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academic/flexbar: incl. patches for newer tbb

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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brobr 2023-11-06 23:36:02 +00:00 committed by Willy Sudiarto Raharjo
parent de08e7bbec
commit f9f97d0290
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4 changed files with 763 additions and 9 deletions
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academic/flexbar/Migrate_from_tbb_to_onetbb_seqan_flexbar_pull_41.patch Normal file
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@ -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;

10
academic/flexbar/flexbar.SlackBuild
View file

@ -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 \

8
academic/flexbar/flexbar.info
View file

@ -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"

44
academic/flexbar/seqan_flexbar_pull_20.patch Normal file
View file

@ -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;
}