SeqAn3 design decisions

Modules

Documents on high-level design decisions in certain modules:

• Argument Parser seqan3/argument_parser
• Alphabet seqan3/alphabet
• ranges
  • Containers seqan3/containers
• Alignment seqan3/alignment
  • core
  • pairwise
  • pairwise (Myers)
  • multiple
  • score
• find
• graph
• search
• Indexes seqan3/index
• Input/Output seqan3/io
  • stream tokenisation, virtual_stream
  • Sequence (Fasta, Fastq...)
  • Alignment (SAM/BAM/CRAM, Blast)
  • Structure (vienna)
  • annotation (GTF, GFF...)

Drafts for new modules:

• Align module

External Submodules

• SDSL

Specifications

• I/O
  • Tokenization -- Specification of Tokenization
  • Stream -- Streams in SeqAn3