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Avg Release Cycle
121 days
Latest Release
1719 days ago

Changelog History

  • v1.9.8 Changes

    June 18, 2019
    • ๐Ÿ”จ Refactor VariantMatrix to manage memory via Sequence::GenotypeCapsule and Sequence::PositionCapsule
    • ๐Ÿ Windows of VariantMatrix objects now do not require copies, and instead use Sequence::NonOwningGenotypeCapsule and Sequence::NonOwningPositionCapsule.
    • ๐Ÿ›  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 Changes

    April 01, 2019

    ๐Ÿ›  A bug in l-Haf from #53 was fixed. Thanks to Alex Nater for spotting that.

    ๐Ÿ—„ The library compiles on OS X again, which required that the path names for deprecated summary stats be changed.

  • v1.9.6 Changes

    November 06, 2018
    • ๐Ÿ›  Fix GitHub issue PR50 via PR51.
    • โž• Added very efficient overload of Sequence::nsl. PR51 and PR52
    • โœ… 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.
    • โž• Added Sequence::lhaf. PR53
    • Include Sequence/variant_matrix/msformat.hpp when installing the library.
    • ๐Ÿ›  Fix GitHub issue 54
  • v1.9.5 Changes

    September 13, 2018
    • ๐Ÿ‘Œ Support for slices of VariantMatrix and AlleleCountMatrix. PR49
    • Faster summary statistic calculation. PR46 PR47 PR48
    • Added Sequence::is_different_matrix. PR45
    • ๐Ÿ›  Fixed a bug in Sequence::label_haplotypes.PR44
  • v1.9.4 Changes

    August 02, 2018

    A major step towards 2.0

    • Summary statistics can now be calculated from a VariantMatrix.
      PR33 PR36
    • ๐Ÿ‘€ More feature deprecation. See Issue 21.
    • ๐Ÿšš Dependency on TBB removed. PR38
    • ๐Ÿšš Dependency on zlib removed. PR39
  • v1.9.3 Changes

    July 12, 2018
    • ๐Ÿ”จ Refactor unit tests to be much faster to compile
    • โœ‚ Remove dependency on htslib.
    • The coalescent simulation machinery is no longer compiled or installed.
    • ๐Ÿ—„ Mark a lot of code as deprecated
    • ๐Ÿง Travis CI is now Linux-only
    • โž• Add Sequence::VariantMatrix and Sequence::StateCounts

    ๐Ÿš€ This release includes the following GitHub PRs: #11, #12, #13, #14, #15, #25, #26, #30, #31, and #32.

  • v1.9.2 Changes

    October 16, 2017

    ๐Ÿš€ 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 Changes

    April 19, 2017
    • ๐Ÿšš Sequence::SeqException was removed. Exceptions from namespace std are preferred, and are easier to wrap in other languages.
    • ๐Ÿ‘ป Sequence::PolySNP::ThetaL throws exception if outrgroup not present
  • v1.9.0 Changes

    October 24, 2016
    • ๐Ÿ›  Fixed issues with Sequence::Comeron95 that made it impossible to allocate on the stack.
    • โšก๏ธ Updated threaded implementation of the l-Haf statistic to use TBB.
    • ๐Ÿ”ง 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.
    • ๐Ÿ›  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.