v11: Chunk Fasta files in parallel with components

[josiahseaman]

Depends on: (pangenome/odgi#88)
component_segmentation read in single FASTA file. It chunks up FASTA in parallel with component dividers and assigns corresponding names for (graph-genome/Schematize#17)

[josiahseaman]

• Start with FASTA mockup file.
• Get sequence out of the bin file, from fresh odgi

partitions, bin2file_mapping = schematic.split(args.cells_per_file) is a good place to start.

• Final output: FASTA files, correlate to chunk boundaries. One FASTA for every chunk.json
• start and stop bin should be in the fasta header and filename is chunk05.fasta

[josiahseaman]

@mandosoft Thomas is working on this issue.

[josiahseaman]

Bin math: Bin 0 is a reserved meaning. Biologists count nucleotide index starting at 1, not 0. That means with bin width 1,000, position 1 -1,000 is in bin 1. Target position X is in Bin label ceil(X /1,000). Fasta position in file (0 indexed) for Bin Y = [(Y - 1) * 1,000 : Y * 1,000] non-inclusive of the last nucleotide (default behavior in Python and Javascript). Nucleotide Index Z for Pangenome is Fasta[Z-1].