Runs the native, streaming bascet minhash-fq command directly on each
TIRP shard (one array job task per shard). Unlike the old BascetMapCell
based path, this never materialises a whole cell's reads in memory, so it is
safe for wildly uneven (e.g. MDA) cells.
Usage
BascetComputeMinhash(
bascetRoot,
inputName = "filtered",
outputName = "minhash",
kmerSize = 31,
numMinhash = 1000,
numThreads = NULL,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard (a TIRP file)
- outputName
Name of output shard
- kmerSize
The KMER size for the hashing (1..32)
- numMinhash
Number of minhashes (features) kept per cell
- numThreads
Number of minhash worker threads. Default is the runner CPU count
- overwrite
Force overwriting of existing files. The default is to do nothing if files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance