.uniq v5
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.
| 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.
License
History
This package was originally maintained in unikmer.
The magic number of binary format is still .unikmer for keeping compatibility.
