Fix divide by zero.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 57596fbb07fb96b951ead13f41697e5f565e13d2..254029e4770ba68834b6a1bed19c5cf0ca4f57cc 100644 (file)
--- a/import.go
+++ b/import.go
@@ -307,7 +307,7 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                tseqs, err := cmd.tileFasta(tilelib, infile2)
                                var kept, dropped int
                                variants[1], kept, dropped = tseqs.Variants()
-                               log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
+                               log.Printf("%s found %d unique tags plus %d repeats", infile2, kept, dropped)
                                return err
                        }
                } else if fastaFilenameRe.MatchString(infile) {
@@ -317,12 +317,20 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                log.Printf("%s starting", infile)
                                defer log.Printf("%s done", infile)
                                tseqs, err := cmd.tileFasta(tilelib, infile)
-                               var kept, dropped int
-                               variants[0], kept, dropped = tseqs.Variants()
-                               variants[1] = variants[0]
-                               log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
-                               return err
+                               if err != nil {
+                                       return err
+                               }
+                               totlen := 0
+                               for _, tseq := range tseqs {
+                                       totlen += len(tseq)
+                               }
+                               log.Printf("%s tiled %d seqs, total len %d", infile, len(tseqs), totlen)
+                               return cmd.encoder.Encode(LibraryEntry{
+                                       CompactSequences: []CompactSequence{{Name: infile, TileSequences: tseqs}},
+                               })
                        }
+                       // Don't write out a CompactGenomes entry
+                       continue
                } else if vcfFilenameRe.MatchString(infile) {
                        for phase := 0; phase < 2; phase++ {
                                phase := phase
@@ -347,20 +355,8 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                        if len(errs) > 0 {
                                return
                        }
-                       ntags := len(variants[0])
-                       if ntags < len(variants[1]) {
-                               ntags = len(variants[1])
-                       }
-                       flat := make([]tileVariantID, ntags*2)
-                       for i := 0; i < ntags; i++ {
-                               for hap := 0; hap < 2; hap++ {
-                                       if i < len(variants[hap]) {
-                                               flat[i*2+hap] = variants[hap][i]
-                                       }
-                               }
-                       }
                        err := cmd.encoder.Encode(LibraryEntry{
-                               CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},
+                               CompactGenomes: []CompactGenome{{Name: infile, Variants: flatten(variants)}},
                        })
                        if err != nil {
                                select {
@@ -391,9 +387,11 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
                                        }
                                }
                                remain := len(todo) + int(atomic.LoadInt64(&running)) - 1
-                               ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
-                               eta := time.Now().Add(ttl)
-                               log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
+                               if remain < cap(todo) {
+                                       ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
+                                       eta := time.Now().Add(ttl)
+                                       log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
+                               }
                        }
                }()
        }
@@ -450,3 +448,21 @@ func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (t
        }
        return
 }
+
+func flatten(variants [][]tileVariantID) []tileVariantID {
+       ntags := 0
+       for _, v := range variants {
+               if ntags < len(v) {
+                       ntags = len(v)
+               }
+       }
+       flat := make([]tileVariantID, ntags*2)
+       for i := 0; i < ntags; i++ {
+               for hap := 0; hap < 2; hap++ {
+                       if i < len(variants[hap]) {
+                               flat[i*2+hap] = variants[hap][i]
+                       }
+               }
+       }
+       return flat
+}