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CHANGELOG.md

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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.

[2.1.4]

  • Add Base.print(::IO, ::Index)
  • Touch up documentation
  • Bump TranscodingStreams to 0.10

[2.1.3]

  • Add short-form show for records
  • Migrate to Automa v1
  • Drop ReTest test dep

[2.1.2]

Bugfix

  • Allow non-PHRED quality scores, such as Solexa scores, which can be negative (#104)

[2.1.0]

Bugfix

  • Fix doc examples for writer with do-syntax (#100)

[2.1.0]

Additions

  • Implement Base.copy! for FASTQRecord and FASTARecord

[2.0.1]

Bugfix

  • Fix Base.read!(::FASTQReader, ::FASTQRecord) (issue #95)

[2.0.0]

Version 2 is a near-complete rewrite of FASTX. It brings strives to provide an easier and more consistent API, while also being faster, more memory efficient, and better tested than v1.

The changes are comprehensive, but code should only need a few minor tweaks to work with v2. I recommend upgrading your packages using a static analysis tool like JET.jl.

Breaking changes

Records

  • description has changed meaning: In v1, it meant the part of the header after the '>' symbol and up until first whitespace. Now it extends to the whole header line until the ending newline. This implies the identifier is a prefix of the description.
  • header has been removed, and is now replaced by description.
  • All Record objects now have an identifier, a description and a sequence, and all FASTQRecords have a quality. These may be empty, but will not throw an error when accessing them.
  • As a consequence, all "checker" functions like hassequence, isfilled, hasdescription and so on has been removed, since the answer now is trivially "yes" in all cases.
  • identifier, description, sequence and quality now returns an AbstractString by default. Although it is an implementation detail, it uses zero-copy string views for performance.
  • You can no longer construct a record using e.g. Record(::String). Instead, use parse(Record, ::String).
  • seqlen is renamed seqsize to emphasize that it returns the data size of the sequence, not necessarily its length.

Readers/writers

  • All readers/writers now take any other arguments than the main IO as a keyword for clarity and consistency.
  • FASTQ.Writers will no longer by default modify FASTQ.Records's second header. An optional keyword forces the reader to always write/skip second header if set to true or false, but it defaults to nothing, meaning it leaves it intact.
  • FASTQ writers now can no longer fill in ambiguous bases in Records transparently, or otherwise transform records, when writing. If the user wishes to transform records, they must do it my manually calling a function that transforms the records.

Other breaking changes

  • FASTQ.Read has been removed. To subset a read, extract the sequence and quality, and construct a new Record object from these.
  • transcribe has been removed, as it is now trivial to do the same thing. It may be added in a future release with new functionality.

New features

  • Function quality_scores return the qualities of a FASTQ record as a lazy, validating iterator of PHRED quality scores.
  • New object: QualityEncoding can be used to construct custom PHRED/ASCII quality encodings. accessing quality scores uses an existing default object.
  • Readers now have a keyword copy that defaults to true. If set to false, iterating over a reader will overwrite the same record for performance. Use with care. This makes the old while !eof(reader)-idiom obsolete in favor of iterating over a reader constructed with copy=false.
  • Users can now use the following syntax to make processing gzipped readers easier: 
    Reader(GzipDecompressorStream(open(path)); kwargs...) do reader
    # stuff
end
    this is a change in BioGenerics.jl, but is guaranteed to work in FASTX.jl v2.
  • FAI (FASTX index) files can now be written as well as read.
  • FASTA files can now be indexed with the new function faidx.
  • Function extract can extract parts of a sequence from an indexed FASTA reader without loading the entire sequence into memory. You can use this to e.g. extract a small part of a large chromosome. (see #29)
  • New functions validate_fasta and validate_fastq validates if an IO is formatted validly, faster and more memory-efficiently than loading in the file.

Other changes

  • All practically useful functions and types are now exported directly from FASTX, so users don't need to prepend identifiers with FASTA. or FASTQ..
  • FASTA readers are more liberal in what formats they will accept (#73)

Removed

  • The method FASTA.sequence(::FASTA.Record) has been removed, since the auto-detection of sequence type chould not be made reliable enough.

[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 [4;1386;2550t]

1.1.0 - 2019-08-07

Added

  • Base.copyto! methods for copying record data to LongSequences.
  • FASTA.seqlen & FASTQ.seqlen for getting the length of a sequence in a record.

Changed

  • Use BioSequence.jl v2.0 or higher.
  • Use TranscodingStreams v0.9.5.

1.0.0 - 2019-06-30

Added

  • FASTA submodule.
  • FASTQ submodule.
  • User manual.
  • API reference.