deletions | additions       diff --git a/implementation.tex b/implementation.tex  index fc6d4e4..4861887 100644  --- a/implementation.tex  +++ b/implementation.tex 
...
Inconsistent or unwrapped sequence lines, spaces in headers and missing or non-standard new lines are considered non-fatal errors. Testing for these issues is optional. If they are detected the decision is made to reformat as requested, report the issue to the analyst and continue the workflow.  The script also automatically adjusts to run the minimal number of steps sufficient to fix and report format issues. If it is included in the set of QC steps then wrapping is the first format issue tested because while repairing FASTA wrapping both headers and new lines can be corrected. New lines are given priority after wrapping because while repairing new lines it is also trivial to repair headers. Finally, headers are evaluated for format issues. If an early test returns a format issue and launches a reformatting that automatically repairs any remaining format issues then Fasta-O-Matic still tests for any additional format errors in the original file. The analyst should be made aware of any unexpected All  format issues are reported in the programs logs  in case they indicate an unexpected issue with the data. Logs can be optionally color coded so that red indicates errors, yellow indicates warnings (e.g. a non-fatal issue was found and automatically reformatted) and green indicates status information. This method of logging is designed to draw the attention of the bioinformatics analyst to relevant warnings or errors even if they have grown accustomed to seeing Fasta-O-Matic output frequently.    \subsection{Workflow integration}   
...
\begin{verbatim}  filename="$(python fasta_o_matic.py -f NC_010473_mock_scaffolds.fna -o ~/out_fasta_o_matic -c)"  echo $filename  \end{verbatim}