Versions in this module Expand all Collapse all v1 v1.0.1 Feb 16, 2017 v1.0.0 Jan 5, 2017 Changes in this version + const BlockCost + const DiffCost + const MatchCost + const MaxIGap + const RMatchCost + const SameCost + var DefaultLength = 400 + var DefaultMinIdentity = 0.94 + var MaxAvgIndexListLen = 15.0 + var MaxKmerLen = 15 + var MinWordLength = 4 + var TubeOffsetDelta = 32 + type Contig string + func (c Contig) Description() string + func (c Contig) End() int + func (c Contig) Len() int + func (c Contig) Location() feat.Feature + func (c Contig) Name() string + func (c Contig) Start() int + func (c Contig) String() string + type Feature struct + From int + ID string + Loc feat.Feature + Pair *Pair + To int + func (f *Feature) Description() string + func (f *Feature) End() int + func (f *Feature) Len() int + func (f *Feature) Location() feat.Feature + func (f *Feature) Mate() *Feature + func (f *Feature) Name() string + func (f *Feature) Start() int + func (f *Feature) String() string + type Logger interface + Print func(v ...interface{}) + Printf func(format string, v ...interface{}) + type PALS struct + DPParams *dp.Params + FilterParams *filter.Params + func New(target, query *linear.Seq, selfComp bool, m *morass.Morass, tubeOffset int, ...) *PALS + func (p *PALS) Align(complement bool) (dp.Hits, error) + func (p *PALS) AlignFrom(traps filter.Trapezoids, complement bool) (dp.Hits, error) + func (p *PALS) AvgIndexListLength(filterParams *filter.Params) float64 + func (p *PALS) BuildIndex() error + func (p *PALS) CleanUp() error + func (p *PALS) MemRequired(filterParams *filter.Params) uintptr + func (p *PALS) Optimise(minHitLen int, minId float64) error + func (p *PALS) Share(m *PALS) + func (p *PALS) Trapezoids() filter.Trapezoids + type Packed struct + type Packer struct + func NewPacker(id string) *Packer + func (pa *Packer) FinalisePack() *Packed + func (pa *Packer) Pack(seq *linear.Seq) (string, error) + type Pair struct + A *Feature + B *Feature + Error float64 + Score int + Strand seq.Strand + func ExpandFeature(f *gff.Feature) (*Pair, error) + func NewPair(target, query *Packed, hit dp.Hit, comp bool) (*Pair, error) + func (fp *Pair) String() string + type PairFilter func(*Pair) bool + type Pile struct + From int + Images []*Feature + Loc feat.Feature + Strand seq.Strand + To int + func (p *Pile) Description() string + func (p *Pile) End() int + func (p *Pile) Len() int + func (p *Pile) Location() feat.Feature + func (p *Pile) Name() string + func (p *Pile) Start() int + func (p *Pile) String() string + type Piler struct + LogFreq int + Logger *log.Logger + func NewPiler(overlap int) *Piler + func (p *Piler) Add(fp *Pair) error + func (p *Piler) Piles(f PairFilter) []*Pile + type Writer struct + func NewWriter(w io.Writer, prec, width int, header bool) *Writer + func (w *Writer) Write(pair *Pair) (n int, err error)