.uniq v5

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This package provides k-mer serialization methods for the package kmers,
TaxIds of k-mers are optionally saved, while there’s no frequency information.

This package is used in project unikmer and kmcp.

Details

K-mers (represented in uint64 in RAM ) are serialized in 8-Byte
(or less Bytes for shorter k-mers in compact format,
or much less Bytes for sorted k-mers) arrays and
optionally compressed in gzip format with extension of .unik.

TaxIds are optionally stored next to k-mers with 4 or less bytes.

Compression rate comparison

No TaxIds stored in this test.

cr.jpg

label encoded-kmera gzip-compressedb compact-formatc sortedd comment
plain plain text
gzip gzipped plain text
unik.default gzipped encoded k-mers in fixed-length byte array
unik.compat gzipped encoded k-mers in shorter fixed-length byte array
unik.sorted gzipped sorted encoded k-mers
  • a One k-mer is encoded as uint64 and serialized in 8 Bytes.
  • b K-mers file is compressed in gzip format by default,
    users can switch on global option -C/--no-compress to output non-compressed file.
  • c One k-mer is encoded as uint64 and serialized in 8 Bytes by default.
    However few Bytes are needed for short k-mers, e.g., 4 Bytes are enough for
    15-mers (30 bits). This makes the file more compact with smaller file size,
    controled by global option -c/--compact .
  • d One k-mer is encoded as uint64, all k-mers are sorted and compressed
    using varint-GB algorithm.
  • In all test, flag --canonical is ON when running unikmer count.

License

MIT License

History

This package was originally maintained in unikmer.

The magic number of binary format is still .unikmer for keeping compatibility.

GitHub

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