config

type Config struct {
	// the config file's version
	Version string `mapstructure:"version"`

	// the cost of each Gibson Assembly
	GibsonAssemblyCost float64 `mapstructure:"gibson-assembly-cost"`

	// the cost of time for each Gibson Assembly
	GibsonAssemblyTimeCost float64 `mapstructure:"gibson-assembly-time-cost"`

	// the cost per bp of synthesized DNA as a fragment (as a step function)
	SyntheticFragmentCost map[int]SynthCost `mapstructure:"synthetic-fragment-cost"`

	// the cost per bp of synthesized clonal DNA  (delivered in a plasmid)
	SyntheticPlasmidCost map[int]SynthCost `mapstructure:"synthetic-plasmid-cost"`

	// the maximum number of fragments in the final assembly
	FragmentsMaxCount int `mapstructure:"fragments-max-count"`

	// the minimum homology between this fragment and the net one
	FragmentsMinHomology int `mapstructure:"fragments-min-junction-length"`

	// maximum length of homology between two adjacent fragments in bp
	FragmentsMaxHomology int `mapstructure:"fragments-max-junction-length"`

	// maximum allowable hairpin melting temperature (celcius)
	FragmentsMaxHairpinMelt float64 `mapstructure:"fragments-max-junction-hairpin"`

	// the cost per bp of primer DNA
	PcrBpCost float64 `mapstructure:"pcr-bp-cost"`

	// the cost of each PCR reaction
	PcrRxnCost float64 `mapstructure:"pcr-rxn-cost"`

	// the cost of time for each PCR reaction
	PcrTimeCost float64 `mapstructure:"pcr-time-cost"`

	// PcrMinLength is the minimum size of a fragment (used to filter BLAST results)
	PcrMinLength int `mapstructure:"pcr-min-length"`

	// the maximum primer3 score allowable
	PcrPrimerMaxPairPenalty float64 `mapstructure:"pcr-primer-max-pair-penalty"`

	// the maximum length of a sequence to embed up or downstream of an amplified sequence
	PcrPrimerMaxEmbedLength int `mapstructure:"pcr-primer-max-embed-length"`

	// PcrPrimerMaxOfftargetTm is the maximum tm of an offtarget, above which PCR is abandoned
	PcrPrimerMaxOfftargetTm float64 `mapstructure:"pcr-primer-max-ectopic-tm"`

	// PcrBufferLength is the length of buffer from the ends of a match in which
	// to allow Primer3 to look for a primer
	PcrBufferLength int `mapstructure:"pcr-buffer-length"`

	// minimum length of a synthesized piece of DNA
	SyntheticMinLength int `mapstructure:"synthetic-min-length"`

	// maximum length of a synthesized piece of DNA
	SyntheticMaxLength int `mapstructure:"synthetic-max-length"`
}

type SynthCost struct {
	// whether it's a fixed or variable cost
	Fixed bool `mapstructure:"fixed"`

	// the cost (either per bp or for the whole stretch)
	Cost float64 `mapstructure:"cost"`
}