dump

kmtricks dump allows to dump kmtricks's file in a human readable format. It works at the file level, in kmtricks this means at partition level. If you want to work with multiple files/partitions see kmtricks aggregate.

Supported files:

• *.kmer (at kmtricks_dir/counts)
• *.hash (at kmtricks_dir/counts)
• *.count (at kmtricks_dir/matrices)
• *.count_hash (at kmtricks_dir/matrices)
• *.pa (at kmtricks_dir/matrices)
• *.pa_hash (at kmtricks_dir/matrices)
• *.hist (at kmtricks_dir/histograms)

Usage

kmtricks dump v1.0.0

DESCRIPTION
  Dump kmtricks's files in human readable format.

USAGE
  kmtricks dump --run-dir <DIR> --input <FILE> [-o/--output <FILE>] [-t/--threads <INT>] [-v/--verbose <STR>] 
                [-h/--help] [--version] 

OPTIONS
  [global]
       --run-dir - kmtricks runtime directory 
       --input   - path to file. 
    -o --output  - output file. {stdout}

  [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}

Examples

Dump counts

> kmtricks dump --input ./km_dir/counts/partition_0/D1.kmer
AAAC 2
...
CCAT 3

Dump counts matrix

> kmtricks dump --input ./km_dir/matrices/matrix_0.count
AAAC 2 5
...
CCAT 3 0

Dump histogram

> kmtricks dump --input ./km_dir/histograms/D1.hist
@LOWER=1
@UPPER=255
@OOB_L=0
@OOB_U=2452
1 150
2 80
...
255 42

kmtricks produces histograms for counts in range [lower, upper] (default is [1, 255]).

• OOB_L = sum of counts lower than lower.
• OOB_U = sum of counts greater than upper.