Drop duplicate tags, fix ref position tracking.

refs #18438

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

diff --git a/slicenumpy.go b/slicenumpy.go
index 91e7cb2622227ec766f74e54b05c0fa3a5f28973..fdaa02e658de2a59dc6b1bbbbdaad0ecb250f1ef 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -192,41 +192,37 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
        type reftileinfo struct {
                variant  tileVariantID
                seqname  string // chr1
        type reftileinfo struct {
                variant  tileVariantID
                seqname  string // chr1

-               pos      int    // distance from start of chr1 to start of tile
+               pos      int    // distance from start of chromosome to starttag

                tiledata []byte // acgtggcaa...
        }
                tiledata []byte // acgtggcaa...
        }

+       isdup := map[tagID]bool{}

        reftile := map[tagID]*reftileinfo{}
        for seqname, cseq := range refseq {
        reftile := map[tagID]*reftileinfo{}
        for seqname, cseq := range refseq {

+               pos := 0

                for _, libref := range cseq {
                for _, libref := range cseq {

-                       reftile[libref.Tag] = &reftileinfo{
-                               seqname:  seqname,
-                               variant:  libref.Variant,
-                               tiledata: reftiledata[libref],
+                       tiledata := reftiledata[libref]
+                       if len(tiledata) == 0 {
+                               err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
+                               return 1

                        }
                        }

-               }
-       }
-
-       throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
-       log.Info("reconstructing reference sequences")
-       for seqname, cseq := range refseq {
-               seqname, cseq := seqname, cseq
-               throttleCPU.Go(func() error {
-                       pos := 0
-                       for _, libref := range cseq {
-                               rt := reftile[libref.Tag]
-                               rt.pos = pos
-                               if len(rt.tiledata) == 0 {
-                                       return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
+                       if isdup[libref.Tag] {
+                               log.Printf("dropping reference tile %+v from %s, tag not unique", libref, seqname)
+                       } else if reftile[libref.Tag] != nil {
+                               log.Printf("dropping reference tile %+v from %s, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname)
+                               delete(reftile, libref.Tag)
+                               log.Printf("dropping reference tile %+v from %s, tag not unique", libref, seqname)
+                               isdup[libref.Tag] = true
+                       } else {
+                               reftile[libref.Tag] = &reftileinfo{
+                                       seqname:  seqname,
+                                       variant:  libref.Variant,
+                                       tiledata: tiledata,
+                                       pos:      pos,

                                }
                                }

-                               pos += len(rt.tiledata) - taglen

                        }
                        }

-                       log.Printf("... %s done, len %d", seqname, pos)
-                       return nil
-               })
-       }
-       err = throttleCPU.Wait()
-       if err != nil {
-               return 1
+                       pos += len(tiledata) - taglen
+               }
+               log.Printf("... %s done, len %d", seqname, pos+taglen)

        }
 
        var mask *mask
        }
 
        var mask *mask