[ANN] BioJulia: CIGARStrings.jl

Package Announcements
1

I’m pleased to announce the latest BioJulia package: CIGARStrings.jl.
This is a small package used to parse Concise Idiosyncratic Gapped Alignment Reports, or, CIGAR strings, for short. CIGARs are a notation for writing a pairwise alignment, and are used in the SAM, GFA and PAF formats.

BioAlignments.jl already contains a CIGAR parser, but the one in CIGARStrings.jl may be preferable for several reasons:

  • The CIGAR isn’t heap allocated, but is a view into memory, and can therefore be constructed from a view into the same buffer used to parse the file containing the CIGAR. This package is generally faster
  • The CIGARStrings.jl package is better documented (I think)
  • The package has recoverable errors which is useful for parsing.

I’ve just registered the package, but since this package is nascent, based on feedback, I’m okay with releasing a breaking version 0.2 soon after release.

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