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scrm Version History

scrm 1.7.2

Released: 2016-04-10

Bug Fixes

  • Fixes a different bug that could occur when using the "-eI" option. The contemporaries buffer was always cleared correctly between repetitions, and could cause scrm to throw an error (#104). Thanks again to @jackkamm for reporting this bug.

scrm 1.7.1

Released: 2016-03-23

Bug Fixes

  • Fixes that bug that could lead to false results when the "-eI" option was used to include non-contemporary samples. In that case, scrm could skip the time interval between the MRCA of the contemporary samples and the time of the "-eI" event (if any), and neglect all events during that time. We recommend to repeat all simulations which used "-eI" with the updated version (#102). Thanks to @jackkamm for reporting this bug.

scrm 1.7.0

Released: 2016-02-07

New Features

  • New command line option "--transpose-segsites" that prints the segregating sites matrix with rows repesenting mutations instead of individuals. This also adds the time at which the mutation occurred as additional information (#85).

Improvements

  • scrm now throws an error when mutation or recombination rate changes have invalid sequence positions (#82).
  • The length of segments between recombinations is now always reported in non-scientific notation (#81).
  • Improved the error message when lines could not coalescence because of missing migration or negative population growth (#87).

Bug Fixes

  • Forest.coalescence_finished has not set to true after a pairwise coalescence event (#89). This had no effect on the command line version of scrm.
  • Fixes scrm's tests suite on 32 bit systems (#98).

scrm 1.6.1

Released: 2015-07-09

Bug Fixes

  • scrm had extensive memory consumption when simulating trees in large models (#79). This is now fixed, it is however no longer possible to use "-O" and "-T" at the same time.

scrm 1.6.0

Released: 2015-06-04

New Features

  • It is now possible to specify the approximation exact window in number of recombination events (#73).
  • scrm now uses a conservative approximation by default (#75).

Bug Fixes

  • Critical: Position based rates changes (-sr and -st) were only applied to the first locus. All other loci are simulated with the rates from the end of the first one (#74).
  • In large models, the Newick trees could get larger than the character limit of a C++ string. In this cases, only incomplete trees were printed (#76).

scrm 1.5.1

Released: 2015-05-18

  • Bug fix: Fixed a cache invalidation error that could lead to runs being aborted after 100k recombinations (#70). Thanks to Jerome Kelleher for report this.
  • Minor: Small updates to the documentation and citation information.

scrm 1.5.0

Released: 2015-04-07

  • New feature: Added flag "--print-model" which prints a textual representation of the demographic model for verification and debugging (#60).
  • Bug fix: When multiple population splits and/or merges occurred at the same time, only one of them affected each line while the others were ignored (#61).
  • New feature: Added support for partial population admixtures (-eps, #62).
  • In addition to using "-seed" scrm now also supports "-seeds", as ms also supports both.

scrm 1.4.1

Released: 2015-04-04

  • Bug fix: Wrong population size where calculated when migration rates changes or population splits and merges occurred in an growth period (#56)
  • Bug fix: When -es was used at time 0, scrm ran into an endless loop (#53)
  • Improvement: Added an error message when a population size is set to 0 (#52)

scrm 1.4.0

Released: 2015-03-29

  • Improved memory management (#36)
  • Added option '-p' to set number of significant digits in output (#47)
  • Switched to std::mt19937_64 as default random generator (#49)
  • Support arguments in scientific notation (#50, #51)

scrm 1.3.2

Released: 2014-12-23

  • Bug fix: Fix reproducibility problem when the large sample optimization was active (#42).

scrm 1.3.1

Released: 2014-10-23

  • Bug fix: Implement missing '-m' and '-em' arguments (#32).

scrm 1.3.0

Released: 2014-10-21

Improvements

  • Improved the autotools configuration to support more compilers and operating systems (#10, #27).
  • Changed the Oriented Forest summary statistic (#25).
  • Various minor cleanups in the code base to simplify creation of an R package containing scrm (#29).

scrm 1.2.0

Released: 2014-09-10

New Features

  • New oriented forest summary statistic as suggested by

    J. Kelleher, A.M. Etheridge, N.H. Barton (2014) Coalescent simulation in continuous space: Algorithms for large neighbourhood size, Theoretical Population Biology, Volume 95, August2014, Pages 13-23, ISSN 0040-5809, http://dx.doi.org/10.1016/j.tpb.2014.05.001.

Improvements

  • Optimized the generation of newick trees (#22) and use a buffer (#23)

scrm 1.1.0

Released: 2014-08-04

Improvements

  • Improved the handling & storage of contemporary nodes. This gives a huge performance boost if scrm is used with large sample sizes (>1000) (#20).
  • Optimized scrm for use with many populations (#20).
  • Added more automatic tests of the produced distribution of trees (#20).

scrm 1.0.0

Released: 2014-07-09

Bug fixes

  • Fixed an access to unmapped memory

scrm 1.0-beta2

Released: 2014-06-18

Improvements

  • Fix file permissions
  • Remove clang warning suppression
  • Added a man page

scrm 1.0-beta1

Released: 2014-06-02

Bug fixes:

  • Option '-es' is now ms-compatible (#16).
  • It is now possible to use 3 seeds (as in ms).

Improvements:

  • Added help and version information.
  • Small performance tweaks.

New Features

  • Added variable recombination & mutation rates

scrm 0.9-1

Bug fixes

  • Very first node in the tree was assigned to wrong population
  • The input time of "-eI" option was not scaled
  • Fixed the scaling of growth rates

scrm 0.9-0

Algorithm passes all tests now, starting explicit versioning.