libsequence changelog

Changelog History

• v1.9.8 Changes

  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 Changes

  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 Changes

  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 Changes

  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 Changes

  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 Changes

  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 Changes

  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 Changes

  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 Changes

  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.