X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/5e4171fb1592e22628929c965e90943dbf50f49b..69b71af4136fdaeeb5c2afbc559208dc5f428c48:/annotate.go

diff --git a/annotate.go b/annotate.go
index 449e64bb34..ff4ab88717 100644
--- a/annotate.go
+++ b/annotate.go
@@ -109,10 +109,10 @@ func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader,
 	bufw := bufio.NewWriter(output)
 
 	tilelib := &tileLibrary{
-		includeNoCalls:      true,
+		retainNoCalls:       true,
 		retainTileSequences: true,
 	}
-	err = tilelib.LoadGob(context.Background(), input, nil)
+	err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
 	if err != nil {
 		return 1
 	}
@@ -152,7 +152,7 @@ func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, tilelib *tileLibrary) er
 	sort.Strings(refs)
 	log.Infof("len(refs) %d", len(refs))
 
-	outch := make(chan string, 1)
+	outch := make(chan string, runtime.NumCPU()*2)
 	var outwg sync.WaitGroup
 	defer outwg.Wait()
 	outwg.Add(1)
@@ -169,7 +169,7 @@ func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, tilelib *tileLibrary) er
 		nseqs += len(refcs)
 	}
 
-	throttle := &throttle{Max: runtime.NumCPU() + nseqs + 1}
+	throttle := &throttle{Max: runtime.NumCPU()*2 + nseqs*2 + 1}
 	defer throttle.Wait()
 
 	for _, refname := range refs {
@@ -185,7 +185,7 @@ func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, tilelib *tileLibrary) er
 			throttle.Acquire()
 			go func() {
 				defer throttle.Release()
-				throttle.Report(cmd.annotateSequence(throttle, outch, tilelib, taglen, refname, seqname, refcs[seqname]))
+				throttle.Report(cmd.annotateSequence(throttle, outch, tilelib, taglen, refname, seqname, refcs[seqname], len(refs) > 1))
 			}()
 		}
 	}
@@ -193,7 +193,7 @@ func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, tilelib *tileLibrary) er
 	return throttle.Err()
 }
 
-func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string, tilelib *tileLibrary, taglen int, refname, seqname string, reftiles []tileLibRef) error {
+func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string, tilelib *tileLibrary, taglen int, refname, seqname string, reftiles []tileLibRef, refnamecol bool) error {
 	var refseq []byte
 	// tilestart[123] is the index into refseq
 	// where the tile for tag 123 was placed.
@@ -232,7 +232,9 @@ func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string
 		for variant := 1; variant <= len(tvs); variant++ {
 			variant, hash := tileVariantID(variant), tvs[variant-1]
 			tileseq := tilelib.TileVariantSequence(tileLibRef{Tag: tag, Variant: variant})
-			if len(tileseq) < taglen {
+			if len(tileseq) == 0 {
+				continue
+			} else if len(tileseq) < taglen {
 				return fmt.Errorf("tilevar %d,%d has sequence len %d < taglen %d", tag, variant, len(tileseq), taglen)
 			}
 			var refpart []byte
@@ -273,7 +275,11 @@ func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string
 					} else {
 						varid = fmt.Sprintf("%d", variant)
 					}
-					outch <- fmt.Sprintf("%d\t%s\t%s\t%s:g.%s\n", tag, varid, refname, seqname, diff.String())
+					refnamefield := ""
+					if refnamecol {
+						refnamefield = "\t" + refname
+					}
+					outch <- fmt.Sprintf("%d\t%s%s\t%s:g.%s\n", tag, varid, refnamefield, seqname, diff.String())
 				}
 			}()
 		}