Fix recomputing diffs N times.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/export.go b/export.go
index 496f5c9cd593f4e2bdbac42bafbc7321d6abdac3..fb07fd329e996ad1139ca2b93392a0e9464d6610 100644 (file)
--- a/export.go
+++ b/export.go
@@ -341,6 +341,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                        log.Printf("exportSeq: %s: refstep %d of %d, %.0f/s, ETA %v", seqname, refstep, len(reftiles), float64(refstep)/time.Now().Sub(t0).Seconds(), eta)
                default:
                }
+               diffs := map[tileLibRef][]hgvs.Variant{}
                refseq := tilelib.TileVariantSequence(libref)
                tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
                for cgidx, cg := range cgs {
@@ -356,30 +357,38 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                if variant == libref.Variant {
                                        continue
                                }
-                               genomeseq := tilelib.TileVariantSequence(tileLibRef{Tag: libref.Tag, Variant: variant})
-                               if len(genomeseq) == 0 {
-                                       // Hash is known but sequence
-                                       // is not, e.g., retainNoCalls
-                                       // was false during import
-                                       continue
-                               }
-                               if len(genomeseq) > cmd.maxTileSize {
-                                       continue
-                               }
-                               refSequence := refseq
-                               // If needed, extend the reference
-                               // sequence up to the tag at the end
-                               // of the genomeseq sequence.
-                               refstepend := refstep + 1
-                               for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
-                                       if &refSequence[0] == &refseq[0] {
-                                               refSequence = append([]byte(nil), refSequence...)
+                               glibref := tileLibRef{Tag: libref.Tag, Variant: variant}
+                               vars, ok := diffs[glibref]
+                               if !ok {
+                                       genomeseq := tilelib.TileVariantSequence(glibref)
+                                       if len(genomeseq) == 0 {
+                                               // Hash is known but sequence
+                                               // is not, e.g., retainNoCalls
+                                               // was false during import
+                                               continue
+                                       }
+                                       if len(genomeseq) > cmd.maxTileSize {
+                                               continue
+                                       }
+                                       refSequence := refseq
+                                       // If needed, extend the
+                                       // reference sequence up to
+                                       // the tag at the end of the
+                                       // genomeseq sequence.
+                                       refstepend := refstep + 1
+                                       for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
+                                               if &refSequence[0] == &refseq[0] {
+                                                       refSequence = append([]byte(nil), refSequence...)
+                                               }
+                                               refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
+                                               refstepend++
                                        }
-                                       refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
-                                       refstepend++
+                                       // (TODO: handle no-calls)
+                                       refstr := strings.ToUpper(string(refSequence))
+                                       genomestr := strings.ToUpper(string(genomeseq))
+                                       vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
+                                       diffs[glibref] = vars
                                }
-                               // (TODO: handle no-calls)
-                               vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genomeseq)), time.Second)
                                for _, v := range vars {
                                        if cmd.outputFormat.PadLeft {
                                                v = v.PadLeft()