Avg Release Cycle
946 days ago
- ♻️ Refactor VariantMatrix to manage memory via Sequence::GenotypeCapsule and Sequence::PositionCapsule
- 🏁 Windows of VariantMatrix objects now do not require copies, and instead use Sequence::NonOwningGenotypeCapsule and Sequence::NonOwningPositionCapsule.
- 🛠 A bug in haplotype labelling is fixed. Issue 59. Statistics like number of haplotypes, haplotype diversity, etc., were affected by this issue, but the errors were small for larger data sets.
- 🛠 Fix GitHub issue PR50 via PR51.
- ➕ Added very efficient overload of Sequence::nsl. PR51 and PR52
- ✅ PR52 added a first implementation of Sequence::nslx, a series of back-end changes to some of the summary statistic code as well as some more testing.
- ➕ Added Sequence::lhaf. PR53
- Include Sequence/variant_matrix/msformat.hpp when installing the library.
- 🛠 Fix GitHub issue 54
- ♻️ Refactor unit tests to be much faster to compile
- ✂ Remove dependency on htslib.
- The coalescent simulation machinery is no longer compiled or installed.
- 🗄 Mark a lot of code as deprecated
- 🐧 Travis CI is now Linux-only
- ➕ Add Sequence::VariantMatrix and Sequence::StateCounts
🚀 This release simplifies these calculations. There is no longer a function to standardize/bin results. Rather, a vector if (nSL/iHS/derived mutation count) tuples are returned.
- 🚚 Sequence::SeqException was removed. Exceptions from namespace std are preferred, and are easier to wrap in other languages.
- 👻 Sequence::PolySNP::ThetaL throws exception if outrgroup not present
- 🛠 Fixed issues with Sequence::Comeron95 that made it impossible to allocate on the stack.
- ⚡️ Updated threaded implementation of the l-Haf statistic to use TBB.
- 🔧 Weights on stop codons used in Grantham distance calculations is now configurable, and defaults to the max value of a double. Previous library versions arbitrarily used 999.0.
- 🛠 PolySIM::ThetaL now correctly will not include fixed differences in the calculation.
- nSL/iHS, H1, H12, H2H1, and haplotype homozygosity statistics are now calculated in parallel.
- Sequence::Disequilibrium parallelized.
- Intel's TBB is now a dependency.