# Specifications for the script

**Use the Nontarget**

- Clusters should have large enough number of fragments (3+ maybe)
- nontarget has a pattern match function.
- Check for chlorinated compounds (has n+2, n+4, ...)

- GPL License (good)
- Script to get output for all of the results

- tabbed-deliminated text file

- Which clusters contain chlorinated compounds, how many fragments, what other
isotopes.

## format

- Readable by R.
- Manipulatable by Tidyverse
- Include it in script?

# Additional Notes

- Independent of the ordering (it might get corrupted)
- Just search for chlorinated/brominated compounds.
- usually, use_charges will be 1
- Headers to use in script.

- Packages to do things in parallel (multiple threads)
- be able to configure the number of cores or threads used.
- make it a requirement to be tab-deliminated.

- eliminate clusters with only m/z.

# Notes

- cutint represents high enough intensity.
- mztol is in terms of ppm.
- mzfrac is in terms of absolute.
- PPM = true always