source: trunk/yat/omic

Revision Log Mode:


Legend:

Added
Modified
Copied or renamed
Diff Rev Age Author Log Message
(edit) @3752   3 years Peter adjust license text to be same as in other files
(edit) @3750   3 years Peter refs #905. Adding class VcfHeader? handling the header section in a VCF …
(edit) @3747   3 years Peter new class for an VCF entry; behaviour of default construction still …
(edit) @3733   4 years Peter convenience functions to access strand of alignment
(edit) @3732   4 years Peter one more convenience function to access BamRead::flag; refs #827 and r3731
(edit) @3731   4 years Peter added functions to access and modify bits in flag; closes #827
(edit) @3727   4 years Peter add output operator for Fasta::Sequence
(edit) @3704   4 years Peter update copyright years
(edit) @3703   4 years Peter docs typo
(edit) @3702   4 years Peter update copyright years
(edit) @3700   4 years Peter improve docs
(edit) @3698   4 years Peter merge release 0.14.4 into trunk
(edit) @3693   4 years Peter clarify exception message
(edit) @3692   4 years Peter OutBamFile::what() was set to 'IO_error: '; change to clarify that …
(edit) @3691   4 years Peter always declare move constructors with noexcept unless constructor may …
(edit) @3682   4 years Peter update copyright years
(edit) @3674   4 years Peter add function to create bam index file
(edit) @3672   4 years Peter for convenience add constructor that creates an iterator that iterates …
(edit) @3661   5 years Peter update copyright years
(edit) @3647   5 years Peter docs typo
(edit) @3646   5 years Peter docs
(edit) @3636   5 years Peter merge 0.14.3 into trunk
(edit) @3631   5 years Peter fix leftover compiler warnings against htslib v1.4
(edit) @3630   5 years Peter Avoid compiler warnings when compiling against HTSLIB 1.4. In struct …
(edit) @3628   5 years Peter merge release 0.14.2 into trunk
(edit) @3600   5 years Peter move constructor aand assignmnet for BamHeader?; refs #878
(edit) @3599   5 years Peter document BamHeader::read_group_iterator. closes #879
(edit) @3596   5 years Peter move constructor and assignment in MatrixWeighted?. Remove declaration …
(edit) @3584   5 years Peter remove include not needed
(edit) @3583   5 years Peter move constructor and move assignment for omic::BamRead?; refs #878
(edit) @3579   5 years Peter merge release 0.14 into trunk
(edit) @3573   5 years Peter fixes #861; throw if allocation fails
(edit) @3550   5 years Peter Update copyright years. Happy New Year
(edit) @3533   5 years Peter prefer scoped_array, which is more appropriate in this context, and …
(edit) @3520   5 years Peter fix docs typo
(edit) @3517   5 years Peter Use boost iterator concepts (refs #803); avoid two loops in …
(edit) @3516   6 years Peter fix recent typo in Codon::amino_acid_long
(edit) @3502   6 years Peter Avoid static variables. fixes #860.
(edit) @3487   6 years Peter add function amino_acid_long
(edit) @3484   6 years Peter implement InBamFile? functions mapped, unmapped, and n_no_coordinate …
(edit) @3481   6 years Peter fix PP conditionals so code compiles against libbam
(edit) @3480   6 years Peter missing includes
(edit) @3479   6 years Peter docs
(edit) @3478   6 years Peter assert on memory failures
(edit) @3477   6 years Peter add functionality to access which RG IDs that are present in a BamHeader?
(edit) @3475   6 years Peter closes #859 New class handling Fasta files that have an index file …
(edit) @3464   6 years Peter implementing idxstats functions against libhts. refs #852
(edit) @3463   6 years Peter fixes #855
(edit) @3439   6 years Peter merge release 0.13 into trunk
(edit) @3423   6 years Peter merge from 0.13-stable branch. Avoid compiler warnings also in trunk.
(edit) @3417   7 years Peter updating copyright statements
(edit) @3415   7 years Peter refs #794 Change logic in configure test looking for libhts/samtools …
(edit) @3412   7 years Peter throw exception rather than returnining empty string when ID or KEY is …
(edit) @3411   7 years Peter remove confusing reference to samtools API
(edit) @3410   7 years Peter add two new functions read_group and program_group to access data in …
(edit) @3409   7 years Peter refs #817. Fix bug that struct was not updated in text(1) function (in …
(edit) @3408   7 years Peter Implement functions to get/set free text in BamHeader?. As setting the …
(edit) @3400   7 years Peter refs #794 Deprecate configure option --without-samtools and add new …
(edit) @3398   7 years Peter refs #794 Global arrays bam_nt16_stable and bam_nt16_rev_table in …
(edit) @3395   7 years Peter closes #830. New function that calculates alignment_score of a bam …
(edit) @3384   7 years Peter closes #826
(edit) @3380   7 years Peter document how to access size of CIGAR array.
(edit) @3363   7 years Peter improve docs. refs #794
(edit) @3362   7 years Peter avoid temp variable. refs #794
(edit) @3361   7 years Peter remove superfluous namespace
(edit) @3360   7 years Peter update copyright years
(edit) @3359   7 years Peter fix issues in OutBamFile::write. refs #794
(edit) @3358   7 years Peter fix how to read from a hts_itr_t. refs #794
(edit) @3357   7 years Peter refs #794. implement open and close functions
(edit) @3355   7 years Peter refs #794. implement BamRead::end() and BamRead::sequence() correctly …
(edit) @3353   7 years Peter refs #794. First version that compiles against htslib. Alibi …
(edit) @3352   7 years Peter implement BamHeader? against htslib, except parse region which requires …
(edit) @3351   7 years Peter make BamRead? compile with htslib. refs #794
(edit) @3350   7 years Peter Make configure htslib aware. Header detection changed to look for …
(edit) @3336   7 years Peter closes #816
(edit) @3335   7 years Peter closes #806
(edit) @3334   7 years Peter Avoid stopping at position one passed a pile, instead fast forward to …
(edit) @3333   7 years Peter correct docs. refs #806
(edit) @3332   7 years Peter In Pileup store reads in a std::list (rather than std::deque) to allow …
(edit) @3330   7 years Peter update copyright years
(edit) @3329   7 years Peter new class CigarIterator? that can be used to (surprise) iterate over a …
(edit) @3328   7 years Peter avoid temporary variables; prefer initialization. refs #806
(edit) @3327   7 years Peter redefine Pileup::const_iterator so it avoids reads that do not overlap …
(edit) @3326   7 years Peter use same variable name (p) in docs as in argument list
(edit) @3325   7 years Peter new functions phred and phred_inv that calculate phred scaled …
(edit) @3324   7 years Peter grammar in comment
(edit) @3323   7 years Peter prefer strcmp over generic std::equal
(edit) @3317   7 years Peter refs #806 add test for Pileup class
(edit) @3310   7 years Peter a first version of new class Pileup. refs #806
(edit) @3306   7 years Peter merge ptach release 0.12.1 into trunk
(edit) @3295   8 years Peter merge release 0.12 into trunk
(edit) @3252   8 years Peter avoid split in Codon
(edit) @3212   8 years Peter move Cigar defines to a separate file
(edit) @3210   8 years Peter update copyright years
(edit) @3202   8 years Peter make Cigar work also without bam.h, refs #785. #define YAT_CIGAR_ etc …
(edit) @3199   8 years Peter fixes #790
(edit) @3198   8 years Peter refs #790. Prefer checking (in configure) whether boost work rather …
(edit) @3197   8 years Peter refs #790. workaround for old boost
(edit) @3193   8 years Peter document limitation due to bug in boost 1.48 (or older)
(edit) @3191   8 years Peter avoid compiler error (with gcc 4.4.6).
Note: See TracRevisionLog for help on using the revision log.