source: trunk/yat/omic

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Diff Rev Age Author Log Message
(edit) @4113   4 months Peter fix docs typo
(edit) @4089   5 months Peter updating copyright years
(edit) @4060   9 months Peter prefer throw_with_nested, when info in the caught expression makes …
(edit) @4057   10 months Peter closes #798; new classes BamPairBuffer? and a more general SortedBuffer?.
(edit) @4056   10 months Peter docs: fix typo and add clarification
(edit) @4041   12 months Peter avoid constructing temporary substring just for comparison
(edit) @4040   12 months Peter speed-up; prefer move instead of copy
(edit) @4025   13 months Peter add move constructor for BamPair?
(edit) @4021   14 months Peter closes #961. Improve message in thrown exceptions.
(edit) @4019   15 months Peter merge 0.18 into trunk
(edit) @4011   15 months Peter Use std smart pointers instead of boost. Prefer initialisation of …
(edit) @3999   16 months Peter update copyright years
(edit) @3996   16 months Peter prefer std smart pointers
(edit) @3991   17 months Peter new constructor in GenomicPosition?
(edit) @3970   18 months Peter explain what position is when inside an insertion
(edit) @3969   18 months Peter docs typo
(edit) @3955   18 months Peter use std::move and friend rather than internal macro (since we can …
(edit) @3938   19 months Peter let configure fail if compiler is not a C++11 compiler. …
(edit) @3920   20 months Peter to handle ALT being <ID> string access to VCFHeader is needed and …
(edit) @3919   20 months Peter alt=* is not an SNV
(edit) @3916   20 months Peter avoid incrementing read if it's being removed on the next line. Get …
(edit) @3913   21 months Peter prefer new PP macro YAT_HAVE_HTSLIB. Deprecated macro YAT_HAVE_LIBBAM …
(edit) @3905   21 months Peter docs: add missing since tag
(edit) @3891   22 months Peter fixes #933
(edit) @3889   22 months Peter closes #941
(edit) @3887   22 months Peter detect error from faidx_fetch_seq in ::fetch rather thasn in function …
(edit) @3883   23 months Peter remove support for building against libbam (which allows us to remove …
(edit) @3881   23 months Peter correct PP guard names
(edit) @3880   23 months Peter In c++11 std::multiset<T>::erase(1) takes an ::iterator, whereas in …
(edit) @3878   23 months Peter New class BamPairIterator2 that takes a sort range of bam reads as …
(edit) @3875   2 years Peter merge release 0.17 into trunk
(edit) @3870   2 years Peter merge changes from 0.17-stable branch
(edit) @3855   2 years Peter updating copyright statements
(edit) @3843   2 years Peter refer to yat's wrapper functions rather than underlying libbam/htslib …
(edit) @3840   2 years Peter merge release yat-0.16.2 into trunk
(edit) @3823   3 years Peter Merge release 0.16 into trunk
(edit) @3809   3 years Peter fixes #925
(edit) @3802   3 years Peter closes #918. implement function Pileup::size
(edit) @3801   3 years Peter implement reverse iterator in Pileup. closes #919
(edit) @3792   3 years Peter update copyright years
(edit) @3790   3 years Peter refs #905. Add functionality to access Info.
(edit) @3789   3 years Peter refs #905. Avoid #include; prefer forward declaration.
(edit) @3774   3 years Peter implement VcfIterator?. refs #905
(edit) @3773   3 years Peter add function in VcfFile? to read next VCF; refs #905
(edit) @3772   3 years Peter improve docsin VCF; refs #905
(edit) @3771   3 years Peter refs #905; improve docs of VcfFile?; fix so object can be re-opened; …
(edit) @3770   3 years Peter remove dead declarations
(edit) @3765   3 years Peter add missing include; refs #905
(edit) @3764   3 years Peter fix compilation in c++98; use boost::scoped_ptr instead of shared_ptr, …
(edit) @3762   3 years Peter a first version of new class VcfFile?; refs #905
(edit) @3760   3 years Peter Fix compiler problems with c++98 compiler. Declare functor privately …
(edit) @3759   3 years Peter refs #905. New class, VcfCompare?, to compare to VCF objects used e.g. …
(edit) @3758   3 years Peter adjust license text to be same as in other files
(edit) @3757   3 years Peter adjust license text to be same as in other files
(edit) @3756   3 years Peter adjust license text to be same as in other files
(edit) @3755   3 years Peter adjust license text to be same as in other files
(edit) @3754   3 years Peter adjust license text to be same as in other files
(edit) @3753   3 years Peter adjust license text to be same as in other files
(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
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