[med-svn] [Git][med-team/flexbar][master] Replace our own onetbb patch by the patch of Liam Keegan
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Feb 9 20:26:44 GMT 2023
Andreas Tille pushed to branch master at Debian Med / flexbar
Commits:
25357847 by Andreas Tille at 2023-02-09T21:25:54+01:00
Replace our own onetbb patch by the patch of Liam Keegan
- - - - -
3 changed files:
- + debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
- debian/patches/onetbb.patch
- debian/patches/series
Changes:
=====================================
debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
=====================================
@@ -0,0 +1,522 @@
+From 195a1ab2c2715b07df5acff58dc2a0396d9cd52d Mon Sep 17 00:00:00 2001
+From: Liam Keegan <liam at keegan.ch>
+Date: Thu, 9 Feb 2023 16:27:37 +0100
+Subject: [PATCH] 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(-)
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -30,9 +30,9 @@ 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} )
+@@ -51,9 +51,4 @@ 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 "" )
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
+@@ -12,9 +12,9 @@
+ #include <iostream>
+ #include <vector>
+
+-#include <tbb/pipeline.h>
+-#include <tbb/task_scheduler_init.h>
+-#include <tbb/concurrent_vector.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>
+@@ -239,14 +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;
+
+--- 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),
+--- 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 @@ public:
+ };
+
+
+- tbb::concurrent_vector<flexbar::TBar> getAdapters(){
++ oneapi::tbb::concurrent_vector<flexbar::TBar> getAdapters(){
+ return adapters;
+ }
+
+--- 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 @@ public:
+ };
+
+
+- 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;
+ }
+
+--- 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;
+--- 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 @@ private:
+ 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 @@ public:
+
+ PairedAlign(Options &o) :
+
+- filter(parallel),
+ m_format(o.format),
+ m_log(o.logAlign),
+ m_runType(o.runType),
+@@ -102,7 +101,7 @@ public:
+ };
+
+
+- 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 @@ public:
+ }
+
+
+- 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 @@ public:
+ }
+
+
+- void trimLeftHPS(flexbar::TSeqRead* seqRead){
++ void trimLeftHPS(flexbar::TSeqRead* seqRead) const{
+
+ using namespace std;
+ using namespace flexbar;
+@@ -223,7 +222,7 @@ public:
+ }
+
+
+- void trimRightHPS(flexbar::TSeqRead* seqRead){
++ void trimRightHPS(flexbar::TSeqRead* seqRead) const{
+
+ using namespace std;
+ using namespace flexbar;
+@@ -275,13 +274,11 @@ public:
+
+
+ // 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){
+--- 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 @@ private:
+ 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 @@ public:
+ }
+
+
+- void* loadPairedReadBundle(){
++ void* loadPairedReadBundle() const{
+
+ using namespace std;
+ using namespace flexbar;
+@@ -207,8 +206,7 @@ public:
+
+
+ // tbb filter operator
+- void* operator()(void*){
+-
++ flexbar::TPairedReadBundle* operator()(oneapi::tbb::flow_control& fc) const {
+ using namespace flexbar;
+
+ TPairedReadBundle *prBundle = NULL;
+--- 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 @@ private:
+ 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 @@ private:
+ 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 @@ public:
+ 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 @@ public:
+ m_adapters2 = &o.adapters2;
+
+ m_mapsize = 0;
+- m_nSingleReads = 0;
+- m_nLowPhred = 0;
+-
++
+ switch(m_runType){
+
+ case PAIRED_BARCODED:{
+@@ -237,7 +236,7 @@ public:
+ };
+
+
+- void writePairedRead(flexbar::TPairedRead* pRead){
++ void writePairedRead(flexbar::TPairedRead* pRead) const{
+
+ using namespace flexbar;
+
+@@ -346,13 +345,11 @@ public:
+
+
+ // 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 @@ public:
+ }
+ delete prBundle;
+ }
+-
+- return NULL;
+ }
+
+
+@@ -457,7 +452,7 @@ public:
+
+ using namespace std;
+
+- tbb::concurrent_vector<flexbar::TBar> *adapters;
++ oneapi::tbb::concurrent_vector<flexbar::TBar> *adapters;
+ const unsigned int maxSpaceLen = 20;
+
+ int startLen = 8;
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -20,16 +20,16 @@ private:
+ 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),
+@@ -50,7 +50,7 @@ public:
+ 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);
+ };
+
+
+--- a/src/SeqAlignPair.h
++++ b/src/SeqAlignPair.h
+@@ -20,8 +20,8 @@ private:
+ 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 @@ public:
+ 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);
+ };
+
+
+--- a/src/SeqInput.h
++++ b/src/SeqInput.h
+@@ -18,7 +18,7 @@ private:
+
+ 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:
+
+--- a/src/SeqOutput.h
++++ b/src/SeqOutput.h
+@@ -18,8 +18,8 @@ private:
+ 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 @@ public:
+ }
+ 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){
+
+--- a/src/SeqOutputFiles.h
++++ b/src/SeqOutputFiles.h
+@@ -14,7 +14,7 @@ public:
+ 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),
=====================================
debian/patches/onetbb.patch
=====================================
@@ -5,8 +5,8 @@ Bug-Debian: https://bugs.debian.org/1008220
Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
---- flexbar.orig/src/Flexbar.h
-+++ flexbar/src/Flexbar.h
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
@@ -12,8 +12,8 @@
#include <iostream>
#include <vector>
@@ -18,9 +18,20 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
#include <tbb/concurrent_vector.h>
#include <seqan/basic.h>
---- flexbar.orig/src/FlexbarTypes.h
-+++ flexbar/src/FlexbarTypes.h
-@@ -126,7 +126,7 @@
+@@ -239,8 +239,8 @@ 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;
++ tbb::task_scheduler_handle init_serial(o.nThreads);
++ tbb::parallel_pipeline pipe;
+
+ pipe.add_filter(inputFilter);
+ pipe.add_filter(alignFilter);
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -126,7 +126,7 @@ namespace flexbar{
FSeqStr seq;
bool rcAdapter;
@@ -29,8 +40,8 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
TBar() :
rmOverlap(0),
---- flexbar.orig/src/PairedAlign.h
-+++ flexbar/src/PairedAlign.h
+--- a/src/PairedAlign.h
++++ b/src/PairedAlign.h
@@ -9,7 +9,7 @@
@@ -40,7 +51,7 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
private:
-@@ -31,7 +31,7 @@
+@@ -31,7 +31,7 @@ private:
const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
const flexbar::PairOverlap m_poMode;
@@ -49,7 +60,7 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
tbb::concurrent_vector<flexbar::TBar> *m_adapters, *m_adapters2;
tbb::concurrent_vector<flexbar::TBar> *m_barcodes, *m_barcodes2;
-@@ -47,7 +47,7 @@
+@@ -47,7 +47,7 @@ public:
PairedAlign(Options &o) :
@@ -58,8 +69,8 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
m_format(o.format),
m_log(o.logAlign),
m_runType(o.runType),
---- flexbar.orig/src/PairedInput.h
-+++ flexbar/src/PairedInput.h
+--- a/src/PairedInput.h
++++ b/src/PairedInput.h
@@ -7,7 +7,7 @@
@@ -69,7 +80,7 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
private:
-@@ -15,14 +15,14 @@
+@@ -15,14 +15,14 @@ private:
const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved;
const unsigned int m_bundleSize;
@@ -86,8 +97,8 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
m_format(o.format),
m_useNumberTag(o.useNumberTag),
m_interleaved(o.interleavedInput),
---- flexbar.orig/src/PairedOutput.h
-+++ flexbar/src/PairedOutput.h
+--- a/src/PairedOutput.h
++++ b/src/PairedOutput.h
@@ -9,7 +9,7 @@
@@ -97,7 +108,7 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
private:
-@@ -18,7 +18,7 @@
+@@ -18,7 +18,7 @@ private:
const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP;
const bool m_twoBarcodes, m_qtrimPostRm;
@@ -106,7 +117,7 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
const std::string m_target;
-@@ -41,7 +41,7 @@
+@@ -41,7 +41,7 @@ public:
PairedOutput(Options &o) :
@@ -115,9 +126,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
m_target(o.targetName),
m_format(o.format),
m_runType(o.runType),
---- flexbar.orig/src/SeqAlign.h
-+++ flexbar/src/SeqAlign.h
-@@ -20,7 +20,7 @@
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -20,7 +20,7 @@ private:
const float m_errorRate;
const unsigned int m_bundleSize;
@@ -126,9 +137,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
tbb::concurrent_vector<flexbar::TBar> *m_queries;
tbb::concurrent_vector<unsigned long> m_rmOverlaps;
---- flexbar.orig/src/SeqAlignPair.h
-+++ flexbar/src/SeqAlignPair.h
-@@ -20,7 +20,7 @@
+--- a/src/SeqAlignPair.h
++++ b/src/SeqAlignPair.h
+@@ -20,7 +20,7 @@ private:
const float m_errorRate;
const unsigned int m_bundleSize;
@@ -137,9 +148,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
tbb::concurrent_vector<unsigned long> m_overlapLengths;
std::ostream *m_out;
---- flexbar.orig/src/SeqInput.h
-+++ flexbar/src/SeqInput.h
-@@ -18,7 +18,7 @@
+--- a/src/SeqInput.h
++++ b/src/SeqInput.h
+@@ -18,7 +18,7 @@ private:
const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput;
const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
@@ -148,9 +159,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
public:
---- flexbar.orig/src/SeqOutput.h
-+++ flexbar/src/SeqOutput.h
-@@ -18,7 +18,7 @@
+--- a/src/SeqOutput.h
++++ b/src/SeqOutput.h
+@@ -18,7 +18,7 @@ private:
const bool m_switch2Fasta, m_writeLenDist, m_useStdout;
const unsigned int m_minLength, m_cutLen_read;
@@ -159,9 +170,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
tbb::concurrent_vector<unsigned long> m_lengthDist;
public:
---- flexbar.orig/src/SeqOutputFiles.h
-+++ flexbar/src/SeqOutputFiles.h
-@@ -14,7 +14,7 @@
+--- a/src/SeqOutputFiles.h
++++ b/src/SeqOutputFiles.h
+@@ -14,7 +14,7 @@ public:
typedef SeqOutput<TSeqStr, TString> TSeqOutput;
TSeqOutput *f1, *f2, *single1, *single2;
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
no_march_native.patch
-onetbb.patch
+# onetbb.patch
+195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/commit/25357847b4ac44308b1cfc134bafca93104dd5a2
--
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/commit/25357847b4ac44308b1cfc134bafca93104dd5a2
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