minor code cleanup, use uint64 for wavefront values

update go mod

Makefile

@@ -1,4 +1,4 @@
-.PHONY: build clean test
+.PHONY: build clean test dev-init
 
 build: clean
 	@echo "======================== Building Binary ======================="
@@ -23,4 +23,8 @@ test:
 	go tool pprof -top mem.prof
 	@rm -f mem.prof
 
-	@rm -f test.test
+	@rm -f test.test
+
+dev-init:
+	apt install minify
+	go get -t wfa/test

README.md

@@ -1,11 +1,13 @@
 # Using WFA-JS
 
-Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/tronnet/WFA-JS/releases) to your project. Add to your script:
+Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/alu/WFA-JS/releases) to your project. Add to your script:
 
 ```
 import wfa from "./wfa.js"
 await wfa("<path to wasm>")
-console.log(wfAlign(...))
+let result = wfAlign(...)
+operations = DecodeCIGAR(result.CIGAR)
+// ...
 ```
 
 Where `<path to wasm>` is the path from the site root ie. `./scripts/wfa.wasm`. This will depend on your project structure.

go.mod

@@ -1,15 +1,15 @@
 module wfa
 
-go 1.23.2
+go 1.23.6
 
 require (
-	github.com/schollz/progressbar/v3 v3.17.0
+	github.com/schollz/progressbar/v3 v3.17.1
-	golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c
+	golang.org/x/exp v0.0.0-20241108190413-2d47ceb2692f
 )
 
 require (
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
-	golang.org/x/sys v0.26.0 // indirect
+	golang.org/x/sys v0.27.0 // indirect
-	golang.org/x/term v0.25.0 // indirect
+	golang.org/x/term v0.26.0 // indirect
 )

main.go

@@ -1,7 +1,6 @@
 package main
 
 import (
-	"fmt"
 	"syscall/js"
 	wfa "wfa/pkg"
 )
@@ -15,32 +14,47 @@ func main() {
 
 func wfAlign(this js.Value, args []js.Value) interface{} {
 	if len(args) != 4 {
-		fmt.Println("invalid number of args, requires 4: s1, s2, penalties, doCIGAR")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "invalid number of args, requires 4: s1, s2, penalties, doCIGAR",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	if args[0].Type() != js.TypeString {
-		fmt.Println("s1 should be a string")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "s1 should be a string",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	s1 := args[0].String()
 
 	if args[1].Type() != js.TypeString {
-		fmt.Println("s2 should be a string")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "s2 should be a string",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	s2 := args[1].String()
 
 	if args[2].Type() != js.TypeObject {
-		fmt.Println("penalties should be a map with key values m, x, o, e")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "penalties should be a map with key values m, x, o, e",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	if args[2].Get("m").IsUndefined() || args[2].Get("x").IsUndefined() || args[2].Get("o").IsUndefined() || args[2].Get("e").IsUndefined() {
-		fmt.Println("penalties should be a map with key values m, x, o, e")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "penalties should be a map with key values m, x, o, e",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	m := args[2].Get("m").Int()
@@ -56,8 +70,11 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 	}
 
 	if args[3].Type() != js.TypeBoolean {
-		fmt.Println("doCIGAR should be a boolean")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "doCIGAR should be a boolean",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	doCIGAR := args[3].Bool()
@@ -65,8 +82,10 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 	// Call the actual func.
 	result := wfa.WFAlign(s1, s2, penalties, doCIGAR)
 	resultMap := map[string]interface{}{
+		"ok":    true,
 		"score": result.Score,
 		"CIGAR": result.CIGAR,
+		"error": "",
 	}
 
 	return js.ValueOf(resultMap)
@@ -74,12 +93,12 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 
 func DecodeCIGAR(this js.Value, args []js.Value) interface{} {
 	if len(args) != 1 {
-		fmt.Println("invalid number of args, requires 1: CIGAR")
+		println("invalid number of args, requires 1: CIGAR")
 		return nil
 	}
 
 	if args[0].Type() != js.TypeString {
-		fmt.Println("CIGAR should be a string")
+		println("CIGAR should be a string")
 		return nil
 	}
 

pkg/custom_slice.go

@@ -6,50 +6,31 @@ type PositiveSlice[T any] struct {
 	defaultValue T
 }
 
-func (a *PositiveSlice[T]) TranslateIndex(idx int) int {
-	return idx
-}
-
 func (a *PositiveSlice[T]) Valid(idx int) bool {
-	actualIdx := a.TranslateIndex(idx)
+	return 0 <= idx && idx < len(a.valid) && a.valid[idx]
-	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
 }
 
 func (a *PositiveSlice[T]) Get(idx int) T {
-	actualIdx := a.TranslateIndex(idx)
+	if 0 <= idx && idx < len(a.valid) && a.valid[idx] { // idx is in the slice
-	if 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx] { // idx is in the slice
+		return a.data[idx]
-		return a.data[actualIdx]
 	} else { // idx is out of the slice
 		return a.defaultValue
 	}
 }
 
 func (a *PositiveSlice[T]) Set(idx int, value T) {
-	actualIdx := a.TranslateIndex(idx)
+	if idx >= len(a.valid) { // idx is outside the slice
-	if actualIdx < 0 || actualIdx >= len(a.valid) { // idx is outside the slice
+		// expand data array to 2*idx
-		// expand data array to actualIdx
+		newData := make([]T, 2*idx+1)
-		newData := make([]T, 2*actualIdx+1)
 		copy(newData, a.data)
 		a.data = newData
 
-		// expand valid array to actualIdx
+		// expand valid array to 2*idx
-		newValid := make([]bool, 2*actualIdx+1)
+		newValid := make([]bool, 2*idx+1)
 		copy(newValid, a.valid)
 		a.valid = newValid
 	}
 
-	a.data[actualIdx] = value
+	a.data[idx] = value
-	a.valid[actualIdx] = true
+	a.valid[idx] = true
-}
-
-func (a *PositiveSlice[T]) Preallocate(hi int) {
-	size := hi
-
-	// expand data array to actualIdx
-	newData := make([]T, size+1)
-	a.data = newData
-
-	// expand valid array to actualIdx
-	newValid := make([]bool, size+1)
-	a.valid = newValid
 }

pkg/debug.go

@@ -1,3 +1,5 @@
+//go:build debug
+
 package wfa
 
 import (
@@ -12,11 +14,13 @@ func (w *WavefrontComponent) String(score int) string {
 	max_hi := math.MinInt
 
 	for i := 0; i <= score; i++ {
-		if w.lo.Valid(i) && w.lo.Get(i) < min_lo {
+		valid := w.W.Valid(i)
-			min_lo = w.lo.Get(i)
+		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
+		if valid && lo < min_lo {
+			min_lo = lo
 		}
-		if w.hi.Valid(i) && w.hi.Get(i) > max_hi {
+		if valid && hi > max_hi {
-			max_hi = w.hi.Get(i)
+			max_hi = hi
 		}
 	}
 
@@ -40,9 +44,7 @@ func (w *WavefrontComponent) String(score int) string {
 
 	for i := 0; i <= score; i++ {
 		s = s + "["
-		lo := w.lo.Get(i)
+		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
-		hi := w.hi.Get(i)
-		// print out wavefront matrix
 		for k := min_lo; k <= max_hi; k++ {
 			valid, val, _ := UnpackWavefrontValue(w.W.Get(i).Get(k))
 			if valid {

pkg/types.go

@@ -25,49 +25,60 @@ const (
 	End
 )
 
-// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 28 bits for the diag distance
+// bitpacked wavefront lo/hi values with 32 bits each
-// technically this restricts to solutions within 268 million score but that should be sufficient for most cases
+type WavefrontLoHi uint64
-type WavefrontValue uint32
 
-// TODO: add 64 bit packed value in case more than 268 million score is needed
+func PackWavefrontLoHi(lo int, hi int) WavefrontLoHi {
+	loBM := int64(int32(lo)) & 0x0000_0000_FFFF_FFFF
+	hiBM := int64(int64(hi) << 32)
+	return WavefrontLoHi(hiBM | loBM)
+}
+
+func UnpackWavefrontLoHi(lohi WavefrontLoHi) (int, int) {
+	loBM := int(int32(lohi & 0x0000_0000_FFFF_FFFF))
+	hiBM := int(int32(lohi & 0xFFFF_FFFF_0000_0000 >> 32))
+	return loBM, hiBM
+}
+
+// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 60 bits for the diag distance
+type WavefrontValue uint64
 
 // PackWavefrontValue: packs a diag value and traceback into a WavefrontValue
-func PackWavefrontValue(value uint32, traceback Traceback) WavefrontValue {
+func PackWavefrontValue(value uint64, traceback Traceback) WavefrontValue {
-	valueBM := value & 0x0FFF_FFFF
+	validBM := uint64(0x8000_0000_0000_0000)
-	tracebackBM := uint32(traceback&0x0000_0007) << 28
+	tracebackBM := uint64(traceback&0x0000_0007) << 60
-	return WavefrontValue(0x8000_0000 | valueBM | tracebackBM)
+	valueBM := uint64(value) & 0x0FFF_FFFF_FFFF_FFFF
+	return WavefrontValue(validBM | tracebackBM | valueBM)
 }
 
 // UnpackWavefrontValue: opens a WavefrontValue into a valid bool, diag value and traceback
-func UnpackWavefrontValue(wfv WavefrontValue) (bool, uint32, Traceback) {
+func UnpackWavefrontValue(wfv WavefrontValue) (bool, uint64, Traceback) {
-	valueBM := uint32(wfv & 0x0FFF_FFFF)
+	validBM := wfv&0x8000_0000_0000_0000 != 0
-	tracebackBM := uint8(wfv & 0x7000_0000 >> 28)
+	tracebackBM := uint8(wfv & 0x7000_0000_0000_0000 >> 60)
-	validBM := wfv&0x8000_0000 != 0
+	valueBM := uint64(wfv & 0x0000_0000_FFFF_FFFF)
 	return validBM, valueBM, Traceback(tracebackBM)
 }
 
 // Wavefront: stores a single wavefront, stores wavefront's lo value and hi is naturally lo + len(data)
 type Wavefront struct { // since wavefronts store diag distance, they should never be negative, and traceback data can be stored as uint8
 	data []WavefrontValue
-	lo   int
+	lohi WavefrontLoHi
 }
 
 // NewWavefront: returns a new wavefront with size accomodating lo and hi (inclusive)
 func NewWavefront(lo int, hi int) *Wavefront {
 	a := &Wavefront{}
-
+	a.lohi = PackWavefrontLoHi(lo, hi)
-	a.lo = lo
+	size := hi - lo
-	size := a.TranslateIndex(hi)
+	a.data = make([]WavefrontValue, size+1)
-
-	newData := make([]WavefrontValue, size+1)
-	a.data = newData
 
 	return a
 }
 
 // TranslateIndex: utility function for getting the data index given a diagonal
 func (a *Wavefront) TranslateIndex(diagonal int) int {
-	return diagonal - a.lo
+	lo := int(int32(a.lohi & 0x0000_0000_FFFF_FFFF))
+	return diagonal - lo
 }
 
 // Get: returns WavefrontValue for given diagonal
@@ -95,27 +106,17 @@ func (a *Wavefront) Set(diagonal int, value WavefrontValue) {
 
 // WavefrontComponent: each M/I/D wavefront matrix including the wavefront data, lo and hi
 type WavefrontComponent struct {
-	lo *PositiveSlice[int]        // lo for each wavefront
+	W *PositiveSlice[*Wavefront] // wavefront diag distance and traceback for each wavefront
-	hi *PositiveSlice[int]        // hi for each wavefront
-	W  *PositiveSlice[*Wavefront] // wavefront diag distance and traceback for each wavefront
 }
 
 // NewWavefrontComponent: returns initialized WavefrontComponent
-func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
+func NewWavefrontComponent() *WavefrontComponent {
 	// new wavefront component = {
 	// lo = [0]
 	// hi = [0]
 	// W = []
 	// }
-	w := WavefrontComponent{
+	w := &WavefrontComponent{
-		lo: &PositiveSlice[int]{
-			data:  []int{0},
-			valid: []bool{true},
-		},
-		hi: &PositiveSlice[int]{
-			data:  []int{0},
-			valid: []bool{true},
-		},
 		W: &PositiveSlice[*Wavefront]{
 			defaultValue: &Wavefront{
 				data: []WavefrontValue{0},
@@ -123,42 +124,27 @@ func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
 		},
 	}
 
-	w.lo.Preallocate(preallocateSize)
-	w.hi.Preallocate(preallocateSize)
-	w.W.Preallocate(preallocateSize)
-
 	return w
 }
 
 // GetVal: get value for wavefront=score, diag=k => returns ok, value, traceback
-func (w *WavefrontComponent) GetVal(score int, k int) (bool, uint32, Traceback) {
+func (w *WavefrontComponent) GetVal(score int, k int) (bool, uint64, Traceback) {
 	return UnpackWavefrontValue(w.W.Get(score).Get(k))
 }
 
 // SetVal: set value, traceback for wavefront=score, diag=k
-func (w *WavefrontComponent) SetVal(score int, k int, val uint32, tb Traceback) {
+func (w *WavefrontComponent) SetVal(score int, k int, val uint64, tb Traceback) {
 	w.W.Get(score).Set(k, PackWavefrontValue(val, tb))
 }
 
 // GetLoHi: get lo and hi for wavefront=score
 func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
-	// if lo[score] and hi[score] are valid
+	lo, hi := UnpackWavefrontLoHi(w.W.Get(score).lohi)
-	if w.lo.Valid(score) && w.hi.Valid(score) {
+	return w.W.Valid(score), lo, hi
-		// return lo[score] hi[score]
-		return true, w.lo.Get(score), w.hi.Get(score)
-	} else {
-		return false, 0, 0
-	}
 }
 
 // SetLoHi: set lo and hi for wavefront=score
 func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
-	// lo[score] = lo
-	w.lo.Set(score, lo)
-	// hi[score] = hi
-	w.hi.Set(score, hi)
-
-	// preemptively setup w.W
 	b := NewWavefront(lo, hi)
 	w.W.Set(score, b)
 }

pkg/utils.go

@@ -7,6 +7,7 @@ import (
 	"golang.org/x/exp/constraints"
 )
 
+// convert an unsigned into to string
 func UIntToString(num uint) string { // num assumed to be positive
 	var builder strings.Builder
 
@@ -25,6 +26,7 @@ func UIntToString(num uint) string { // num assumed to be positive
 	return string(str)
 }
 
+// decode runlength encoded string such as CIGARs
 func RunLengthDecode(encoded string) string {
 	decoded := strings.Builder{}
 	length := len(encoded)
@@ -51,32 +53,17 @@ func RunLengthDecode(encoded string) string {
 	return decoded.String()
 }
 
+// given the min index, return the item in values at that index
 func SafeMin[T constraints.Integer](values []T, idx int) T {
 	return values[idx]
 }
 
+// given the max index, return the item in values at that index
 func SafeMax[T constraints.Integer](values []T, idx int) T {
 	return values[idx]
 }
 
-func SafeArgMax[T constraints.Integer](valids []bool, values []T) (bool, int) {
+// given array of values and corresponding array of valid flags, find the min of value which is valid or return false if there does not exist any
-	hasValid := false
-	maxIndex := 0
-	maxValue := math.MinInt
-	for i := 0; i < len(valids); i++ {
-		if valids[i] && int(values[i]) > maxValue {
-			hasValid = true
-			maxIndex = i
-			maxValue = int(values[i])
-		}
-	}
-	if hasValid {
-		return true, maxIndex
-	} else {
-		return false, 0
-	}
-}
-
 func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	minIndex := 0
@@ -95,7 +82,23 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	}
 }
 
-func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) (int, int) {
+// given array of values and corresponding array of valid flags, find the max of value which is valid or return false if there does not exist any
+func SafeArgMax[T constraints.Integer](valids []bool, values []T) (bool, int) {
+	hasValid := false
+	maxIndex := 0
+	maxValue := math.MinInt
+	for i := range valids {
+		if valids[i] && int(values[i]) > maxValue {
+			hasValid = true
+			maxIndex = i
+			maxValue = int(values[i])
+		}
+	}
+	return hasValid, maxIndex
+}
+
+// set the lext lo and hi bounds for wavefronts M, I, D
+func NextLoHi(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) (int, int) {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E
@@ -125,35 +128,38 @@ func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent,
 	return lo, hi
 }
 
-func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalties Penalty) {
+// set the traceback and diag value for the next I wavefront
+func NextI(M *WavefrontComponent, I *WavefrontComponent, score int, k int, penalties Penalty) {
 	o := penalties.O
 	e := penalties.E
 
 	a_ok, a, _ := M.GetVal(score-o-e, k-1)
 	b_ok, b, _ := I.GetVal(score-e, k-1)
 
-	ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint64{a, b})
-	nextIVal := SafeMax([]uint32{a, b}, nextITraceback) + 1 // important that the +1 is here
+	nextIVal := SafeMax([]uint64{a, b}, nextITraceback) + 1 // important that the +1 is here
 	if ok {
 		I.SetVal(score, k, nextIVal, []Traceback{OpenIns, ExtdIns}[nextITraceback])
 	}
 }
 
-func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalties Penalty) {
+// set the traceback and diag value for the next D wavefront
+func NextD(M *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) {
 	o := penalties.O
 	e := penalties.E
 
 	a_ok, a, _ := M.GetVal(score-o-e, k+1)
 	b_ok, b, _ := D.GetVal(score-e, k+1)
 
-	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint64{a, b})
-	nextDVal := SafeMax([]uint32{a, b}, nextDTraceback)
+	nextDVal := SafeMax([]uint64{a, b}, nextDTraceback)
 	if ok {
 		D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
 	}
 }
 
-func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, k int, penalties Penalty) {
+// set the traceback and diag value for the next M wavefront
+func NextM(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) {
 	x := penalties.X
 
 	a_ok, a, _ := M.GetVal(score-x, k)
@@ -161,8 +167,8 @@ func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sco
 	b_ok, b, _ := I.GetVal(score, k)
 	c_ok, c, _ := D.GetVal(score, k)
 
-	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []uint32{a, b, c})
+	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []uint64{a, b, c})
-	nextMVal := SafeMax([]uint32{a, b, c}, nextMTraceback)
+	nextMVal := SafeMax([]uint64{a, b, c}, nextMTraceback)
 	if ok {
 		M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
 	}

pkg/wfa.go

@@ -4,23 +4,23 @@ import (
 	"strings"
 )
 
+// WFAlign takes strings s1, s2, penalties, and returns the score and CIGAR if doCIGAR is true
 func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	n := len(s1)
 	m := len(s2)
-	A_k := m - n
+	A_k := m - n          // diagonal where both sequences end
-	A_offset := uint32(m)
+	A_offset := uint64(m) // offset along a_k diagonal corresponding to end
 	score := 0
-	estimatedScore := (max(n, m) * max(penalties.M, penalties.X, penalties.O, penalties.E)) / 4
+	M := NewWavefrontComponent()
-	M := NewWavefrontComponent(estimatedScore)
 	M.SetLoHi(0, 0, 0)
 	M.SetVal(0, 0, 0, End)
-	I := NewWavefrontComponent(estimatedScore)
+	I := NewWavefrontComponent()
-	D := NewWavefrontComponent(estimatedScore)
+	D := NewWavefrontComponent()
 
 	for {
 		WFExtend(M, s1, n, s2, m, score)
 		ok, val, _ := M.GetVal(score, A_k)
-		if ok && val >= A_offset {
+		if ok && val >= A_offset { // exit when M_(s,a_k) >= A_offset, ie the wavefront has reached the end
 			break
 		}
 		score = score + 1
@@ -28,7 +28,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	}
 
 	CIGAR := ""
-	if doCIGAR {
+	if doCIGAR { // if doCIGAR, then perform backtrace, otherwise just return the score
 		CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, A_offset, s1, s2)
 	}
 
@@ -38,40 +38,41 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	}
 }
 
-func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
+func WFExtend(M *WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
 	_, lo, hi := M.GetLoHi(score)
-	for k := lo; k <= hi; k++ {
+	for k := lo; k <= hi; k++ { // for each diagonal in current wavefront
 		// v = M[score][k] - k
 		// h = M[score][k]
-		ok, hu, _ := M.GetVal(score, k)
+		ok, uh, tb := M.GetVal(score, k)
-		h := int(hu)
+		// exit early if M_(s,l) is invalid
-		v := h - k
-
-		// exit early if v or h are invalid
 		if !ok {
 			continue
 		}
-		for v < n && h < m && s1[v] == s2[h] {
+		h := int(uh)
-			_, val, tb := M.GetVal(score, k)
+		v := h - k
-			M.SetVal(score, k, val+1, tb)
+		// in the paper, we do v++, h++, M_(s,k)++
+		// however, note that h = M_(s,k) so instead we just do v++, h++ and set M_(s,k) at the end
+		// this saves a some memory reads and writes
+		for v < n && h < m && s1[v] == s2[h] { // extend diagonal for the next set of matches
 			v++
 			h++
 		}
+		M.SetVal(score, k, uint64(h), tb)
 	}
 }
 
-func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) {
+func WFNext(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) {
 	// get this score's lo, hi
 	lo, hi := NextLoHi(M, I, D, score, penalties)
 
-	for k := lo; k <= hi; k++ {
+	for k := lo; k <= hi; k++ { // for each diagonal, extend the matrices for the next wavefronts
 		NextI(M, I, score, k, penalties)
 		NextD(M, D, score, k, penalties)
 		NextM(M, I, D, score, k, penalties)
 	}
 }
 
-func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint32, s1 string, s2 string) string {
+func WFBacktrace(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint64, s1 string, s2 string) string {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E

test/wfa_test.go

@@ -12,6 +12,7 @@ import (
 	wfa "wfa/pkg"
 
 	"github.com/schollz/progressbar/v3"
+	"golang.org/x/exp/constraints"
 )
 
 const testJsonPath = "tests.json"
@@ -29,14 +30,14 @@ type TestCase struct {
 	Solutions string      `json:"solutions"`
 }
 
-func randRange(min, max int) uint32 {
+func randRange[T constraints.Integer](min, max int) T {
-	return uint32(rand.IntN(max-min) + min)
+	return T(rand.IntN(max-min) + min)
 }
 
 func TestWavefrontPacking(t *testing.T) {
 	for range 1000 {
-		val := randRange(0, 1000)
+		val := randRange[uint64](0, 1000)
-		tb := wfa.Traceback(randRange(0, 7))
+		tb := wfa.Traceback(randRange[uint64](0, 7))
 		v := wfa.PackWavefrontValue(val, tb)
 
 		valid, gotVal, gotTB := wfa.UnpackWavefrontValue(v)
@@ -47,6 +48,20 @@ func TestWavefrontPacking(t *testing.T) {
 	}
 }
 
+func TestLoHiPacking(t *testing.T) {
+	for range 1000 {
+		lo := randRange[int](-1000, 1000)
+		hi := randRange[int](-1000, 1000)
+		v := wfa.PackWavefrontLoHi(lo, hi)
+
+		gotLo, gotHi := wfa.UnpackWavefrontLoHi(v)
+
+		if gotLo != lo || gotHi != hi {
+			t.Errorf(`test WavefrontPack/Unpack, lo: %d, hi: %d, packedval: %x, gotlo: %d, gothi: %d`, lo, hi, v, gotLo, gotHi)
+		}
+	}
+}
+
 func GetScoreFromCIGAR(CIGAR string, penalties wfa.Penalty) int {
 	unpackedCIGAR := wfa.RunLengthDecode(CIGAR)
 	previousOp := '~'