Cutoff Adjustments

The consensus calculation can be tuned by changing the threshhold at which a particular base type is considered to have the 'majority'; a dash (-) is displayed when the majority is not sufficiently high. See the staden package manual for precise details on this.

An additiona quality cutoff can be applied to each base. This determines the contribution that each base makes to the consensus calculation and also the colour used when displaying bases on the screen. Bases with a quality lower than the cutoff are displayed in qualColour and qualForeground colours, as defined in the configuration Options listed above.

set_ccutoff ?value?

If value is specified the consensus cutoff is set to value. Otherwise the existing consensus cutoff value is returned without making any changes.

set_qcutoff ?value?

If value is specified the quality cutoff is set to value. Otherwise the existing quality cutoff value is returned without making any changes.