From 37ce3536e18ea352c08ee1412330d8efbc824468 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 18 Feb 2022 10:01:23 +0100
Subject: [PATCH] New more functionnal version of obiuniq. But it has a memory
 leak

---
 pkg/obitools/obiuniq/options.go | 15 ++++++++++--
 pkg/obitools/obiuniq/unique.go  | 42 +++++++++++++++++++++------------
 2 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/pkg/obitools/obiuniq/options.go b/pkg/obitools/obiuniq/options.go
index 2820b65..b06f4d8 100644
--- a/pkg/obitools/obiuniq/options.go
+++ b/pkg/obitools/obiuniq/options.go
@@ -9,18 +9,25 @@ var _StatsOn = make([]string, 0, 10)
 var _Keys = make([]string, 0, 10)
 var _OnDisk = false
 var _chunks = 100
+var _NAValue = "NA"
 
 func UniqueOptionSet(options *getoptions.GetOpt) {
 	options.StringSliceVar(&_StatsOn, "merge",
-		1, 1000,
+		1, 1,
 		options.Alias("m"),
 		options.Description("Adds a merged attribute containing the list of sequence record ids merged within this group."))
+
 	options.StringSliceVar(&_Keys, "category-attribute",
-		1, 1000,
+		1, 1,
 		options.Alias("c"),
 		options.Description("Adds one attribute to the list of attributes used to define sequence groups (this option can be used several times)."))
+
+	options.StringVar(&_NAValue, "na-value", _NAValue,
+		options.Description("Value used when the classifier tag is not defined for a sequence."))
+
 	options.BoolVar(&_OnDisk, "on-disk", true,
 		options.Description("Allows for using a disk cache during the dereplication process. "))
+
 	options.IntVar(&_chunks, "chunk-count", _chunks,
 		options.Description("In how many chunk the dataset is pre-devided for speeding up the process."))
 
@@ -52,3 +59,7 @@ func CLINumberOfChunks() int {
 
 	return _chunks
 }
+
+func CLINAValue() string {
+	return _NAValue
+}
diff --git a/pkg/obitools/obiuniq/unique.go b/pkg/obitools/obiuniq/unique.go
index 7bbcaf2..20aa0cb 100644
--- a/pkg/obitools/obiuniq/unique.go
+++ b/pkg/obitools/obiuniq/unique.go
@@ -10,29 +10,41 @@ import (
 
 func Unique(sequences obiseq.IBioSequenceBatch) obiseq.IBioSequenceBatch {
 
-	classifier := obiseq.HashClassifier(CLINumberOfChunks())
-	var newIter obiseq.IBioSequenceBatch
-	var err error
+	options := make([]obichunk.WithOption, 0, 30)
+
+	options = append(options,
+		obichunk.OptionBatchCount(CLINumberOfChunks()),
+	)
 
 	if CLIUniqueInMemory() {
 		log.Printf("Running dereplication in memory on %d chunks", CLINumberOfChunks())
-		newIter, err = obichunk.ISequenceChunk(sequences, classifier, 2)
+		options = append(options, obichunk.OptionSortOnMemory())
 	} else {
 		log.Printf("Running dereplication on disk with %d chunks", CLINumberOfChunks())
-		newIter, err = obichunk.ISequenceChunkOnDisk(sequences, classifier, 2)
+		options = append(options, obichunk.OptionSortOnDisk())
 	}
 
+	options = append(options,
+		obichunk.OptionStatOn(CLIStatsOn()...))
+
+	options = append(options,
+		obichunk.OptionSubCategory(CLIKeys()...))
+
+	options = append(options,
+		obichunk.OptionsParallelWorkers(
+			obioptions.CLIParallelWorkers()),
+		obichunk.OptionsBufferSize(
+			obioptions.CLIBufferSize()),
+		obichunk.OptionsBatchSize(
+			obioptions.CLIBatchSize()),
+		obichunk.OptionNAValue(CLINAValue()),
+	)
+
+	iUnique, err := obichunk.IUniqueSequence(sequences, options...)
+
 	if err != nil {
-		log.Fatalf("error in spliting the dataset : %v", err)
+		log.Fatal(err)
 	}
 
-	statsOn := CLIStatsOn()
-	keys := CLIKeys()
-	parallelWorkers := obioptions.CLIParallelWorkers()
-	buffSize := obioptions.CLIBufferSize()
-
-	newIter = newIter.MakeISliceWorker(obiseq.UniqueSliceWorker(statsOn, keys...),
-		parallelWorkers, buffSize)
-
-	return newIter
+	return iUnique
 }