- depcorr
float depcorr()
void depcorr(float f)
- errmod
ErrorModel errmod()
Undocumented in source. Be warned that the author may not have intended to support it.
- eta
float eta()
- eta
void eta(float f)
- findSNPs
auto findSNPs(P pileup_columns, string reference, string sample)
main method of this class
- genotypeLikelihoodInfo
GenotypeLikelihoodInfo genotypeLikelihoodInfo(C column)
- makeCall
Nullable!DiploidCall5 makeCall(C column, string reference, string sample)
Make call on a pileup column
- minimum_base_quality
ubyte minimum_base_quality()
Discard reads with base quality less than this at a site
- minimum_base_quality
void minimum_base_quality(ubyte q)
Undocumented in source. Be warned that the author may not have intended to support it.
- minimum_call_quality
float minimum_call_quality()
void minimum_call_quality(float f)
Class for calling SNPs using MAQ model.
Typical usage: auto caller = new MaqSnpCaller(); caller.minimum_call_quality = 20.0f; caller.minimum_base_quality = 13; foreach (snp; caller.findSNPs(reads)) { ... }