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.
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.
No TaxIds stored in this test.
| 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
uint64and serialized in 8 Bytes. - b K-mers file is compressed in gzip format by default,
users can switch on global option
-C/--no-compressto output non-compressed file. - c One k-mer is encoded as
uint64and 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
--canonicalis ON when runningunikmer count.
Please open an issue to report bugs, propose new functions or ask for help.
This package was originally maintained in unikmer.
The magic number of binary format is still .unikmer for keeping compatibility.