Ensure that reads that are already marked as duplicate are handled co…

…rrectly in mark duplicates / mark optical duplicates.
ExaScience · Aug 19, 2020 · 78ce9b8 · 78ce9b8
1 parent 1712531
commit 78ce9b8
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,5 +1,5 @@
 elPrep: a high-performance tool for preparing SAM/BAM files.
-Copyright (c) 2017, 2018 imec vzw.
+Copyright (c) 2017-2020 imec vzw.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as

diff --git a/cmd/util.go b/cmd/util.go
@@ -37,7 +37,7 @@ const (
 	// ProgramName is "elprep"
 	ProgramName = "elprep"
 	// ProgramVersion is the version of the elprep binary
-	ProgramVersion = "4.1.5"
+	ProgramVersion = "4.1.6"
 	// ProgramURL is the repository for the elprep source code
 	ProgramURL = "http://github.com/exascience/elprep"
 )

diff --git a/filters/mark-duplicates.go b/filters/mark-duplicates.go
@@ -423,7 +423,7 @@ func MarkDuplicates(alsoOpticals bool) (sam.Filter, *sync.Map, *sync.Map) {
 		if alsoOpticals {
 			return func(aln *sam.Alignment) bool {
 				addLIBID(aln, lbTable) // need this for all reads when marking optical duplicates
-				if aln.FlagNotAny(sam.Unmapped | sam.Secondary | sam.Duplicate | sam.Supplementary) {
+				if aln.FlagNotAny(sam.Unmapped | sam.Secondary | sam.Supplementary) {
 					adaptAlignment(aln)
 					classifyFragment(aln, fragments)
 					classifyPair(aln, pairsFragments, pairs)
@@ -432,7 +432,7 @@ func MarkDuplicates(alsoOpticals bool) (sam.Filter, *sync.Map, *sync.Map) {
 			}
 		}
 		return func(aln *sam.Alignment) bool {
-			if aln.FlagNotAny(sam.Unmapped | sam.Secondary | sam.Duplicate | sam.Supplementary) {
+			if aln.FlagNotAny(sam.Unmapped | sam.Secondary | sam.Supplementary) {
 				addLIBID(aln, lbTable) // don't need this for all reads when not marking optical duplicates
 				adaptAlignment(aln)
 				classifyFragment(aln, fragments)