v1.2.0

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

v1.1.3

FASTX v1.1.3

Diff since v1.1.2

Closed issues:

• Different slicing methods for FASTX.FASTA.sequences produces inconsistent behavior (#23)

Merged pull requests:

• Fix zero-length copy (#24) (@jakobnissen)

v1.1.2

FASTX v1.1.2

Diff since v1.1.1

Closed issues:

• Unexpected behaviour when reading FASTA files with read!(reader, record) (#13)
• LoadError: UndefVarError: LongSequence not defined during precompilation step (#19)

Merged pull requests:

• Add docs on reading gzipped files (#17) (@kescobo)
• Remove use of internal encode_copy! [DO NOT MERGE] (#18) (@jakobnissen)
• Inbounds FASTQ parser (#20) (@jakobnissen)
• Run on Julia LTS (#21) (@benjward)

v1.1.1

FASTX v1.1.1

Diff since v1.1.0

Closed issues:

• Release version 1.1 (#7)
• Reading fastq from TranscodingStream (#8)
• Bug in Reader with stream (#14)

Merged pull requests:

• Handle case where input is a TranscodingStream. (#9) (@blaiseli)
• Implement hashing and equality for Records (#10) (@harryscholes)
• Implement generic methods for commonly used functions and export them (#11) (@harryscholes)
• add FASTA.identifier(record) example in docs (#15) (@dehann)
• CompatHelper: bump compat for "Automa" to "0.8" (#16) (@github-actions[bot])

Version 1.1.0

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.

v1.0.0

v1.0.0 (2019-06-30)

Diff since b42484c5faade55b416a8a150ac76e3a2c23f1a0

Closed issues:

• Test issue (#2)