All Versions
9
Latest Version
Avg Release Cycle
121 days
Latest Release
414 days ago

Changelog History

  • v1.9.8

    June 18, 2019
    • ♻️ 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.
  • v1.9.7

    April 01, 2019

    🛠 A bug in l-Haf from #53 was fixed. Thanks to Alex Nater for spotting that.

    🗄 The library compiles on OS X again, which required that the path names for deprecated summary stats be changed.

  • v1.9.6

    November 06, 2018
    • 🛠 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
  • v1.9.5

    September 13, 2018
    • 👌 Support for slices of VariantMatrix and AlleleCountMatrix. PR49
    • Faster summary statistic calculation. PR46 PR47 PR48
    • Added Sequence::is_different_matrix. PR45
    • 🛠 Fixed a bug in Sequence::label_haplotypes.PR44
  • v1.9.4

    August 02, 2018

    A major step towards 2.0

    • Summary statistics can now be calculated from a VariantMatrix.
      PR33 PR36
    • 👀 More feature deprecation. See Issue 21.
    • 🚚 Dependency on TBB removed. PR38
    • 🚚 Dependency on zlib removed. PR39
  • v1.9.3

    July 12, 2018
    • ♻️ 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 includes the following GitHub PRs: #11, #12, #13, #14, #15, #25, #26, #30, #31, and #32.

  • v1.9.2

    October 16, 2017

    🚀 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.

  • v1.9.1

    April 19, 2017
    • 🚚 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
  • v1.9.0

    October 24, 2016
    • 🛠 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.