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This crate provides the command line interface for fireflow.

It currently only supports a subset of features provided by the full Rust interface (and other wrappers such as Python).

Supported features:

  • reading HEADER and TEXT as JSON blobs
  • exporting DATA as a TSV stream
  • raw and standard mode
  • most repair flags
  • dumping the spillover or compensation matrices
  • dumping the measurement keywords as a table

Installation

This is not yet available on crates.io so it must be built locally. Ensure cargo is installed and run the following:

clone https://github.com/usnistgov/fireflow
cd fireflow/crates/fireflow-cli
cargo install --path .

Ensure $PATH includes $CARGO_HOME/bin.

Now fireflow can be invoked from any shell.

Examples

fireflow by default will only read an FCS file if it follows the standard perfectly.

However, flags may be provided which can repair most deviations. Pass --help for any subcommand (header, raw, std, etc) depicted below to see available flags.

Show the header

For a pristine file:

fireflow header -i <path/to/file>

For a file with a DATA segment which is has an end offset one greater than it should be (which will be beyond the length of the file and thus trigger an error):

fireflow header -i <path/to/file> --data-correction-end=-1

Show the TEXT segment in raw mode

For a pristine file:

fireflow raw -i <path/to/file>

For a file which doesn't use escaped delimiters (which also likely means some keyword values are empty):

fireflow raw -i <path/to/file> --use-literal-delims --allow-empty

If successful, this will output the keywords (split by standard and non-standard) as written in TEXT, along with some miscellaneous data from parsing (such as the delimiter).

Show the TEXT segment in standardized mode

For a pristine file:

fireflow std -i <path/to/file>

For a file which "lies" about its version (HEADER says 3.0 but should say 3.1).

fireflow std -i <path/to/file> --version-override=3.1

This will output a JSON object with the keywords neatly decomposed into primitive types and arranged hierarchically (for example, $TR will have two fields for name and threshold, measurements will be arranged in an array, the data layout will be a separate array, etc). The exact structure is version-specific.

Show the DATA segment

For now, this requires reading TEXT in standardized mode (in theory raw is also possible but not supported yet).

For a pristine file:

fireflow data -i <path/to/file>

For a file which has the wrong value for $TOT:

fireflow data -i <path/to/file> --allow-tot-mismatch

This will output the DATA segment as a tab-separated value stream to stdout with $PnN as the headers.

Show the measurements as a table

This will print all measurement keywords as a table, where each row is a measurement and each column is a measurement keyword (ie $Pn*).

fireflow measurements -i <path/to/file>

Show compensation or spillover matrix

Depending on version, this will print the value(s) for the $DFCmTOn keywords (2.0), the $COMP keyword (3.0), or the $SPILLOVER keyword (3.1+).

fireflow spillover -i <path/to/file>