academic/flexbar: incl. patches for newer tbb

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 763 insertions, 9 deletions

diff --git a/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch
new file mode 100644
index 000000000000..12068e9337c7
--- /dev/null
+++ b/academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch
@@ -0,0 +1,710 @@
+From 195a1ab2c2715b07df5acff58dc2a0396d9cd52d Mon Sep 17 00:00:00 2001
+From: Liam Keegan <liam@keegan.ch>
+Date: Thu, 9 Feb 2023 16:27:37 +0100
+Subject: [PATCH 1/4] Migrate from tbb to onetbb
+
+- add `FlexbarAtomic`
+  - a simple wrapper around `std::atomic` which adds a copy constructor
+  - to replace `tbb::atomic` member variables in classes with default copy constructors
+- replace removed `tbb::atomic`
+  - with `FlexbarAtomic` if copy constructor was assumed
+  - with `std::atomic` otherwise
+- filters (PairedAlign, PairedInput, PairedOutput)
+  - no longer inherit from tbb::filter
+  - take and return pointers to actual type instead of void*
+  - operator() is now const
+- pipeline
+  - use parallel_pipeline and make_filter
+- use global_control to set max threads
+- use `oneapi::tbb` namespace
+- add find_package for TBB to CMakeLists.txt
+---
+ src/CMakeLists.txt   |  9 ++-------
+ src/Flexbar.h        | 27 +++++++++++++++------------
+ src/FlexbarTypes.h   | 16 +++++++++++++++-
+ src/LoadAdapters.h   |  4 ++--
+ src/LoadFasta.h      |  6 +++---
+ src/Options.h        |  2 +-
+ src/PairedAlign.h    | 23 ++++++++++-------------
+ src/PairedInput.h    | 10 ++++------
+ src/PairedOutput.h   | 29 ++++++++++++-----------------
+ src/SeqAlign.h       | 12 ++++++------
+ src/SeqAlignPair.h   |  6 +++---
+ src/SeqInput.h       |  2 +-
+ src/SeqOutput.h      |  6 +++---
+ src/SeqOutputFiles.h |  2 +-
+ 14 files changed, 78 insertions(+), 76 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index a5643ca..ca4e5db 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -32,9 +32,9 @@ else()
+ endif()
+ 
+ add_executable( flexbar Flexbar.cpp )
+-target_link_libraries( flexbar tbb -lpthread )
+-
+ 
++find_package(TBB CONFIG REQUIRED)
++target_link_libraries(flexbar TBB::tbb)
+ find_package( ZLIB )
+ if( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
+@@ -53,9 +53,4 @@ else()
+ 	message( STATUS "Build will not support bzip2." )
+ endif()
+ 
+-# find_package( TBB REQUIRED )
+-# if( NOT TBB_FOUND )
+-# 	message( FATAL_ERROR "TBB library not found." )
+-# endif()
+-
+ set( SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} flexbar CACHE INTERNAL "" )
+diff --git a/src/Flexbar.h b/src/Flexbar.h
+index 67c07d7..d1a8f31 100644
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
+@@ -12,10 +12,9 @@
+ #include <iostream>
+ #include <vector>
+ 
+-#include <tbb/pipeline.h>
+-#include <tbb/task_scheduler_init.h>
+-#include <tbb/concurrent_vector.h>
+-#include <tbb/mutex.h>
++#include <oneapi/tbb/parallel_pipeline.h>
++#include <oneapi/tbb/global_control.h>
++#include <oneapi/tbb/concurrent_vector.h>
+ 
+ #include <seqan/basic.h>
+ #include <seqan/sequence.h>
+@@ -240,14 +239,18 @@ void startProcessing(Options &o){
+ 	PairedAlign<TSeqStr, TString>  alignFilter(o);
+ 	PairedOutput<TSeqStr, TString> outputFilter(o);
+ 	
+-	tbb::task_scheduler_init init_serial(o.nThreads);
+-	tbb::pipeline pipe;
+-	
+-	pipe.add_filter(inputFilter);
+-	pipe.add_filter(alignFilter);
+-	pipe.add_filter(outputFilter);
+-	pipe.run(o.nThreads);
+-	
++    oneapi::tbb::global_control control(
++            oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads);
++    oneapi::tbb::parallel_pipeline(o.nThreads,
++                                   oneapi::tbb::make_filter<void, TPairedReadBundle *>(
++                                           oneapi::tbb::filter_mode::serial_in_order, inputFilter)
++                                   &
++                                   oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>(
++                                           oneapi::tbb::filter_mode::parallel, alignFilter)
++                                   &
++                                   oneapi::tbb::make_filter<TPairedReadBundle *, void>(
++                                           oneapi::tbb::filter_mode::serial_in_order, outputFilter)
++    );
+ 	if(o.logAlign == TAB) *out << "\n";
+ 	*out << "done.\n" << endl;
+ 	
+diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h
+index 8abdf66..f1bce0f 100644
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -3,6 +3,20 @@
+ #ifndef FLEXBAR_FLEXBARTYPES_H
+ #define FLEXBAR_FLEXBARTYPES_H
+ 
++#include <atomic>
++
++// A simple wrapper around std::atomic<T> with a copy-constructor
++// This is a drop-in replacement for the previously used tbb::atomic (which is copyable),
++// to avoid having to add copy-constructors to classes that used it
++template<typename T>
++struct FlexbarAtomic : public std::atomic<T> {
++    FlexbarAtomic() = default;
++    explicit constexpr FlexbarAtomic(T t) : std::atomic<T>(t) {}
++    constexpr FlexbarAtomic(const FlexbarAtomic<T>& other) :
++            FlexbarAtomic(other.load(std::memory_order_acquire))
++    {}
++};
++
+ 
+ template <typename TSeqStr, typename TString>
+ class SeqRead {
+@@ -126,7 +140,7 @@ namespace flexbar{
+ 		FSeqStr seq;
+ 		bool rcAdapter;
+ 		
+-		tbb::atomic<unsigned long> rmOverlap, rmFull;
++        FlexbarAtomic<unsigned long> rmOverlap, rmFull;
+ 		
+ 		TBar() :
+ 			rmOverlap(0),
+diff --git a/src/LoadAdapters.h b/src/LoadAdapters.h
+index 046e799..6168775 100644
+--- a/src/LoadAdapters.h
++++ b/src/LoadAdapters.h
+@@ -10,7 +10,7 @@ class LoadAdapters {
+ private:
+ 	
+ 	std::ostream *out;
+-	tbb::concurrent_vector<flexbar::TBar> adapters;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> adapters;
+ 	
+ 	flexbar::Adapters a;
+ 	
+@@ -134,7 +134,7 @@ class LoadAdapters {
+ 	};
+ 	
+ 	
+-	tbb::concurrent_vector<flexbar::TBar> getAdapters(){
++	oneapi::tbb::concurrent_vector<flexbar::TBar> getAdapters(){
+ 		return adapters;
+ 	}
+ 	
+diff --git a/src/LoadFasta.h b/src/LoadFasta.h
+index 3e69594..ccd0550 100644
+--- a/src/LoadFasta.h
++++ b/src/LoadFasta.h
+@@ -10,7 +10,7 @@ class LoadFasta {
+ private:
+ 	
+ 	std::ostream *out;
+-	tbb::concurrent_vector<flexbar::TBar> bars;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> bars;
+ 	
+ 	const bool m_isAdapter;
+ 	const flexbar::RevCompMode m_rcMode;
+@@ -94,12 +94,12 @@ class LoadFasta {
+ 	};
+ 	
+ 	
+-	tbb::concurrent_vector<flexbar::TBar> getBars(){
++	oneapi::tbb::concurrent_vector<flexbar::TBar> getBars(){
+ 		return bars;
+ 	}
+ 	
+ 	
+-	void setBars(tbb::concurrent_vector<flexbar::TBar> &newBars){
++	void setBars(oneapi::tbb::concurrent_vector<flexbar::TBar> &newBars){
+ 		bars = newBars;
+ 	}
+ 	
+diff --git a/src/Options.h b/src/Options.h
+index 6299c50..21d7710 100644
+--- a/src/Options.h
++++ b/src/Options.h
+@@ -46,7 +46,7 @@ struct Options{
+ 	flexbar::AdapterPreset   aPreset;
+ 	flexbar::AdapterTrimmed  aTrimmed;
+ 	
+-	tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> barcodes, adapters, barcodes2, adapters2;
+ 	
+ 	std::ostream *out;
+ 	std::fstream fstrmOut;
+diff --git a/src/PairedAlign.h b/src/PairedAlign.h
+index d6f9956..59c4473 100644
+--- a/src/PairedAlign.h
++++ b/src/PairedAlign.h
+@@ -9,7 +9,7 @@
+ 
+ 
+ template <typename TSeqStr, typename TString>
+-class PairedAlign : public tbb::filter {
++class PairedAlign {
+ 
+ private:
+ 	
+@@ -31,9 +31,9 @@ class PairedAlign : public tbb::filter {
+ 	const flexbar::TrimEnd        m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
+ 	const flexbar::PairOverlap    m_poMode;
+ 	
+-	tbb::atomic<unsigned long> m_unassigned;
+-	tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2;
+-	tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2;
++    mutable FlexbarAtomic<unsigned long> m_unassigned;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2;
+ 	
+ 	typedef SeqAlign<TSeqStr, TString, SeqAlignAlgo<TSeqStr> > TSeqAlign;
+ 	TSeqAlign *m_a1, *m_b1, *m_a2, *m_b2;
+@@ -47,7 +47,6 @@ class PairedAlign : public tbb::filter {
+ 	
+ 	PairedAlign(Options &o) :
+ 		
+-		filter(parallel),
+ 		m_format(o.format),
+ 		m_log(o.logAlign),
+ 		m_runType(o.runType),
+@@ -102,7 +101,7 @@ class PairedAlign : public tbb::filter {
+ 	};
+ 	
+ 	
+-	void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode){
++	void alignPairedReadToBarcodes(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode) const {
+ 		
+ 		using namespace flexbar;
+ 		
+@@ -122,7 +121,7 @@ class PairedAlign : public tbb::filter {
+ 	}
+ 	
+ 	
+-	void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd){
++	void alignPairedReadToAdapters(flexbar::TPairedRead* pRead, flexbar::TAlignBundle &alBundle, std::vector<flexbar::ComputeCycle> &cycle, std::vector<unsigned int> &idxAl, const flexbar::AlignmentMode &alMode, const flexbar::TrimEnd trimEnd) const {
+ 		
+ 		using namespace flexbar;
+ 		
+@@ -173,7 +172,7 @@ class PairedAlign : public tbb::filter {
+ 	}
+ 	
+ 	
+-	void trimLeftHPS(flexbar::TSeqRead* seqRead){
++	void trimLeftHPS(flexbar::TSeqRead* seqRead) const{
+ 		
+ 		using namespace std;
+ 		using namespace flexbar;
+@@ -223,7 +222,7 @@ class PairedAlign : public tbb::filter {
+ 	}
+ 	
+ 	
+-	void trimRightHPS(flexbar::TSeqRead* seqRead){
++	void trimRightHPS(flexbar::TSeqRead* seqRead) const{
+ 		
+ 		using namespace std;
+ 		using namespace flexbar;
+@@ -275,13 +274,11 @@ class PairedAlign : public tbb::filter {
+ 	
+ 	
+ 	// tbb filter operator
+-	void* operator()(void* item){
++    flexbar::TPairedReadBundle* operator()(flexbar::TPairedReadBundle* prBundle) const{
+ 		
+ 		using namespace flexbar;
+ 		
+-		if(item != NULL){
+-			
+-			TPairedReadBundle *prBundle = static_cast<TPairedReadBundle* >(item);
++		if(prBundle != NULL){
+ 			
+ 			if(m_umiTags){
+ 				for(unsigned int i = 0; i < prBundle->size(); ++i){
+diff --git a/src/PairedInput.h b/src/PairedInput.h
+index 94a54e5..f7a6c9e 100644
+--- a/src/PairedInput.h
++++ b/src/PairedInput.h
+@@ -7,7 +7,7 @@
+ 
+ 
+ template <typename TSeqStr, typename TString>
+-class PairedInput : public tbb::filter {
++class PairedInput {
+ 
+ private:
+ 	
+@@ -15,14 +15,13 @@ class PairedInput : public tbb::filter {
+ 	const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved;
+ 	const unsigned int m_bundleSize;
+ 	
+-	tbb::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles;
++    mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles;
+ 	SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b;
+ 	
+ public:
+ 	
+ 	PairedInput(const Options &o) :
+ 		
+-		filter(serial_in_order),
+ 		m_format(o.format),
+ 		m_useNumberTag(o.useNumberTag),
+ 		m_interleaved(o.interleavedInput),
+@@ -55,7 +54,7 @@ class PairedInput : public tbb::filter {
+ 	}
+ 	
+ 	
+-	void* loadPairedReadBundle(){
++	void* loadPairedReadBundle() const{
+ 		
+ 		using namespace std;
+ 		using namespace flexbar;
+@@ -207,8 +206,7 @@ class PairedInput : public tbb::filter {
+ 	
+ 	
+ 	// tbb filter operator
+-	void* operator()(void*){
+-		
++    flexbar::TPairedReadBundle* operator()(oneapi::tbb::flow_control& fc) const {
+ 		using namespace flexbar;
+ 		
+ 		TPairedReadBundle *prBundle = NULL;
+diff --git a/src/PairedOutput.h b/src/PairedOutput.h
+index 6c3fad7..c0d3626 100644
+--- a/src/PairedOutput.h
++++ b/src/PairedOutput.h
+@@ -9,7 +9,7 @@
+ 
+ 
+ template <typename TSeqStr, typename TString>
+-class PairedOutput : public tbb::filter {
++class PairedOutput {
+ 
+ private:
+ 	
+@@ -18,8 +18,8 @@ class PairedOutput : public tbb::filter {
+ 	const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP;
+ 	const bool m_twoBarcodes, m_qtrimPostRm;
+ 	
+-	tbb::atomic<unsigned long> m_nSingleReads, m_nLowPhred;
+-	
++    mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred;
++
+ 	const std::string m_target;
+ 	
+ 	const flexbar::FileFormat     m_format;
+@@ -34,14 +34,13 @@ class PairedOutput : public tbb::filter {
+ 	TOutFiles *m_outMap;
+ 	std::ostream *out;
+ 	
+-	tbb::concurrent_vector<flexbar::TBar> *m_adapters,  *m_barcodes;
+-	tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters,  *m_barcodes;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters2, *m_barcodes2;
+ 	
+ public:
+ 	
+ 	PairedOutput(Options &o) :
+ 		
+-		filter(serial_in_order),
+ 		m_target(o.targetName),
+ 		m_format(o.format),
+ 		m_runType(o.runType),
+@@ -57,6 +56,8 @@ class PairedOutput : public tbb::filter {
+ 		m_writeSingleReads(o.writeSingleReads),
+ 		m_writeSingleReadsP(o.writeSingleReadsP),
+ 		m_twoBarcodes(o.barDetect == flexbar::WITHIN_READ_REMOVAL2 || o.barDetect == flexbar::WITHIN_READ2),
++        m_nSingleReads(0),
++        m_nLowPhred(0),
+ 		out(o.out){
+ 		
+ 		using namespace std;
+@@ -68,9 +69,7 @@ class PairedOutput : public tbb::filter {
+ 		m_adapters2 = &o.adapters2;
+ 		
+ 		m_mapsize      = 0;
+-		m_nSingleReads = 0;
+-		m_nLowPhred    = 0;
+-		
++
+ 		switch(m_runType){
+ 			
+ 			case PAIRED_BARCODED:{
+@@ -237,7 +236,7 @@ class PairedOutput : public tbb::filter {
+ 	};
+ 	
+ 	
+-	void writePairedRead(flexbar::TPairedRead* pRead){
++	void writePairedRead(flexbar::TPairedRead* pRead) const{
+ 		
+ 		using namespace flexbar;
+ 		
+@@ -346,13 +345,11 @@ class PairedOutput : public tbb::filter {
+ 	
+ 	
+ 	// tbb filter operator
+-	void* operator()(void* item){
++	void operator()(flexbar::TPairedReadBundle* prBundle) const{
+ 		
+ 		using namespace flexbar;
+ 		
+-		if(item != NULL){
+-			
+-			TPairedReadBundle *prBundle = static_cast< TPairedReadBundle* >(item);
++		if(prBundle != NULL){
+ 			
+ 			for(unsigned int i = 0; i < prBundle->size(); ++i){
+ 				
+@@ -361,8 +358,6 @@ class PairedOutput : public tbb::filter {
+ 			}
+ 			delete prBundle;
+ 		}
+-		
+-		return NULL;
+ 	}
+ 	
+ 	
+@@ -457,7 +452,7 @@ class PairedOutput : public tbb::filter {
+ 		
+ 		using namespace std;
+ 		
+-		tbb::concurrent_vector<flexbar::TBar> *adapters;
++		oneapi::tbb::concurrent_vector<flexbar::TBar> *adapters;
+ 		const unsigned int maxSpaceLen = 20;
+ 		
+ 		int startLen = 8;
+diff --git a/src/SeqAlign.h b/src/SeqAlign.h
+index 221a901..b10aafa 100644
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -3,7 +3,7 @@
+ #ifndef FLEXBAR_SEQALIGN_H
+ #define FLEXBAR_SEQALIGN_H
+ 
+-tbb::mutex ouputMutex;
++std::mutex ouputMutex;
+ 
+ template <typename TSeqStr, typename TString, class TAlgorithm>
+ class SeqAlign {
+@@ -21,16 +21,16 @@ class SeqAlign {
+ 	const float m_errorRate;
+ 	const unsigned int m_bundleSize;
+ 	
+-	tbb::atomic<unsigned long> m_nPreShortReads, m_modified;
+-	tbb::concurrent_vector<flexbar::TBar> *m_queries;
+-	tbb::concurrent_vector<unsigned long> m_rmOverlaps;
++	std::atomic<unsigned long> m_nPreShortReads, m_modified;
++	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_queries;
++	oneapi::tbb::concurrent_vector<unsigned long> m_rmOverlaps;
+ 	
+ 	std::ostream *m_out;
+ 	TAlgorithm m_algo;
+ 	
+ public:
+ 	
+-	SeqAlign(tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding):
++	SeqAlign(oneapi::tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding):
+ 			
+ 			m_minOverlap(minOverlap),
+ 			m_errorRate(errorRate),
+@@ -51,7 +51,7 @@ class SeqAlign {
+ 			m_algo(TAlgorithm(o, match, mismatch, gapCost, ! isBarcoding)){
+ 		
+ 		m_queries    = queries;
+-		m_rmOverlaps = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0);
++		m_rmOverlaps = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0);
+ 	};
+ 	
+ 	
+diff --git a/src/SeqAlignPair.h b/src/SeqAlignPair.h
+index d5d1079..2479242 100644
+--- a/src/SeqAlignPair.h
++++ b/src/SeqAlignPair.h
+@@ -20,8 +20,8 @@ class SeqAlignPair {
+ 	const float m_errorRate;
+ 	const unsigned int m_bundleSize;
+ 	
+-	tbb::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified;
+-	tbb::concurrent_vector<unsigned long> m_overlapLengths;
++	std::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified;
++	oneapi::tbb::concurrent_vector<unsigned long> m_overlapLengths;
+ 	
+ 	std::ostream *m_out;
+ 	TAlgorithm m_algo;
+@@ -45,7 +45,7 @@ class SeqAlignPair {
+ 			m_modified(0),
+ 			m_algo(TAlgorithm(o, match, mismatch, gapCost, true)){
+ 		
+-		m_overlapLengths = tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0);
++		m_overlapLengths = oneapi::tbb::concurrent_vector<unsigned long>(flexbar::MAX_READLENGTH + 1, 0);
+ 	};
+ 	
+ 	
+diff --git a/src/SeqInput.h b/src/SeqInput.h
+index 4dcbe74..7a8f8d0 100644
+--- a/src/SeqInput.h
++++ b/src/SeqInput.h
+@@ -18,7 +18,7 @@ class SeqInput {
+ 	
+ 	const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput;
+ 	const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
+-	tbb::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred;
++	std::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred;
+ 	
+ public:
+ 	
+diff --git a/src/SeqOutput.h b/src/SeqOutput.h
+index 9a63e6a..64cab91 100644
+--- a/src/SeqOutput.h
++++ b/src/SeqOutput.h
+@@ -18,8 +18,8 @@ class SeqOutput {
+ 	const bool m_switch2Fasta, m_writeLenDist, m_useStdout;
+ 	const unsigned int m_minLength, m_cutLen_read;
+ 	
+-	tbb::atomic<unsigned long> m_countGood, m_countGoodChars;
+-	tbb::concurrent_vector<unsigned long> m_lengthDist;
++	std::atomic<unsigned long> m_countGood, m_countGoodChars;
++	oneapi::tbb::concurrent_vector<unsigned long> m_lengthDist;
+ 	
+ public:
+ 	
+@@ -48,7 +48,7 @@ class SeqOutput {
+ 		}
+ 		m_filePath += o.outCompression;
+ 		
+-		m_lengthDist = tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0);
++		m_lengthDist = oneapi::tbb::concurrent_vector<unsigned long>(MAX_READLENGTH + 1, 0);
+ 		
+ 		if(m_useStdout){
+ 			
+diff --git a/src/SeqOutputFiles.h b/src/SeqOutputFiles.h
+index fe6b50e..8ece58c 100644
+--- a/src/SeqOutputFiles.h
++++ b/src/SeqOutputFiles.h
+@@ -14,7 +14,7 @@ class SeqOutputFiles {
+ 	typedef SeqOutput<TSeqStr, TString> TSeqOutput;
+ 	
+ 	TSeqOutput *f1, *f2, *single1, *single2;
+-	tbb::atomic<unsigned long> m_nShort_1, m_nShort_2;
++	std::atomic<unsigned long> m_nShort_1, m_nShort_2;
+ 	
+ 	SeqOutputFiles() :
+ 		f1(0),
+
+From 1c872fa10d474f090633fc95d409aa60607a3f96 Mon Sep 17 00:00:00 2001
+From: Liam Keegan <liam@keegan.ch>
+Date: Fri, 10 Feb 2023 09:55:58 +0100
+Subject: [PATCH 2/4] Fix parallel_pipeline issues
+
+- pass a lambda with a reference to the filter instead of directly passing the filter to parallel_pipeline
+  - passed filters may be copied and/or deleted by tbb
+  - flexbar continues to use the filter objects after the pipeline is finished
+- call fc.stop() in PairedInput when there is no more input
+  - required control flow for first filter in parallel_pipeline that was previously missing
+---
+ src/Flexbar.h     | 9 ++++++---
+ src/PairedInput.h | 9 +++++++--
+ 2 files changed, 13 insertions(+), 5 deletions(-)
+
+diff --git a/src/Flexbar.h b/src/Flexbar.h
+index d1a8f31..46261cf 100644
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
+@@ -243,13 +243,16 @@ void startProcessing(Options &o){
+             oneapi::tbb::global_control::max_allowed_parallelism, o.nThreads);
+     oneapi::tbb::parallel_pipeline(o.nThreads,
+                                    oneapi::tbb::make_filter<void, TPairedReadBundle *>(
+-                                           oneapi::tbb::filter_mode::serial_in_order, inputFilter)
++                                           oneapi::tbb::filter_mode::serial_in_order,
++                                           [&inputFilter](auto &fc) { return inputFilter(fc); })
+                                    &
+                                    oneapi::tbb::make_filter<TPairedReadBundle *, TPairedReadBundle *>(
+-                                           oneapi::tbb::filter_mode::parallel, alignFilter)
++                                           oneapi::tbb::filter_mode::parallel,
++                                           [&alignFilter](TPairedReadBundle *tprb) { return alignFilter(tprb); })
+                                    &
+                                    oneapi::tbb::make_filter<TPairedReadBundle *, void>(
+-                                           oneapi::tbb::filter_mode::serial_in_order, outputFilter)
++                                           oneapi::tbb::filter_mode::serial_in_order,
++                                           [&outputFilter](TPairedReadBundle *tprb) { return outputFilter(tprb); })
+     );
+ 	if(o.logAlign == TAB) *out << "\n";
+ 	*out << "done.\n" << endl;
+diff --git a/src/PairedInput.h b/src/PairedInput.h
+index f7a6c9e..4fc4441 100644
+--- a/src/PairedInput.h
++++ b/src/PairedInput.h
+@@ -221,9 +221,14 @@ class PairedInput {
+ 				
+ 				prBundle = static_cast< TPairedReadBundle* >(loadPairedReadBundle());
+ 				
+-				if(prBundle == NULL) return prBundle;
++				if(prBundle == NULL){
++                    fc.stop();
++                    return prBundle;
++                }
+ 			}
+-		}
++		} else {
++            fc.stop();
++        }
+ 		
+ 		return prBundle;
+ 	}
+
+From 19722f2743c96235ff57948eda82f963cf734131 Mon Sep 17 00:00:00 2001
+From: Liam Keegan <liam@keegan.ch>
+Date: Fri, 10 Feb 2023 10:21:22 +0100
+Subject: [PATCH 3/4] revert accidental removal of pthread linking in
+ src/CMakeLists.txt
+
+---
+ src/CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index ca4e5db..fb42cc4 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -32,6 +32,7 @@ else()
+ endif()
+ 
+ add_executable( flexbar Flexbar.cpp )
++target_link_libraries( flexbar -lpthread )
+ 
+ find_package(TBB CONFIG REQUIRED)
+ target_link_libraries(flexbar TBB::tbb)
+
+From a9b0eb87a391aeaf760f8116dca777749c8b4f96 Mon Sep 17 00:00:00 2001
+From: Liam Keegan <liam@keegan.ch>
+Date: Fri, 10 Feb 2023 10:52:35 +0100
+Subject: [PATCH 4/4] use `std::atomic` instead of `FlexbarAtomic` in filters
+ as they are no longer require copy constructors
+
+---
+ src/FlexbarTypes.h | 2 +-
+ src/PairedAlign.h  | 2 +-
+ src/PairedInput.h  | 2 +-
+ src/PairedOutput.h | 2 +-
+ 4 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h
+index f1bce0f..3cf241e 100644
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -139,7 +139,7 @@ namespace flexbar{
+ 		FString id;
+ 		FSeqStr seq;
+ 		bool rcAdapter;
+-		
++
+         FlexbarAtomic<unsigned long> rmOverlap, rmFull;
+ 		
+ 		TBar() :
+diff --git a/src/PairedAlign.h b/src/PairedAlign.h
+index 59c4473..d3b50ae 100644
+--- a/src/PairedAlign.h
++++ b/src/PairedAlign.h
+@@ -31,7 +31,7 @@ class PairedAlign {
+ 	const flexbar::TrimEnd        m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
+ 	const flexbar::PairOverlap    m_poMode;
+ 	
+-    mutable FlexbarAtomic<unsigned long> m_unassigned;
++    mutable std::atomic<unsigned long> m_unassigned;
+ 	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2;
+ 	oneapi::tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2;
+ 	
+diff --git a/src/PairedInput.h b/src/PairedInput.h
+index 4fc4441..230474b 100644
+--- a/src/PairedInput.h
++++ b/src/PairedInput.h
+@@ -15,7 +15,7 @@ class PairedInput {
+ 	const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved;
+ 	const unsigned int m_bundleSize;
+ 	
+-    mutable FlexbarAtomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles;
++    mutable std::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles;
+ 	SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b;
+ 	
+ public:
+diff --git a/src/PairedOutput.h b/src/PairedOutput.h
+index c0d3626..fae5d3f 100644
+--- a/src/PairedOutput.h
++++ b/src/PairedOutput.h
+@@ -18,7 +18,7 @@ class PairedOutput {
+ 	const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP;
+ 	const bool m_twoBarcodes, m_qtrimPostRm;
+ 	
+-    mutable FlexbarAtomic<unsigned long> m_nSingleReads, m_nLowPhred;
++    mutable std::atomic<unsigned long> m_nSingleReads, m_nLowPhred;
+ 
+ 	const std::string m_target;
+ 	
diff --git a/academic/flexbar/flexbar.SlackBuild b/academic/flexbar/flexbar.SlackBuild
index 69ec0db8d0f4..803163e04612 100644
--- a/academic/flexbar/flexbar.SlackBuild
+++ b/academic/flexbar/flexbar.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for flexbar
 
-# Copyright 2017-2021 Rob van Nues
+# Copyright 2017-2023 Rob van Nues
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=flexbar
 VERSION=${VERSION:-3.5.0}
-BUILD=${BUILD:-1}
+BUILD=${BUILD:-2}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
@@ -41,9 +41,6 @@ if [ -z "$ARCH" ]; then
   esac
 fi
 
-# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
-# the name of the created package would be, and then exit. This information
-# could be useful to other scripts.
 if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
   echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
   exit 0
@@ -83,6 +80,9 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
   -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
+patch -p 1 < $CWD/seqan_flexbar_pull_20.patch
+patch -p 1 < $CWD/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch
+
 mkdir -p build
 cd build
   cmake \
diff --git a/academic/flexbar/flexbar.info b/academic/flexbar/flexbar.info
index 23efa136d830..6ac4dd092077 100644
--- a/academic/flexbar/flexbar.info
+++ b/academic/flexbar/flexbar.info
@@ -1,12 +1,12 @@
 PRGNAM="flexbar"
 VERSION="3.5.0"
 HOMEPAGE="https://github.com/seqan/flexbar"
-DOWNLOAD="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="https://github.com/seqan/flexbar/archive/v3.5.0/flexbar-3.5.0.tar.gz \
           https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz"
-MD5SUM="0e07bf4afebfd731c4718b401383224a \
+MD5SUM_x86_64="0e07bf4afebfd731c4718b401383224a \
         eeadf5544555c1e196537a888d02d09f"
-DOWNLOAD_x86_64=""
-MD5SUM_x86_64=""
 REQUIRES="tbb"
 MAINTAINER="Rob van Nues"
 EMAIL="sborg63@disroot.org"
diff --git a/academic/flexbar/seqan_flexbar_pull_20.patch b/academic/flexbar/seqan_flexbar_pull_20.patch
new file mode 100644
index 000000000000..96db258a6bd8
--- /dev/null
+++ b/academic/flexbar/seqan_flexbar_pull_20.patch
@@ -0,0 +1,44 @@
+From 707f9381be5d42c6acd122a3c268deb66600cf9a Mon Sep 17 00:00:00 2001
+From: svnbgnk <swb@live.de>
+Date: Thu, 25 Jul 2019 16:35:47 +0200
+Subject: [PATCH] added mutex lock to log output
+
+---
+ src/Flexbar.h  | 1 +
+ src/SeqAlign.h | 3 +++
+ 2 files changed, 4 insertions(+)
+
+diff --git a/src/Flexbar.h b/src/Flexbar.h
+index 2f82f18..67c07d7 100644
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
+@@ -15,6 +15,7 @@
+ #include <tbb/pipeline.h>
+ #include <tbb/task_scheduler_init.h>
+ #include <tbb/concurrent_vector.h>
++#include <tbb/mutex.h>
+ 
+ #include <seqan/basic.h>
+ #include <seqan/sequence.h>
+diff --git a/src/SeqAlign.h b/src/SeqAlign.h
+index 979d05f..221a901 100644
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -3,6 +3,7 @@
+ #ifndef FLEXBAR_SEQALIGN_H
+ #define FLEXBAR_SEQALIGN_H
+ 
++tbb::mutex ouputMutex;
+ 
+ template <typename TSeqStr, typename TString, class TAlgorithm>
+ class SeqAlign {
+@@ -305,7 +306,9 @@ class SeqAlign {
+ 			  << "read seq  " << seqRead.seq << "\n\n" << endl;
+ 		}
+ 		
++		ouputMutex.lock();
+ 		*m_out << s.str();
++		ouputMutex.unlock();
+ 		
+ 		return ++qIndex;
+ 	}