Peter Update copyright years. Happy New Year
(edit) @3549   5 years Peter improve docs English
(edit) @3548   5 years Peter The concept 'Distance' now requires that operator() works on iterator …
(edit) @3547   5 years Peter refs #803; use boost iterator concepts in qQuantileNormalizer.
(edit) @3546   5 years Peter prefer using constructor rather empty construction + std::copy
(edit) @3545   5 years Peter remove ws
(edit) @3544   5 years Peter refs #803. use boost iterator categories in normalizer::Gauss
(edit) @3543   5 years Peter refs #803. use boost iterator categories in normalizer::Spearman
(edit) @3542   5 years Peter fix sort_index so it works with iterators that are …
(edit) @3541   5 years Peter refs #803; use boost iterator concepts in Centralizer and Zscore
(edit) @3540   5 years Peter refs #871 and #873
(edit) @3539   5 years Peter docs
(edit) @3538   5 years Peter convenience classes for archetypes of data iterators
(edit) @3537   5 years Peter remove trailing ws
(edit) @3536   5 years Peter remove a trailing space
(edit) @3535   5 years Peter docs: clarify that functions can be private; refs #871
(edit) @3534   5 years Peter move test::weighted_iterator_archetype to …
(edit) @3533   5 years Peter prefer scoped_array, which is more appropriate in this context, and …
(edit) @3532   5 years Peter Distance base class; refs #871
(edit) @3531   5 years Peter remove ws
(edit) @3530   5 years Peter refs #803. use new iterator concept in AveragerPairWeighted?
(edit) @3529   5 years Peter refs #803. use new iterator concept in AveragerPair?
(edit) @3528   5 years Peter refs #803. use new iterator concept in AveragerWeighted?
(edit) @3527   5 years Peter refs #803. use new iterator concept in Averager
(edit) @3526   5 years Peter prefer boost traits classes rather than std or accessing ::value_type …
(edit) @3525   5 years Peter improve docs
(edit) @3524   5 years Peter remove ws
(edit) @3523   5 years Peter refs #803. use new iterator concepts. Require forward traversal and …
(edit) @3522   5 years Peter refs #803. In Histogram no need to require forrward iterator but allow …
(edit) @3521   5 years Peter refs #803 In WeightIterator? and DataIterator? require that BASE models …
(edit) @3520   5 years Peter fix docs typo
(edit) @3519   5 years Peter remove trailing ws
(edit) @3518   5 years Peter refs #803; let std::random_shuffle do the concept check
(edit) @3517   5 years Peter Use boost iterator concepts (refs #803); avoid two loops in …
(edit) @3516   5 years Peter fix recent typo in Codon::amino_acid_long
(edit) @3515   5 years Peter docs
(edit) @3514   5 years Peter refs #803. relax requirement for Smoother so it works with …
(edit) @3513   5 years Peter remove ws
(edit) @3512   5 years Peter TukeyWeight? same requirement as mad. refs #803
(edit) @3511   5 years Peter Reduce requirement on Percentiler (and functions that use Percentiler: …
(edit) @3510   5 years Peter doc type requirements. refs #803
(edit) @3509   5 years Peter concept checks in MergeIterator?. refs #803
(edit) @3508   5 years Peter make thread assignment operator thread safe in Queue and PriorityQueue?
(edit) @3507   5 years Peter refs #865 and refs #803. Concept checks for binary_weight.
(edit) @3506   5 years Peter refs #803. require readable iterator rather than input iterator.
(edit) @3505   5 years Peter closes #864; yat-config: do not filter out duplicated flags
(edit) @3503   5 years Peter It's confusing to have variable name 'boost_version' as it's not …
(edit) @3502   5 years Peter Avoid static variables. fixes #860.
(edit) @3501   5 years Peter remove training spaces
(edit) @3500   5 years Peter change README to reflect that we accept samtools v1.2 (again)
(edit) @3499   5 years Peter extend test. refs #803
(edit) @3498   5 years Peter remove trailing spaces
(edit) @3497   5 years Peter move tests for htslib and samtools into file 'm4/yat_check_htslib.m4' …
(edit) @3496   5 years Peter only use samtools executable, if samtools 1.3 (or newer) is available
(edit) @3495   5 years Peter copy change r3494 into trunk manually (as code is different in trunk …
(edit) @3493   5 years Jari Häkkinen Relaxing test accuracy to pass test on my mac.
(edit) @3492   5 years Peter mention Samtools in header
(edit) @3491   5 years Peter use consistently 'false' to indicate samtools is missing (not 'no')
(edit) @3490   5 years Peter extend spaces for sort_index (refs #803).
(edit) @3489   5 years Peter remove spaces
(edit) @3488   5 years Peter add function compare_3way(segment, element)
(edit) @3487   5 years Peter add function amino_acid_long
(edit) @3486   5 years Peter remove commented code
(edit) @3485   5 years Peter linking against libbam is deprecated; it still works, but users are …
(edit) @3484   5 years Peter implement InBamFile? functions mapped, unmapped, and n_no_coordinate …
(edit) @3483   5 years Peter reject older samtools executable (0.1.19 and older)
(edit) @3482   5 years Peter docs
(edit) @3481   5 years Peter fix PP conditionals so code compiles against libbam
(edit) @3480   5 years Peter missing includes
(edit) @3479   5 years Peter docs
(edit) @3478   5 years Peter assert on memory failures
(edit) @3477   5 years Peter add functionality to access which RG IDs that are present in a BamHeader?
(edit) @3476   5 years Peter remove created fasta file with 'make clean'
(edit) @3475   5 years Peter closes #859 New class handling Fasta files that have an index file …
(edit) @3474   5 years Peter no need to clean things we no longer create
(edit) @3473   5 years Peter put back dirstamp dependency which was accidentally removed in …
(edit) @3472   5 years Peter generate sorted bam file directly from unsorted sam file; skip …
(edit) @3471   5 years Peter merge r3470 into trunk
(edit) @3469   5 years Peter New class for NegativeHyperGeometric?. closes #857. The implementation …
(edit) @3467   5 years Peter add VectorMutable? assignment operator to the API (using already …
(edit) @3466   5 years Peter closes #842. Document how to combine compose_f_gx_hy, PairFirst?, and …
(edit) @3465   5 years Peter closes #856
(edit) @3464   5 years Peter implementing idxstats functions against libhts. refs #852
(edit) @3463   5 years Peter fixes #855
(edit) @3462   6 years Peter add function to reverse an Aligner::Cigar
(edit) @3461   6 years Peter docs
(edit) @3460   6 years Peter prefer boost:: traits (rather than std::), clarify that iterators must …
(edit) @3459   6 years Peter utility::WeightedIterator? is now always tagged as …
(edit) @3458   6 years Peter some functions to do compiler tests on iterators.
(edit) @3457   6 years Peter remove ws
(edit) @3456   6 years Peter docs: add missing word
(edit) @3455   6 years Peter update copyright years
(edit) @3454   6 years Peter closes #838
(edit) @3453   6 years Peter closes #839 Simplify code by looping over different cblas …
(edit) @3452   6 years Peter fix typo, leftover from mother code
Note: See TracRevisionLog for help on using the revision log.