From: Tom Clegg <tom@curii.com>
Date: Thu, 25 Nov 2021 19:41:01 +0000 (-0500)
Subject: More debug messages and error checks.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/ab0f3eebd739cb10951a6907f41d49d7ce6bf8b1

More debug messages and error checks.

refs #18438

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

diff --git a/mask.go b/mask.go
index 7d614fa4aa..9daf606d66 100644
--- a/mask.go
+++ b/mask.go
@@ -27,6 +27,9 @@ type mask struct {
 }
 
 func (m *mask) Add(seqname string, start, end int) {
+	if m.frozen {
+		panic("bug: (*mask)Add() called after Freeze()")
+	}
 	if m.intervals == nil {
 		m.intervals = map[string][]interval{}
 	}
@@ -48,6 +51,17 @@ func (m *mask) Check(seqname string, start, end int) bool {
 	return m.itrees[seqname].check(0, interval{start, end})
 }
 
+func (m *mask) Len() int {
+	if !m.frozen {
+		return 0
+	}
+	n := 0
+	for _, intervals := range m.intervals {
+		n += len(intervals)
+	}
+	return n
+}
+
 func (m *mask) freeze(in []interval) intervalTree {
 	if len(in) == 0 {
 		return nil
diff --git a/slicenumpy.go b/slicenumpy.go
index fe1a77497e..91e7cb2622 100644
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -211,7 +211,6 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
 	for seqname, cseq := range refseq {
 		seqname, cseq := seqname, cseq
 		throttleCPU.Go(func() error {
-			defer log.Printf("... %s done", seqname)
 			pos := 0
 			for _, libref := range cseq {
 				rt := reftile[libref.Tag]
@@ -221,23 +220,30 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
 				}
 				pos += len(rt.tiledata) - taglen
 			}
+			log.Printf("... %s done, len %d", seqname, pos)
 			return nil
 		})
 	}
-	throttleCPU.Wait()
+	err = throttleCPU.Wait()
+	if err != nil {
+		return 1
+	}
 
 	var mask *mask
 	if *regionsFilename != "" {
+		log.Printf("loading regions from %s", *regionsFilename)
 		mask, err = makeMask(*regionsFilename, *expandRegions)
 		if err != nil {
 			return 1
 		}
-		// Delete reftile entries for masked-out regions.
+		log.Printf("before applying mask, len(reftile) == %d", len(reftile))
+		log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 		for tag, rt := range reftile {
 			if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 				delete(reftile, tag)
 			}
 		}
+		log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 	}
 
 	var toMerge [][]int16