Add PadLeft func to help avoid empty ref/new fields.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/hgvs/diff.go b/hgvs/diff.go
index e5377d6bacff8eb3860df99a3592a491df088144..d920663f4403b6b06f75ef977951d4368168ba06 100644 (file)
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -11,6 +11,7 @@ type Variant struct {
        Position int
        Ref      string
        New      string
+       Left     string // base preceding an indel, if Ref or New is empty
 }
 
 func (v *Variant) String() string {
@@ -32,6 +33,24 @@ func (v *Variant) String() string {
        }
 }
 
+// PadLeft returns a Variant that is equivalent to v but (if possible)
+// uses the stashed preceding base (the Left field) to avoid having a
+// non-empty Ref or New part, even for an insertion or deletion.
+//
+// For example, if v is {Position: 45, Ref: "", New: "A"}, PadLeft
+// might return {Position: 44, Ref: "T", New: "TA"}.
+func (v *Variant) PadLeft() Variant {
+       if len(v.Ref) == 0 || len(v.New) == 0 {
+               return Variant{
+                       Position: v.Position - len(v.Left),
+                       Ref:      v.Left + v.Ref,
+                       New:      v.Left + v.New,
+               }
+       } else {
+               return *v
+       }
+}
+
 func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
        dmp := diffmatchpatch.New()
        var deadline time.Time
@@ -44,12 +63,18 @@ func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
                timedOut = true
        }
        diffs = cleanup(dmp.DiffCleanupEfficiency(diffs))
+       left := "" // last char before an insertion or deletion
        pos := 1
        var variants []Variant
        for i := 0; i < len(diffs); i++ {
                switch diffs[i].Type {
                case diffmatchpatch.DiffEqual:
                        pos += len(diffs[i].Text)
+                       if tlen := len(diffs[i].Text); tlen > 0 {
+                               left = diffs[i].Text[tlen-1:]
+                       } else {
+                               left = ""
+                       }
                case diffmatchpatch.DiffDelete:
                        if i+1 < len(diffs) && diffs[i+1].Type == diffmatchpatch.DiffInsert {
                                // deletion followed by insertion
@@ -57,9 +82,10 @@ func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
                                pos += len(diffs[i].Text)
                                i++
                        } else {
-                               variants = append(variants, Variant{Position: pos, Ref: diffs[i].Text})
+                               variants = append(variants, Variant{Position: pos, Ref: diffs[i].Text, Left: left})
                                pos += len(diffs[i].Text)
                        }
+                       left = ""
                case diffmatchpatch.DiffInsert:
                        if i+1 < len(diffs) && diffs[i+1].Type == diffmatchpatch.DiffDelete {
                                // insertion followed by deletion
@@ -67,8 +93,9 @@ func Diff(a, b string, timeout time.Duration) ([]Variant, bool) {
                                pos += len(diffs[i+1].Text)
                                i++
                        } else {
-                               variants = append(variants, Variant{Position: pos, New: diffs[i].Text})
+                               variants = append(variants, Variant{Position: pos, New: diffs[i].Text, Left: left})
                        }
+                       left = ""
                }
        }
        return variants, timedOut