From 6c78b1f73e00a341cddb4f4b4b56bbaba25b4289 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Fri, 24 Apr 2020 16:03:10 -0400
Subject: [PATCH] Log # duplicate tags.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---
 import.go  | 12 +++++++++---
 tilelib.go | 10 ++++++++--
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/import.go b/import.go
index 36558ca8d6..a396636fcb 100644
--- a/import.go
+++ b/import.go
@@ -264,7 +264,9 @@ 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)
-				variants[0] = tseqs.Variants()
+				var kept, dropped int
+				variants[0], kept, dropped = tseqs.Variants()
+				log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
 				return err
 			}
 			infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
@@ -273,7 +275,9 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
 				log.Printf("%s starting", infile2)
 				defer log.Printf("%s done", infile2)
 				tseqs, err := cmd.tileFasta(tilelib, infile2)
-				variants[1] = tseqs.Variants()
+				var kept, dropped int
+				variants[1], kept, dropped = tseqs.Variants()
+				log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
 				return err
 			}
 		} else {
@@ -284,7 +288,9 @@ func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
 					log.Printf("%s phase %d starting", infile, phase+1)
 					defer log.Printf("%s phase %d done", infile, phase+1)
 					tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
-					variants[phase] = tseqs.Variants()
+					var kept, dropped int
+					variants[phase], kept, dropped = tseqs.Variants()
+					log.Printf("%s phase %d found %d unique tags plus %d repeats", infile, phase+1, kept, dropped)
 					return err
 				}
 			}
diff --git a/tilelib.go b/tilelib.go
index be60ab2e1d..5b4b30754c 100644
--- a/tilelib.go
+++ b/tilelib.go
@@ -20,7 +20,7 @@ type tileLibRef struct {
 
 type tileSeq map[string][]tileLibRef
 
-func (tseq tileSeq) Variants() []tileVariantID {
+func (tseq tileSeq) Variants() ([]tileVariantID, int, int) {
 	maxtag := 0
 	for _, refs := range tseq {
 		for _, ref := range refs {
@@ -30,12 +30,18 @@ func (tseq tileSeq) Variants() []tileVariantID {
 		}
 	}
 	vars := make([]tileVariantID, maxtag+1)
+	var kept, dropped int
 	for _, refs := range tseq {
 		for _, ref := range refs {
+			if vars[int(ref.tag)] != 0 {
+				dropped++
+			} else {
+				kept++
+			}
 			vars[int(ref.tag)] = ref.variant
 		}
 	}
-	return vars
+	return vars, kept, dropped
 }
 
 type tileLibrary struct {
-- 
2.30.2