# Patternmatch

This is a short R pattern.search wrapper that takes in a CSV file containing
HRMS Peaks and prints all of the fragment numbers that may contain isotopes of one's
choosing (preferably halogenated compounds).

## Installation

The script uses the following packages:

- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget) 
(It is recommended to install this package through the devtools package)
- [enviPat](https://rdocumentation.org/packages/enviPat/versions/2.2)
- [stringr](https://www.rdocumentation.org/packages/stringr/versions/1.4.0)
- [parallel](https://www.rdocumentation.org/packages/parallel/versions/3.6.2)

Before running/configuring the script, call `make` while in the `/src`
directory or simply copy `/src/script.def.R` to `/src/script.R`.

## Configuration

All configuration variables are located at the top of the script.

## Output

The script should print a list with data for all clusters that contain the
isotopes to be searched for.

If `verbose.enable` is set to `TRUE`, files of the form `(fragment number).txt`
containing the `pattern.search` output will be printed to the directory
specified in `verbose.outputdir`, assuming the directory already exists.

## Additional Notes

As windows does not allow forking, the number of cores used on it will be
constrained to 1.