Progress indicator for exportSeq.

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

diff --git a/export.go b/export.go
index a1831fbcf2e0d70f82ebd7785372e5a57dd21865..ac7f5292beb9812fe81187242973819365fd69c7 100644 (file)
--- a/export.go
+++ b/export.go
@@ -318,11 +318,26 @@ func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrar
 // Align genome tiles to reference tiles, write diffs to outw, and (if
 // bedw is not nil) write tile coverage to bedw.
 func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome) {
+       t0 := time.Now()
+       progressbar := time.NewTicker(time.Minute)
+       defer progressbar.Stop()
        var outmtx sync.Mutex
        defer outmtx.Lock()
        refpos := 0
        variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
        for refstep, libref := range reftiles {
+               select {
+               case <-progressbar.C:
+                       var eta interface{}
+                       if refstep > 0 {
+                               fin := t0.Add(time.Now().Sub(t0) * time.Duration(len(reftiles)) / time.Duration(refstep))
+                               eta = fmt.Sprintf("%v (%v)", fin.Format(time.RFC3339), fin.Sub(time.Now()))
+                       } else {
+                               eta = "N/A"
+                       }
+                       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:
+               }
                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 {