Changelog¶
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Unreleased¶
v0.5.0 - 2023-07-22¶
Changed¶
Bump Cython dependency to
v3.0
.
Fixed¶
Add missing signature of
Sketch.index
to type stubs.PyPy builds failing on missing
PyInterpreterState_GetID
function.
v0.4.1 - 2022-08-20¶
Changed¶
Use lists instead of arrays to store state of
Minimizers
when pickling.Skip serialization of minimizer index to reduce total state size.
Make
Mapper.query_draft
andMapper.query_genome
return hits sorted by identity in descending order.
v0.4.0 - 2022-08-04¶
Added¶
Multi-threaded computation of fragment mapping in
Mapper.query_draft
andMapper.query_genome
.
Fixed¶
NEON-specific compile flags in
setup.py
for Aarch64 target platforms.Broken compilation for Arm platforms because of missing header guards.
v0.3.1 - 2022-07-22¶
Added¶
Slightly improve documentation in some classes.
Sphinx documentation for the project hosted on ReadTheDocs.
Links and instructions to install package from the Bioconda channel.
v0.3.0 - 2022-07-17¶
Added¶
pickle
protocol implementation toMapper
andSketch
via__getstate__
and__setstate__
.Minimizers
class to access the minimizers of aSketch
orMapper
object.
Changed¶
Make
Sketcher
andMapper
final.Prevent direct instantiation of
Mapper
objects.Update
Mapper._query_draft
to recycle memory between fragments.Vendor
Boost::math
headers (v1.79
) to allow compiling without depdendencies.
Fixed¶
Broken compilation of
_fastani
extension module asuniversal2
binaries on MacOS.
v0.2.1 - 2021-06-20¶
Fixed¶
Missing header files in the
tar.gz
distribution, preventing compilation of the wheel from source.
v0.2.0 - 2021-06-20¶
Added¶
Sketch.clear
method to remove all sequences currently in aSketch
and reset the list of minimizers.SIMD code to read and reverse-complement the input sequences efficiently on supported platforms (x86-64 with SSE2 or SSSE3, and ARM with NEON).
Changed¶
Split the
Sketch
type in two depending on whether the object is at the sketching stage (Sketch
) or at the querying stage (Mapper
).Sketch.add_genome
,Sketch.add_draft
,Mapper.query_genome
andMapper.query_draft
can now be passed a Unicode string for the sequence.
Fixed¶
Integer underflow causing minimizers out of the block window to be added to the final minimizers list.
v0.1.2 - 2021-06-15¶
Changed¶
Querying functions now release GIL to allow efficient parallel querying.
v0.1.1 - 2021-06-13¶
Fixed¶
Source distribution missing Cython and C++ sources, thus preventing compilation.
v0.1.0 - 2021-06-13¶
Initial release.