merge

kmtricks merge

kmtricks merge allows to merge equivalent counted k-mers/hashes partition(s) between samples in order to obtain matrices. It can be run only after run kmtricks pipeline --until count.

• --from kmer: build matrix from counted k-mers.

• --from hash: build matrix from counted hashes.

• --mode count: output count matrix.

• --mode pa: output membership matrix.

• --mode bf: output column-major bloom filters matrix (only with --from hash).

• --mode bft: output row-major bloom filters (only with --from hash).

• --out-format text: human readable output (only with --mode count or --mode pa).

• --out-format bin: kmtricks format output.

Usage

kmtricks merge v1.0.0

DESCRIPTION
  Merge partitions.

USAGE
  kmtricks merge --run-dir <DIR> [--partition-id <INT>] [--abundance-min <INT/STR/FLOAT>] 
                 [--recurrence-min <INT>] [--save-if <INT>] [--mode <MODE:FORMAT:OUT>] 
                 [-t/--threads <INT>] [-v/--verbose <STR>] [--clear] [--cpr] [-h/--help] 
                 [--version] 

OPTIONS
  [global]
     --run-dir        - kmtricks runtime directory. 
     --partition-id   - partition id (-1 = all partitions are processed). {-1}
     --abundance-min  - min abundance to keep a k-mer/hash, see README. {1}
     --recurrence-min - min recurrence to keep a k-mer/hash. {1}
     --share-min      - save a non-solid k-mer if it occurs in N other samples. {0}
     --mode           - matrix mode <mode:format:out>, see README {kmer:count:bin}
     --clear          - clear partition files. [⚑]
     --cpr            - output compressed matrices. [⚑]

  [common]
    -t --threads - number of threads. {8}
    -h --help    - show this message and exit. [⚑]
       --version - show version and exit. [⚑]
    -v --verbose - verbosity level [debug|info|warning|error]. {info}