FASTX.jl Versions Save

FASTX v2.1.5

Diff since v2.1.4

Merged pull requests:

• Update issue and PR template to match BioJulia guidelines (#117) (@jakobnissen)
• Do not reach into TranscodingSteams internals (#119) (@jakobnissen)

Closed issues:

• Next release of TranscodingStreams will likely break this package (#118)

FASTX v2.1.4

Diff since v2.1.3

Merged pull requests:

• Drop ReTest test dep (#112) (@jakobnissen)
• Make documentation more approachable (#113) (@jakobnissen)
• Add Base.print(::IO, ::Index) (#114) (@jakobnissen)
• Bump TranscodingStreams to 0.10 (#116) (@jakobnissen)

Closed issues:

• Non-indexed FASTA: access sequence by genomic region (#110)

FASTX v2.1.3

Diff since v2.1.2

Closed issues:

• FASTX.Records need a single-line representation (#54)
• Multiline FASTQ records? (#78)
• Migrate to new Automa release (#82)
• ERROR: Error when parsing FASTX file. Saw unexpected byte 'C' on line 1 (#107)

Merged pull requests:

• Add short-form show for records (#106) (@jakobnissen)
• Migrate to Automa v1 (#108) (@jakobnissen)

FASTX v2.1.2

Diff since v2.1.0

Closed issues:

• package does not precompile (#101)
• Issue with QualityEncoding for the Solexa format (#104)

Merged pull requests:

• Fix doc examples for writer with do-syntax (#100) (@jakobnissen)
• Bump ScanByte (#102) (@jakobnissen)
• Fix: Allow non-PHRED quality scores e.g. Solexa (#105) (@jakobnissen)

FASTX v2.1.1

Diff since v2.1.0

Merged pull requests:

• Fix doc examples for writer with do-syntax (#100) (@jakobnissen)
• Bump ScanByte (#102) (@jakobnissen)

FASTX v2.1.0

Diff since v2.0.1

Merged pull requests:

• Migrate from SnoopPrecompile to PrecompileTools (#98) (@timholy)
• Implement copy! for records (#99) (@jakobnissen)

FASTX v2.0.1

Diff since v2.0.0

Closed issues:

• Make Documenter preview builds work. (#81)
• subset FASTX.FASTQ.Record (#89)
• Make BioSequences an optional dependency (#90)
• Reading with the iteration protocole in 2.0 (#94)
• read! doesn't work in v2.0.0? (#95)

Merged pull requests:

• Try to get preview build to work (#86) (@kescobo)
• Add SnoopPrecompile (#87) (@jakobnissen)
• Improve type stability slightly (#88) (@jakobnissen)
• Improve precompilation (#92) (@jakobnissen)
• Make BioSequences a weak dependency (#93) (@jakobnissen)
• Fix Base.read!(::Reader, ::Record) and add tests (#96) (@jakobnissen)

FASTX v2.0.0

Diff since v1.3.0

Closed issues:

• so slowly of extract sequence by coord (#29)
• Refactor tests (#37)
• Have accesor functions return views? (#56)
• Deal better with missingness (#63)
• bump compatibility for BioSymbols v5 and BioSequences v3? (#65)
• Documenter clearer that writers/readers take ownership of underlying IO (#70)
• Erratum in documentation (#71)
• Include period (.) in valid letters (#73)
• No good way to flush writers? (#77)
• Use ReTest or similar niceness? (#83)

Merged pull requests:

• Return header, identifier and desc as string views (#62) (@jakobnissen)
• Rewrite for v2 (#68) (@jakobnissen)
• Clarify that streams take ownership of IO (#72) (@jakobnissen)
• Fix missing character in docs example (#74) (@jakobnissen)
• Use ReTest (#84) (@kescobo)
• Rollup of a few changes (#85) (@jakobnissen)

FASTX v1.3.0

Diff since v1.2.0

Closed issues:

• Converting FASTQ to FASTA (#50)
• TagBot trigger issue (#51)
• Why export only a few names? (#57)
• More conservative autodetection of sequence type (#59)

Merged pull requests:

• Allow trailing whitespace in sequences (#52) (@jakobnissen)
• Transcode between FASTQ & FASTA files (#53) (@SabrinaJaye)
• Export all user-facing functions (#58) (@jakobnissen)
• Disallow record construction from anything (#60) (@jakobnissen)
• Update authors (#61) (@jakobnissen)
• Update Julia requirement to 1.6 (#64) (@jakobnissen)
• Bump BioSequences/BioSymbols to v3/v5 (#66) (@jakobnissen)
• Update TagBot.yml (#67) (@CiaranOMara)

FASTX v1.2.0

Diff since v1.1.3

[1.2.0] - 2021-07-13

Added:

• header(::Union{FASTA.Record, FASTQ.Record}) returns the full header line.
• sequence_iter(::Union{FASTA.Record, FASTQ.Record}) returns a no-copy iterator over the sequence. If the record is mutated, this iterator will be in an invalid state.
• quality_iter(::FASTQ.Record) - same as above, but for PHRED quality.
• New type FASTQRead stores the same data as a FASTQ record, but in a Julia native format instead of a ASCII-encoding byte vector. (PR #35)

Bugfixes

• Allow trailing newlines after last record of FASTA and FASTQ
• Fix parser FSM ambiguity
• Fix off-by-one error in line counting of FASTQ files
• Various small fixes to the internal parsing regex
• Writers are now parametric and buffered for increased writing speed
• Fixed a bug where Windows-style newlines would break the parser