add an augument to 'AlignmentResult.AlignmentText()' and 'AlignmentRe…

…sult.CIGAR'

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+- v0.4.0
+    - add an augument to `AlignmentResult.AlignmentText()` and `AlignmentResult.CIGAR`.
+    - wfa-go: add a new flag `-t` for only showing the aligned region.
 - v0.3.1
     - use a more efficient data structure to store cigar operations.
     - slight speed improvement.

wfa-go/wfa-go.go

@@ -31,7 +31,7 @@ import (
 	"github.com/shenwei356/wfa"
 )
 
-var version = "0.3.1"
+var version = "0.4.0"
 
 func main() {
 	app := filepath.Base(os.Args[0])
@@ -72,6 +72,7 @@ Options/Flags:
 	noGlobal := flag.Bool("g", false, "do not use global alignment")
 	noAdaptive := flag.Bool("a", false, "do not use adaptive reduction")
 	noOutput := flag.Bool("N", false, "do not output alignment (for benchmark)")
+	trim := flag.Bool("t", false, "only show the aligned region")
 
 	pprofCPU := flag.Bool("p", false, "cpu pprof. go tool pprof -http=:8080 cpu.pprof")
 	pprofMem := flag.Bool("m", false, "mem pprof. go tool pprof -http=:8080 mem.pprof")
@@ -118,13 +119,13 @@ Options/Flags:
 		}
 
 		if !*noOutput {
-			Q, A, T := result.AlignmentText(&_q, &_t)
+			Q, A, T := result.AlignmentText(&_q, &_t, *trim)
 
 			// fmt.Fprintln(outfh, q, t)
 			fmt.Fprintf(outfh, "query   %s\n", *Q)
 			fmt.Fprintf(outfh, "        %s\n", *A)
 			fmt.Fprintf(outfh, "target  %s\n", *T)
-			fmt.Fprintf(outfh, "cigar   %s\n", result.CIGAR())
+			fmt.Fprintf(outfh, "cigar   %s\n", result.CIGAR(*trim))
 			fmt.Fprintln(outfh)
 			fmt.Fprintf(outfh, "align-score : %d\n", result.Score)
 			fmt.Fprintf(outfh, "match-region: q[%d, %d]/%d vs t[%d, %d]/%d\n",

wfa.go

@@ -710,7 +710,7 @@ func (algn *Aligner) backTrace(q, t *[]byte, s uint32, Ak int) *AlignmentResult
 	lenQ := len(*q)
 	lenT := len(*t)
 
-	cigar := NewAlignmentResult()
+	cigar := NewAlignmentResult(algn.opt.GlobalAlignment)
 	cigar.Score = s
 
 	var ok bool

wfa_cigar.go

@@ -43,6 +43,8 @@ type AlignmentResult struct {
 	GapRegions uint32
 
 	proccessed bool
+
+	globalAlignment bool
 }
 
 // // CIGARRecord records the operation and the number.
@@ -64,9 +66,10 @@ const OpH = uint64('H')
 const MaskLower32 = 4294967295
 
 // NewAlignmentResult returns a new CIGAR from the object pool.
-func NewAlignmentResult() *AlignmentResult {
+func NewAlignmentResult(globalAlignment bool) *AlignmentResult {
 	cigar := poolCIGAR.Get().(*AlignmentResult)
 	cigar.reset()
+	cigar.globalAlignment = globalAlignment
 	return cigar
 }
 
@@ -210,13 +213,36 @@ func (cigar *AlignmentResult) process() {
 	cigar.proccessed = true
 }
 
+// trimOps trim ops to keep only aligned region
+func trimOps(ops []uint64) []uint64 {
+	var start, end int
+	start, end = -1, -1
+	for i, op := range ops {
+		if op>>32 == OpM {
+			start = i
+			break
+		}
+	}
+	for i := len(ops) - 1; i >= 0; i-- {
+		if ops[i]>>32 == OpM {
+			end = i
+			break
+		}
+	}
+	return ops[start : end+1]
+}
+
 // CIGAR returns the CIGAR string.
-func (cigar *AlignmentResult) CIGAR() string {
+func (cigar *AlignmentResult) CIGAR(onlyAignedRegion bool) string {
 	cigar.process()
 	buf := poolBytesBuffer.Get().(*bytes.Buffer)
 	buf.Reset()
 
-	for _, op := range cigar.Ops {
+	ops := cigar.Ops
+	if onlyAignedRegion {
+		ops = trimOps(cigar.Ops)
+	}
+	for _, op := range ops {
 		// buf.WriteString(strconv.Itoa(int(op.N)))
 		buf.WriteString(strconv.Itoa(int(op & MaskLower32)))
 		// buf.WriteByte(op.Op)
@@ -230,9 +256,21 @@ func (cigar *AlignmentResult) CIGAR() string {
 
 // AlignmentText returns the formated alignment text for Query, Alignment, and Target.
 // Do not forget to recycle them with RecycleAlignmentText().
-func (cigar *AlignmentResult) AlignmentText(q, t *[]byte) (*[]byte, *[]byte, *[]byte) {
+func (cigar *AlignmentResult) AlignmentText(q0, t0 *[]byte, onlyAignedRegion bool) (*[]byte, *[]byte, *[]byte) {
 	cigar.process()
 
+	var q, t []byte
+	ops := cigar.Ops
+	if !onlyAignedRegion {
+		q = *q0
+		t = *t0
+	} else {
+		q = (*q0)[cigar.QBegin-1 : cigar.QEnd]
+		t = (*t0)[cigar.TBegin-1 : cigar.TEnd]
+
+		ops = trimOps(cigar.Ops)
+	}
+
 	Q := poolBytes.Get().(*[]byte)
 	A := poolBytes.Get().(*[]byte)
 	T := poolBytes.Get().(*[]byte)
@@ -245,7 +283,7 @@ func (cigar *AlignmentResult) AlignmentText(q, t *[]byte) (*[]byte, *[]byte, *[]
 	v, h = 0, 0
 	// var i uint32
 	var i, n uint64
-	for _, op := range cigar.Ops {
+	for _, op := range ops {
 		n = op & MaskLower32
 
 		// switch op.Op {
@@ -254,19 +292,19 @@ func (cigar *AlignmentResult) AlignmentText(q, t *[]byte) (*[]byte, *[]byte, *[]
 		case OpM:
 			// for i = 0; i < op.N; i++ {
 			for i = 0; i < n; i++ {
-				*Q = append(*Q, (*q)[v])
+				*Q = append(*Q, q[v])
 				*A = append(*A, '|')
-				*T = append(*T, (*t)[h])
+				*T = append(*T, t[h])
 				v++
 				h++
 			}
 		// case 'X':
 		case OpX:
 			// for i = 0; i < op.N; i++ {
 			for i = 0; i < n; i++ {
-				*Q = append(*Q, (*q)[v])
+				*Q = append(*Q, q[v])
 				*A = append(*A, ' ')
-				*T = append(*T, (*t)[h])
+				*T = append(*T, t[h])
 				v++
 				h++
 			}
@@ -276,14 +314,14 @@ func (cigar *AlignmentResult) AlignmentText(q, t *[]byte) (*[]byte, *[]byte, *[]
 			for i = 0; i < n; i++ {
 				*Q = append(*Q, '-')
 				*A = append(*A, ' ')
-				*T = append(*T, (*t)[h])
+				*T = append(*T, t[h])
 				h++
 			}
 		// case 'D', 'H':
 		case OpD, OpH:
 			// for i = 0; i < op.N; i++ {
 			for i = 0; i < n; i++ {
-				*Q = append(*Q, (*q)[v])
+				*Q = append(*Q, q[v])
 				*A = append(*A, ' ')
 				*T = append(*T, '-')
 				v++

wfa_test.go

@@ -136,6 +136,10 @@ func TestWFA(_t *testing.T) {
 	// t = []byte("AAATTCTTGGTCAGAAAAGCAACCCCCCACAAGGTCGTCACACCTGGTTCACAGGGATCCTTCTGGTTAGCCAGTGCGAAGGCGATACGGGGGGAGAGCAGACAATTGCGTACAGGTTGAACTGTACTGGCTGAAAAAATTCCTGGCTCAACCCAAAGTTAAGTAGTATAATCGACAACGCAGTCTACAGATGCGGCCCGCGGATATAATTGTCCCCCGTGAAGTCACTGTGTCAAACGCGGAACGGTAATGCTCACCCCAATTCGTCGAAACAGTTAACTCCAGGCTAGATCTCACAAAACCGGAGCGGGACACCGATCACGATTTCACCCGTTATCGGAAGGCAGTTCTCGCTGCTGGTTACCTAGTGACTCACCCTAGCGGAACGTAGACTTGGTATCAAGCTTGCTTAACGCGTTCTCCCCCTTCAAGATAGTAAAATAACGCTGCCGTTTCATCCAAACTATTCTATATCCTTACCGTACTGGTTATTACTCTGGTAGACCGATCATGGTCAGACCACTATTTCACCAAGGGTAGCCACTCCATGCCGTAGGAGACACGCAAATAGCCACCGGGCATGTTGTAGACTGGAGAATCCCTTTGCCTCAGATCCGCATGTGCACTAAAGGCCCCTTGTAGCACGGAGAGATGGATTTTATGGAAGTTCTAAAAGTTTTGTTACTTCTTCCAACCTCCAACCCTGTATATGAAATACTTTCCAGTCACCGGGTTTCTATGCGCGTCCTTATTGCTCAAGGTAAGAAATCTCTGTCCATCAAATTCGAGTGAGTTATGCGTAATGTAAAACAAGTTACTGAGTTCAAAGCTGGTCCTGGTGATGGTGTCCCGTACACCCAAGAAAGTGATACTTAGCTTTACGCGTTAATGCCTCGGCAGACATCAGGTCCATACGAAGCAAGGAAAGCCCCGCCACTGCCACACTGGCTAGTCCCCCGAGTCACTCCCAAGCCTGGCAACCTCGATACCCAAGAGGAGTA")
 	// q = []byte("AAATTCTTGGTCAGAAAAGCAACCCCTCACAAGATCGTCACAGCTGGTTCAAGGGATCCTTCTGGTTAGCCAGTGCGAAGGCGATACGGGGGAGAGCAGACAATTGCGTCAGGTTGAACTGTCTGGCTGAAAAAATTCCTGGCCCAACCCAAAGTTAAGTAGTATAATCGGAAAGCAGTCTACAGATGCGGCCCGCGGATATAATTGTCCCCGTGAAGTCACTGTGTCAAACTCGGAACGGTAATGCTCACCCCAATTCATGCGAAACAGTTGAACTCCAGGCTAGATCCTCACAACCGGAGCGGGACACCGATCACGATTTCACCCGTTATCGGAAGGCATTCTCGCTGCTGGTTACCTAGTGACTCACGCCCTAGCGGAACGTAGACTTGGTATCAAGCTTGCTTAACGCGTTCTCCCCCTTCAGGATAGTAAATTAACGCTGCCGTTTCATCCAAACTATTCTTATACCTTACCGTACTGGTTATTACTCAGGAGTAGCCGAGTCATGGTCAGACCACTATTTCACCAAGGGTAGCCGATCCATGCCGTAGGAGACACGCAAATAGCCACCGGGCATGTTTGCTAGACTGGAGGATACCCTTTGCCTCAGATCCGCATGTGCACTAAAGGCCCCTTGTAGCACGGAAGATGGATTTTATGGCAAGTTCTAAAAGTTTTGTTACTTCTTCGCAACCTCCAACCCGTACTATGAAATACTTTCCAGTCCCGGGTTTCTATGCGCGTCCTTATTGCTCAAGGTAAGAAATCTCTGTCCATCAAATTCGAGTGAGTCATGCGTAATTTAAAACAAGTTACTGAGTTCAAAGCTGGTCCTGGTGATGGTGTCCCGTACACCCAGAGAAAGTGATACTTAGCTTTACGCGTTAATGCCTCGGCAGACATCAGGTCCATACGAAGCAAGGAAAGCCCCGCCACTGCCACACGGCTAGTCCCCCGAGTCACTCCCAAGCCTGGCAACCTCGATACCCAAGAGGGA")
 
+	// repeat sequence in the end of query
+	// q = []byte("GACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCGACTGCCTCAGTGCCCGGCGCTCAAGCCTCAAGCCTCAAGCCTCAGGTCTCGCAGCCCACCGCATTCACCCGTGACACCGAACTGCATCGCGAACGCATTTCTCGCCGCAGCCGCGCGCACGGGCGACGCGGACTTGCCGGCAAGCCCGCGCGCCGCCCGATGCGCG")
+	// t = []byte("GACTGCCGACTGCCGACTGCCGACTGCCTCAGTGCCCGGCGCTCAAGCCTCAAGCCTCAAGCCTCAGGCCTCAGGCCTCGCAGCCCACCGCATTCACCCGTGACACCGAACTTCATCGCGAACGCATTTCTCGCCGCAGCCGCGCGCGCAGGCGACGCGGACTTGCCGGCAAGCCCGCGCGCCGCCCGATGCGCG")
+
 	q = bytes.ToUpper(q)
 	t = bytes.ToUpper(t)
 	result, err := algn.Align(q, t)
@@ -159,8 +163,8 @@ func TestWFA(_t *testing.T) {
 
 	if result != nil {
 		fmt.Println()
-		fmt.Printf("CIGAR:  %s\n", result.CIGAR())
-		Q, A, T := result.AlignmentText(&q, &t)
+		fmt.Printf("CIGAR:  %s\n", result.CIGAR(false))
+		Q, A, T := result.AlignmentText(&q, &t, false)
 		fmt.Printf("query   %s\n", *Q)
 		fmt.Printf("        %s\n", *A)
 		fmt.Printf("target  %s\n", *T)