Rewrite for v2 #68
Merged
Rewrite for v2 #68
Commits on Aug 9, 2022
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Bump BioSequences/BioSymbols to v3/v5 (BioJulia#66)
* Bump BioSequences/BioSymbols to v3/v5 * Bump Julia version
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Return header, identifier and desc as string views
Currently, `header`, `identifier` and `description` returns `String`, which forces needless allocations. This PR adds the dependency `StringViews`, which allows the creation of an `AbstractString` from any `AbstractVector{UInt8}`. The aforementioned functions now return these string views backed by a view into the data buffer. -
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Make identifier and header always return a string
Rename FASTQ.FASTQRead to FASTQ.Read
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Apply suggestions from code review
Co-authored-by: Ciarán O'Mara <[email protected]>
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This returns a view into the sequence part of a FASTA/FASTQ record.
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Instead of relying on the fallback implementation of iterate from BioGenerics, make the Readers carry their own Record object which is being read into when iterated. A new keyword argument `copy` of the Readers then control if the internal Record or a copy is yielded on iteration. This simplifies the current while-loop idiom for efficiently iterating over records in an IO, while also speeding up copied iteration
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Remove apparently unneeded BioGenerics
I'm not 100% sure what BioGenerics really does. I can see the idea of having abstract types for readers/writers, and have kept these. But the basic methods like sequence and isfilled doesn't seem to do anything. I've removed them.
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Do not allow > in FASTA sequence
This allows detecting if two records have been concatenated erroneously
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Add quality(String, record, part)
This is used when displaying the string to avoid future errors when a valid FASTQ record's quality cannot be decoded. This would occur if we change the default quality encoding
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Make quality return string views like other accessors
New function quality_scores now return a generator of decoded PHRED scores.
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Allow constructing FASTQ with string quality
Add constructor covering `Record(::String, ::String, ::String)`.
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Commits on Aug 10, 2022
Commits on Aug 13, 2022
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