minor code cleanup, use uint64 for wavefront values

pkg/custom_slice.go

@@ -19,7 +19,7 @@ func (a *PositiveSlice[T]) Get(idx int) T {
 }
 
 func (a *PositiveSlice[T]) Set(idx int, value T) {
-	if idx < 0 || idx >= len(a.valid) { // idx is outside the slice
+	if idx >= len(a.valid) { // idx is outside the slice
 		// expand data array to 2*idx
 		newData := make([]T, 2*idx+1)
 		copy(newData, a.data)

pkg/types.go

@@ -40,25 +40,22 @@ func UnpackWavefrontLoHi(lohi WavefrontLoHi) (int, int) {
 	return loBM, hiBM
 }
 
-// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 28 bits for the diag distance
+// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 60 bits for the diag distance
-// technically this restricts to alignments with less than 268 million characters but that should be sufficient for most cases
+type WavefrontValue uint64
-type WavefrontValue uint32
-
-// TODO: add 64 bit packed value in case more than 268 million characters are needed
 
 // PackWavefrontValue: packs a diag value and traceback into a WavefrontValue
-func PackWavefrontValue(value uint32, traceback Traceback) WavefrontValue {
+func PackWavefrontValue(value uint64, traceback Traceback) WavefrontValue {
-	validBM := uint32(0x8000_0000)
+	validBM := uint64(0x8000_0000_0000_0000)
-	tracebackBM := uint32(traceback&0x0000_0007) << 28
+	tracebackBM := uint64(traceback&0x0000_0007) << 60
-	valueBM := value & 0x0FFF_FFFF
+	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) {
-	validBM := wfv&0x8000_0000 != 0
+	validBM := wfv&0x8000_0000_0000_0000 != 0
-	tracebackBM := uint8(wfv & 0x7000_0000 >> 28)
+	tracebackBM := uint8(wfv & 0x7000_0000_0000_0000 >> 60)
-	valueBM := uint32(wfv & 0x0FFF_FFFF)
+	valueBM := uint64(wfv & 0x0000_0000_FFFF_FFFF)
 	return validBM, valueBM, Traceback(tracebackBM)
 }
 
@@ -131,12 +128,12 @@ func NewWavefrontComponent() *WavefrontComponent {
 }
 
 // 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))
 }
 

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)
@@ -51,28 +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 := range valids {
-		if valids[i] && int(values[i]) > maxValue {
-			hasValid = true
-			maxIndex = i
-			maxValue = int(values[i])
-		}
-	}
-	return hasValid, maxIndex
-}
-
 func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	minIndex := 0
@@ -91,6 +82,22 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, 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
@@ -121,6 +128,7 @@ func NextLoHi(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponen
 	return lo, hi
 }
 
+// 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
@@ -128,13 +136,14 @@ func NextI(M *WavefrontComponent, I *WavefrontComponent, score int, k int, penal
 	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])
 	}
 }
 
+// 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
@@ -142,13 +151,14 @@ func NextD(M *WavefrontComponent, D *WavefrontComponent, score int, k int, penal
 	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])
 	}
 }
 
+// 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
 
@@ -157,8 +167,8 @@ func NextM(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent,
 	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

@@ -4,11 +4,12 @@ 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
 	M := NewWavefrontComponent()
 	M.SetLoHi(0, 0, 0)
@@ -19,7 +20,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	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
@@ -27,7 +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)
 	}
 
@@ -39,23 +40,24 @@ 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) {
 	_, 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)
 	}
 }
 
@@ -63,14 +65,14 @@ func WFNext(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent,
 	// 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

@@ -36,8 +36,8 @@ func randRange[T constraints.Integer](min, max int) T {
 
 func TestWavefrontPacking(t *testing.T) {
 	for range 1000 {
-		val := randRange[uint32](0, 1000)
+		val := randRange[uint64](0, 1000)
-		tb := wfa.Traceback(randRange[uint32](0, 7))
+		tb := wfa.Traceback(randRange[uint64](0, 7))
 		v := wfa.PackWavefrontValue(val, tb)
 
 		valid, gotVal, gotTB := wfa.UnpackWavefrontValue(v)