0.0.80 (2015-08-10)

  • Added multiprocessing capabilities during census step.
  • Added a simple command line interface.
  • Removed prepare-evaluate paradigm from strategies and now perform counts directly on input data in one step.
  • Skip slides (and set all counts to 0) if their end_pos falls outside of the region on that particular genome’s chromosome/contig.
  • Rename KMerCounterStrategy to MotifCounterStrategy
  • Fixed bug causing use_and to not work as expected for chromosomes not explicitly listed in the exceptions dict when also using use_chrom.
  • Support use of FASTA files which must be supplied with a samtools faidx style index.
  • Stopped supporting Python 3 due to incompatability with buffer and memoryview.
  • Prevent query from deep copying itself on return. Note this means that a query will alter the original Goldilocks object.
  • Now using a 3D numpy matrix to store counters with memory shared to support multiprocessing during census.
  • Removed StrategyValue as these cannot be stored in shared memory. This makes ratio-based strategies a bit of a hack currently (but still work...)
  • tldr; Goldilocks is at least 2-4x faster than previously, even without multiprocessing

0.0.71 (2015-07-11)

  • Officially add MIT license to repository.

  • Deprecate _filter.

  • Update and tidy examples.py.

  • is_seq argument to initialisation removed and replaced with is_pos.

  • Use is_pos to indicate the expected input is positional, not sequence.

  • Force use of PositionCounterStrategy when is_pos is True.

  • Sequence data now read in to 0-indexed arrays to avoid the overhead of string

    re-allocation by having to append a padding character to the beginning of very long strings.

  • Region metadata continues to use 1-indexed positions for user output.

  • VariantCounterStrategy now PositionCounterStrategy.

  • PositionCounterStrategy expects 1-indexed lists of positions;

    prepare populates the listed locations with 1 and then evaluate returns the sum as before.

  • test_regression2 updated to account for converting 1-index to 0-index when

    manually handling the sequence for expected results.

  • query accepts gmax and gmin arguments to filter candidate regions by the group-track value.

  • CandidateList removed and replaced with simply returning a new Goldilocks.

0.0.6 (2015-06-23)

  • Goldilocks.sorted_regions stores a list of region ids to represent the result of a sorting operation following a call to query.
  • Regions in Goldilocks.regions now always have a copy of their “id” as a key.
  • __check_exclusions now accepts a group and track for more complex exclusion-based operations.
  • region_group_lte and region_group_gte added to usable exclusion fields to remove regions where the value of the desired group/track combination is less/greater than or equal to the value of the group/track set by the current query.
  • query now returns a new Goldilocks instance, rather than a CandidateList.
  • Goldilocks.candidates property now allows access to regions, this property will maintain the order of sorted_regions if it has one.
  • export_meta now allows group=None
  • CandidateList class deleted.
  • Test data that is no longer used has been deleted.
  • Scripts for generating test data added to test_gen/ directory.
  • Tests updated to reflect the fact CandidateList lists are no longer returned by query.
  • _filter is to be deprecated in favour of query by 0.0.7

Beta (2014-10-08)

  • Massively updated! Compatability with previous versions very broken.
  • Software retrofitted to be much more flexible to support a wider range of problems.

0.0.2 (2014-08-18)

  • Remove incompatible use of print

0.0.1 (2014-08-18)

  • Initial package