More debugging info for -debug-tag.

refs #18581

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

diff --git a/slicenumpy.go b/slicenumpy.go
index cb218041efbf503c2e67c306e525137015467628..2bd892eb15ed6882b1dec04e65694944d85da9c2 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -433,9 +433,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                        throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
                        for tag, variants := range seq {
                                tag, variants := tag, variants
-                               throttleCPU.Acquire()
-                               go func() {
-                                       defer throttleCPU.Release()
+                               throttleCPU.Go(func() error {
                                        count := make(map[[blake2b.Size256]byte]int, len(variants))
 
                                        rt := reftile[tag]
@@ -449,9 +447,9 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                                        v := cg.Variants[idx+allele]
                                                        if v > 0 && len(variants[v].Sequence) > 0 {
                                                                count[variants[v].Blake2b]++
-                                                               if tag == cmd.debugTag {
-                                                                       log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
-                                                               }
+                                                       }
+                                                       if v > 0 && tag == cmd.debugTag {
+                                                               log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
                                                        }
                                                }
                                        }
@@ -490,7 +488,11 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                                remap[i] = rank[tv.Blake2b]
                                        }
                                        if tag == cmd.debugTag {
-                                               log.Printf("tag %d remap %+v", tag, remap)
+                                               for in, out := range remap {
+                                                       if out > 0 {
+                                                               log.Printf("tag %d remap %d => %d", tag, in, out)
+                                                       }
+                                               }
                                        }
                                        variantRemap[tag-tagstart] = remap
                                        if rt != nil {
@@ -500,7 +502,8 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                                }
                                                rt.variant = refrank
                                        }
-                               }()
+                                       return nil
+                               })
                        }
                        throttleCPU.Wait()
 
@@ -522,7 +525,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        continue
                                }
                                if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
-                                       continue
+                                       break
                                }
                                remap := variantRemap[tag-tagstart]
                                maxv := tileVariantID(0)
@@ -532,11 +535,6 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                        }
                                }
                                if *onehotChunked || *onehotSingle {
-                                       if tag == cmd.debugTag {
-                                               log.WithFields(logrus.Fields{
-                                                       "cgs[2].Variants[tag*2:(tag+1)*2]": cgs[cmd.cgnames[2]].Variants[(tag-tagstart)*2 : (tag-tagstart+1)*2],
-                                               }).Info("before tv2homhet")
-                                       }
                                        onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart)
                                        if tag == cmd.debugTag {
                                                log.WithFields(logrus.Fields{
@@ -683,19 +681,26 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
                                cols := 2 * outcol
                                out := make([]int16, rows*cols)
                                for row, name := range cmd.cgnames {
-                                       out := out[row*cols:]
-                                       outcol := 0
+                                       outidx := row * cols
                                        for col, v := range cgs[name].Variants {
                                                tag := tagstart + tagID(col/2)
-                                               if mask != nil && reftile[tag] == nil || (cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag)) {
+                                               if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
+                                                       break
+                                               }
+                                               if mask != nil && reftile[tag] == nil {
                                                        continue
                                                }
-                                               if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
-                                                       out[outcol] = int16(variantRemap[tag-tagstart][v])
+                                               if v == 0 {
+                                                       out[outidx] = -1 // 0 better?
+                                               } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
+                                                       out[outidx] = int16(variantRemap[tag-tagstart][v])
                                                } else {
-                                                       out[outcol] = -1
+                                                       out[outidx] = -1
+                                               }
+                                               if tag == cmd.debugTag {
+                                                       log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
                                                }
-                                               outcol++
+                                               outidx++
                                        }
                                }
                                seq = nil