v2.0.5

BioSequences v2.0.5

Diff since v2.0.4

Merged pull requests:

• hotfix for reverse_complementing a slice of a longseq (#111) (@cjprybol)

v2.0.4

BioSequences v2.0.4

Diff since v2.0.3

v2.0.3

BioSequences v2.0.3

Diff since v2.0.2

Merged pull requests:

• Fixup addition with a BitIndex (#108) (@benjward)

v2.0.2

BioSequences v2.0.2

Diff since v2.0.1

Closed issues:

• Faster random LongSequence{NucleicAcidAlphabet{4}} generation (#77)

Merged pull requests:

• Support LTS (#101) (@CiaranOMara)
• Fix reverse_complement orphan bug (#104) (@jakobnissen)
• Use stable RNG (take two) (#106) (@jakobnissen)
• Add StableRNGs Compat entry (#107) (@kescobo)

v2.0.1

BioSequences v2.0.1

Diff since v2.0.0

v2.0.0

BioSequences v2.0.0

Diff since v1.1.0

Closed issues:

• Change Varargs to vectors or array (#24)
• Further generalise the bitparallel counting code (#27)
• map(f, seq) raises an exception (#58)
• Test Issue (#60)
• FASTA.Reader doesn't recognize the correct alphabet with ambiguous sites (#64)

Merged pull requests:

• Fix sequence search docs (#51) (@ivirshup)
• Rename types in BioSequences (#53) (@benjward)
• Add unsafe_setindex for more Base.setindex methods (#54) (@benjward)
• Reworked random LongSequence generation (#55) (@jakobnissen)
• Move and generalise sequence transformation methods (#56) (@benjward)
• SkipmerFactory (#57) (@benjward)
• Remove IO submodules (#62) (@benjward)
• Project TOML file (#63) (@benjward)
• Performance improvement to minhash (#67) (@harryscholes)
• Version 2 Changes (#69) (@benjward)

More performance, more methods!

This release improves the performance of iterating over kmers in sequences, and adds methods for the translate function for more sequence types. Indexing ABIF files has also been fixed.

The Julia v0.7 / v1.0 release

v1.0.0

Fixup documentation

Bug fix for `sequence` method of FASTA Records

Previously if the user did not specify that the version of sequence they wanted came from the FASTA namespace (which is not always possible if writing generic code to work with any record reader type we offer), then a version of sequence which does type prediction would always be used, resulting in highly type unstable code, puzzling to some first time BioJulia users. This fixes that so as the sequence type can be specified, allowing type-stable efficient code generation.

Bugfix release for FASTA.Writer

This release fixes a bug present in FASTA.Record writing where the width parameter of a FASTA.Writer is less than or equal to zero.