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Better Reporting and Removal of false attL sites

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@AlisonMacFadyen AlisonMacFadyen released this 07 Apr 10:48
· 15 commits to main since this release
989d7bb

This release provides better reporting of extracted SCC elements e.g. SCC for non-mec carrying or SCC_mec_ for mec carrying. There reason for no extraction is now within a column named "failure_reason" to easily identify the reason for no extraction.

The typing report now provides the location of the mec and ccr genes, rather than simply reporting their presence.

Finally, the attL15 and attL16 search patterns have been removed, due to being false positives.