[med-svn] [Git][med-team/flexbar][debian/experimental] 2 commits: Added patch for the explicit seqan2 namespace.
Enrico Seiler (@eseiler)
gitlab at salsa.debian.org
Tue Nov 26 14:52:33 GMT 2024
Enrico Seiler pushed to branch debian/experimental at Debian Med / flexbar
Commits:
e1684b7a by Enrico Seiler at 2024-11-26T15:49:20+01:00
Added patch for the explicit seqan2 namespace.
- - - - -
8a5d0ee4 by Enrico Seiler at 2024-11-26T15:49:41+01:00
ready for uploading to experimental
- - - - -
8 changed files:
- debian/changelog
- + debian/patches/0006-Upgrade-to-SeqAn-2.5.0.patch
- debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
- debian/patches/19722f2743c96235ff57948eda82f963cf734131.patch
- debian/patches/1c872fa10d474f090633fc95d409aa60607a3f96.patch
- debian/patches/a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
- debian/patches/no_march_native.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,11 @@
-flexbar (1:3.5.0-6) UNRELEASED; urgency=medium
+flexbar (1:3.5.0-6) experimental; urgency=medium
* Team upload.
* d/control: Experimental rebuild using the 3rd release candidate of
SeqAn 2.5.0
+ * Added patch for the explicit seqan2 namespace.
- -- Enrico Seiler <enrico.seiler.debian at outlook.com> Mon, 25 Nov 2024 21:13:13 +0100
+ -- Enrico Seiler <enrico.seiler.debian at outlook.com> Tue, 26 Nov 2024 15:49:33 +0100
flexbar (1:3.5.0-5) unstable; urgency=medium
=====================================
debian/patches/0006-Upgrade-to-SeqAn-2.5.0.patch
=====================================
@@ -0,0 +1,479 @@
+From: Enrico Seiler <enrico.seiler.debian at outlook.com>
+Date: Tue, 26 Nov 2024 15:48:30 +0100
+Subject: Upgrade to SeqAn 2.5.0.
+
+---
+ src/CMakeLists.txt | 8 ++++----
+ src/Flexbar.cpp | 2 +-
+ src/Flexbar.h | 4 ++--
+ src/FlexbarIO.h | 12 ++++++------
+ src/FlexbarTypes.h | 18 +++++++++---------
+ src/LoadAdapters.h | 4 ++--
+ src/LoadFasta.h | 6 +++---
+ src/Options.h | 14 +++++++-------
+ src/PairedAlign.h | 4 ++--
+ src/QualTrimming.h | 2 +-
+ src/SeqAlign.h | 4 ++--
+ src/SeqAlignAlgo.h | 16 ++++++++--------
+ src/SeqAlignPair.h | 2 +-
+ src/SeqInput.h | 16 ++++++++--------
+ src/SeqOutput.h | 8 ++++----
+ 15 files changed, 60 insertions(+), 60 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index f8df09b..6e2b7d4 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -2,12 +2,12 @@ cmake_minimum_required( VERSION 2.8.2 )
+
+ include(CheckCXXCompilerFlag)
+
+-CHECK_CXX_COMPILER_FLAG("-std=c++14" COMPILER_SUPPORTS_CXX14)
++CHECK_CXX_COMPILER_FLAG("-std=c++17" COMPILER_SUPPORTS_CXX17)
+
+-if(COMPILER_SUPPORTS_CXX14)
+- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
++if(COMPILER_SUPPORTS_CXX17)
++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17")
+ else()
+- message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++14 support. Use a different compiler.")
++ message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++17 support. Use a different compiler.")
+ endif()
+
+
+diff --git a/src/Flexbar.cpp b/src/Flexbar.cpp
+index 5846ad3..1a527e4 100644
+--- a/src/Flexbar.cpp
++++ b/src/Flexbar.cpp
+@@ -27,7 +27,7 @@
+ int main(int argc, const char* argv[]){
+
+ using namespace std;
+- using namespace seqan;
++ using namespace seqan2;
+
+ const string version = "3.5.0";
+ const string date = "May 2019";
+diff --git a/src/Flexbar.h b/src/Flexbar.h
+index 46261cf..7b67486 100644
+--- a/src/Flexbar.h
++++ b/src/Flexbar.h
+@@ -119,7 +119,7 @@ void loadAdapters(Options &o, const bool secondSet, const bool useAdapterFile){
+ }
+ if(o.rcMode == RCON || o.rcMode == RCONLY){
+ TSeqStr adapterSeqRC = o.adapterSeq;
+- seqan::reverseComplement(adapterSeqRC);
++ seqan2::reverseComplement(adapterSeqRC);
+
+ TBar barRC;
+ barRC.id = "cmdline_rc";
+@@ -356,7 +356,7 @@ void startProcessing(Options &o){
+ void performTest(){
+
+ using namespace std;
+- using namespace seqan;
++ using namespace seqan2;
+
+ }
+
+diff --git a/src/FlexbarIO.h b/src/FlexbarIO.h
+index 19ee000..86a05a6 100644
+--- a/src/FlexbarIO.h
++++ b/src/FlexbarIO.h
+@@ -47,7 +47,7 @@ void closeFile(std::fstream &strm){
+ }
+
+
+-namespace seqan{
++namespace seqan2{
+
+ // Extension for input fasta file with dat ending
+
+@@ -222,9 +222,9 @@ void checkFileCompression(const std::string path){
+ using namespace std;
+ using namespace flexbar;
+
+- using seqan::CharString;
+- using seqan::suffix;
+- using seqan::length;
++ using seqan2::CharString;
++ using seqan2::suffix;
++ using seqan2::length;
+
+ CompressionType cmprsType = UNCOMPRESSED;
+
+@@ -285,7 +285,7 @@ void checkInputType(const std::string path, flexbar::FileFormat &format, const b
+ }
+ }
+ else{
+- seqan::FlexbarReadsSeqFileIn seqFileIn;
++ seqan2::FlexbarReadsSeqFileIn seqFileIn;
+
+ if(! open(seqFileIn, path.c_str())){
+ cerr << "\nERROR: Could not open file " << path << "\n" << endl;
+@@ -308,7 +308,7 @@ void checkInputType(const std::string path, flexbar::FileFormat &format, const b
+ exit(1);
+ }
+ }
+- catch(seqan::Exception const &e){
++ catch(seqan2::Exception const &e){
+ cerr << "\nERROR: " << e.what() << "\nProgram execution aborted.\n" << endl;
+ close(seqFileIn);
+ exit(1);
+diff --git a/src/FlexbarTypes.h b/src/FlexbarTypes.h
+index 3cf241e..0cd8f7f 100644
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -93,19 +93,19 @@ namespace flexbar{
+
+ const unsigned int MAX_READLENGTH = 2048;
+
+- typedef seqan::Dna5String FSeqStr;
+- typedef seqan::CharString FString;
++ typedef seqan2::Dna5String FSeqStr;
++ typedef seqan2::CharString FString;
+
+- typedef seqan::StringSet<FSeqStr> TSeqStrs;
+- typedef seqan::StringSet<FString> TStrings;
+- typedef seqan::StringSet<bool> TBools;
++ typedef seqan2::StringSet<FSeqStr> TSeqStrs;
++ typedef seqan2::StringSet<FString> TStrings;
++ typedef seqan2::StringSet<bool> TBools;
+
+ typedef SeqRead<FSeqStr, FString> TSeqRead;
+ typedef PairedRead<FSeqStr, FString> TPairedRead;
+
+- typedef seqan::Align<FSeqStr, seqan::ArrayGaps> TAlign;
+- typedef seqan::StringSet<TAlign> TAlignSet;
+- typedef seqan::String<int> TAlignScores;
++ typedef seqan2::Align<FSeqStr, seqan2::ArrayGaps> TAlign;
++ typedef seqan2::StringSet<TAlign> TAlignSet;
++ typedef seqan2::String<int> TAlignScores;
+
+ struct Alignments {
+ TAlignSet aset;
+@@ -115,7 +115,7 @@ namespace flexbar{
+ typedef std::vector<Alignments> TAlignBundle;
+ typedef std::vector<TPairedRead* > TPairedReadBundle;
+
+- // typedef seqan::StringSet<TAlign, seqan::Dependent<seqan::Tight> > TAlignSet;
++ // typedef seqan2::StringSet<TAlign, seqan2::Dependent<seqan2::Tight> > TAlignSet;
+
+
+ // struct SeqReadData {
+diff --git a/src/LoadAdapters.h b/src/LoadAdapters.h
+index 6168775..018bd38 100644
+--- a/src/LoadAdapters.h
++++ b/src/LoadAdapters.h
+@@ -103,7 +103,7 @@ public:
+ TSeqStr seqRC = seq;
+
+ append(idRC, "_rc");
+- seqan::reverseComplement(seqRC);
++ seqan2::reverseComplement(seqRC);
+
+ TBar adapterRC;
+ adapterRC.id = idRC;
+@@ -124,7 +124,7 @@ public:
+ adapters.push_back(adapter);
+
+ append(idc, "_rc");
+- seqan::reverseComplement(seqc);
++ seqan2::reverseComplement(seqc);
+
+ TBar adapterRC;
+ adapterRC.id = idc;
+diff --git a/src/LoadFasta.h b/src/LoadFasta.h
+index ccd0550..ec7c445 100644
+--- a/src/LoadFasta.h
++++ b/src/LoadFasta.h
+@@ -33,7 +33,7 @@ public:
+ using namespace std;
+ using namespace flexbar;
+
+- seqan::DatFastaSeqFileIn seqFileIn;
++ seqan2::DatFastaSeqFileIn seqFileIn;
+
+ if(! open(seqFileIn, filePath.c_str())){
+ cerr << "\nERROR: Could not open file " << filePath << "\n" << endl;
+@@ -74,7 +74,7 @@ public:
+ TSeqStr seq = seqs[i];
+
+ append(id, "_rc");
+- seqan::reverseComplement(seq);
++ seqan2::reverseComplement(seq);
+
+ TBar barRC;
+ barRC.id = id;
+@@ -84,7 +84,7 @@ public:
+ }
+ }
+ }
+- catch(seqan::Exception const &e){
++ catch(seqan2::Exception const &e){
+ cerr << "\nERROR: " << e.what() << "\nProgram execution aborted.\n" << endl;
+ close(seqFileIn);
+ exit(1);
+diff --git a/src/Options.h b/src/Options.h
+index 21d7710..7694143 100644
+--- a/src/Options.h
++++ b/src/Options.h
+@@ -122,7 +122,7 @@ struct Options{
+ };
+
+
+-const std::string getFlexbarBanner(const seqan::CharString version){
++const std::string getFlexbarBanner(const seqan2::CharString version){
+
+ std::string banner = "";
+
+@@ -157,9 +157,9 @@ const std::string getFlexbarDescription(){
+ }
+
+
+-void defineOptions(seqan::ArgumentParser &parser, const std::string version, const std::string date){
++void defineOptions(seqan2::ArgumentParser &parser, const std::string version, const std::string date){
+
+- using namespace seqan;
++ using namespace seqan2;
+
+ typedef ArgParseArgument ARG;
+
+@@ -426,11 +426,11 @@ void printLocalTime(Options &o){
+ }
+
+
+-void parseCmdLine(seqan::ArgumentParser &parser, std::string version, int argc, char const ** argv){
++void parseCmdLine(seqan2::ArgumentParser &parser, std::string version, int argc, char const ** argv){
+
+ using namespace std;
+
+- using seqan::ArgumentParser;
++ using seqan2::ArgumentParser;
+
+ bool useLogFile = true;
+
+@@ -497,7 +497,7 @@ void parseCmdLine(seqan::ArgumentParser &parser, std::string version, int argc,
+ }
+
+
+-void initOptions(Options &o, seqan::ArgumentParser &parser){
++void initOptions(Options &o, seqan2::ArgumentParser &parser){
+
+ using namespace std;
+ using namespace flexbar;
+@@ -533,7 +533,7 @@ void initOptions(Options &o, seqan::ArgumentParser &parser){
+ }
+
+
+-void loadOptions(Options &o, seqan::ArgumentParser &parser){
++void loadOptions(Options &o, seqan2::ArgumentParser &parser){
+
+ using namespace std;
+ using namespace flexbar;
+diff --git a/src/PairedAlign.h b/src/PairedAlign.h
+index d3b50ae..8fc937b 100644
+--- a/src/PairedAlign.h
++++ b/src/PairedAlign.h
+@@ -141,7 +141,7 @@ public:
+ }
+ }
+ }
+- seqan::reverseComplement(addBarcode);
++ seqan2::reverseComplement(addBarcode);
+ }
+
+ m_a1->alignSeqRead(pRead->r1, true, alBundle[0], cycle[0], idxAl[0], alMode, trimEnd, addBarcode);
+@@ -163,7 +163,7 @@ public:
+ }
+ }
+ }
+- seqan::reverseComplement(addBarcode);
++ seqan2::reverseComplement(addBarcode);
+ }
+
+ if(m_adapRem != NORMAL2) m_a1->alignSeqRead(pRead->r2, true, alBundle[1], cycle[1], idxAl[1], alMode, trimEnd, addBarcode);
+diff --git a/src/QualTrimming.h b/src/QualTrimming.h
+index a70f713..8c63e99 100644
+--- a/src/QualTrimming.h
++++ b/src/QualTrimming.h
+@@ -94,7 +94,7 @@ unsigned qualTrimming(const TString& qual, unsigned const cutoff, BWA const &){
+ template <typename TSeqStr, typename TString>
+ bool qualTrim(TSeqStr &seq, TString &qual, const flexbar::QualTrimType qtrim, const int cutoff, const int wSize){
+
+- using namespace seqan;
++ using namespace seqan2;
+
+ unsigned cutPos;
+
+diff --git a/src/SeqAlign.h b/src/SeqAlign.h
+index dc7a032..f96df7e 100644
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -59,8 +59,8 @@ public:
+ using namespace std;
+ using namespace flexbar;
+
+- using seqan::prefix;
+- using seqan::suffix;
++ using seqan2::prefix;
++ using seqan2::suffix;
+
+ TSeqRead &seqRead = *sr;
+ int readLength = length(seqRead.seq);
+diff --git a/src/SeqAlignAlgo.h b/src/SeqAlignAlgo.h
+index d967965..758a32f 100644
+--- a/src/SeqAlignAlgo.h
++++ b/src/SeqAlignAlgo.h
+@@ -9,14 +9,14 @@ class SeqAlignAlgo {
+
+ private:
+
+- typedef typename seqan::Value<TSeqStr>::Type TChar;
+- typedef typename seqan::Row<flexbar::TAlign>::Type TRow;
+- typedef typename seqan::Iterator<TRow>::Type TRowIterator;
++ typedef typename seqan2::Value<TSeqStr>::Type TChar;
++ typedef typename seqan2::Row<flexbar::TAlign>::Type TRow;
++ typedef typename seqan2::Iterator<TRow>::Type TRowIterator;
+
+ typedef AlignResults<TSeqStr> TAlignResults;
+
+- typedef seqan::Score<int, seqan::Simple> TScoreSimple;
+- typedef seqan::Score<int, seqan::ScoreMatrix<TChar, seqan::Default> > TScoreMatrix;
++ typedef seqan2::Score<int, seqan2::Simple> TScoreSimple;
++ typedef seqan2::Score<int, seqan2::ScoreMatrix<TChar, seqan2::Default> > TScoreMatrix;
+
+ // TScoreSimple m_score;
+ TScoreMatrix m_scoreMatrix;
+@@ -31,7 +31,7 @@ public:
+ m_isAdapterRm(isAdapterRm),
+ m_log(o.logAlign){
+
+- using namespace seqan;
++ using namespace seqan2;
+
+ // m_score = Score<int, Simple>(match, mismatch, gapCost);
+ m_scoreMatrix = TScoreMatrix(gapCost);
+@@ -52,7 +52,7 @@ public:
+ void alignGlobal(TAlignResults &a, flexbar::Alignments &alignments, flexbar::ComputeCycle &cycle, const unsigned int idxAl, const flexbar::TrimEnd trimEnd){
+
+ using namespace std;
+- using namespace seqan;
++ using namespace seqan2;
+ using namespace flexbar;
+
+ // int band1 = overhang;
+@@ -142,7 +142,7 @@ public:
+ void printScoreMatrix(TScoreMatrix &scoreMatrix){
+
+ using namespace std;
+- using namespace seqan;
++ using namespace seqan2;
+
+ cout << endl;
+ for(unsigned i = 0; i < ValueSize<TChar>::VALUE; ++i)
+diff --git a/src/SeqAlignPair.h b/src/SeqAlignPair.h
+index 2479242..989de23 100644
+--- a/src/SeqAlignPair.h
++++ b/src/SeqAlignPair.h
+@@ -73,7 +73,7 @@ public:
+ if(idxAl == 0) reserve(alignments.aset, m_bundleSize);
+
+ TSeqStr rcSeq2 = seqRead2.seq;
+- seqan::reverseComplement(rcSeq2);
++ seqan2::reverseComplement(rcSeq2);
+
+ TAlign align;
+ appendValue(alignments.aset, align);
+diff --git a/src/SeqInput.h b/src/SeqInput.h
+index 7a8f8d0..312bca0 100644
+--- a/src/SeqInput.h
++++ b/src/SeqInput.h
+@@ -12,7 +12,7 @@ class SeqInput {
+
+ private:
+
+- seqan::FlexbarReadsSeqFileIn seqFileIn;
++ seqan2::FlexbarReadsSeqFileIn seqFileIn;
+ const flexbar::QualTrimType m_qtrim;
+ const flexbar::FileFormat m_format;
+
+@@ -61,14 +61,14 @@ public:
+
+
+ // returns number of read SeqReads
+- unsigned int loadSeqReads(seqan::StringSet<bool> &uncalled, flexbar::TStrings &ids, flexbar::TSeqStrs &seqs, flexbar::TStrings &quals, const unsigned int nReads){
++ unsigned int loadSeqReads(seqan2::StringSet<bool> &uncalled, flexbar::TStrings &ids, flexbar::TSeqStrs &seqs, flexbar::TStrings &quals, const unsigned int nReads){
+
+ using namespace std;
+ using namespace flexbar;
+
+- using seqan::prefix;
+- using seqan::suffix;
+- using seqan::length;
++ using seqan2::prefix;
++ using seqan2::suffix;
++ using seqan2::length;
+
+ try{
+ if(! atEnd(seqFileIn)){
+@@ -88,7 +88,7 @@ public:
+ }
+ }
+ else{
+- seqan::StringSet<seqan::IupacString> seqsIupac;
++ seqan2::StringSet<seqan2::IupacString> seqsIupac;
+
+ reserve(seqsIupac, nReads);
+
+@@ -160,7 +160,7 @@ public:
+
+ else return 0; // end of file
+ }
+- catch(seqan::Exception const &e){
++ catch(seqan2::Exception const &e){
+ cerr << "\nERROR: " << e.what() << "\nProgram execution aborted.\n" << endl;
+ close(seqFileIn);
+ exit(1);
+@@ -171,7 +171,7 @@ public:
+ // returns TRUE if read contains too many uncalled bases
+ bool isUncalledSequence(TSeqStr &seq){
+
+- using namespace seqan;
++ using namespace seqan2;
+
+ typename Iterator<TSeqStr>::Type it, itEnd;
+
+diff --git a/src/SeqOutput.h b/src/SeqOutput.h
+index 64cab91..8448c2e 100644
+--- a/src/SeqOutput.h
++++ b/src/SeqOutput.h
+@@ -9,7 +9,7 @@ class SeqOutput {
+
+ private:
+
+- seqan::FlexbarReadsSeqFileOut seqFileOut;
++ seqan2::FlexbarReadsSeqFileOut seqFileOut;
+ std::string m_filePath;
+
+ const TString m_tagStr;
+@@ -53,8 +53,8 @@ public:
+ if(m_useStdout){
+
+ if(m_format == FASTA || m_switch2Fasta)
+- setFormat(seqFileOut, seqan::Fasta());
+- else setFormat(seqFileOut, seqan::Fastq());
++ setFormat(seqFileOut, seqan2::Fasta());
++ else setFormat(seqFileOut, seqan2::Fastq());
+
+ if(! open(seqFileOut, cout)){
+ cerr << "\nERROR: Could not open output stream." << "\n" << endl;
+@@ -123,7 +123,7 @@ public:
+ writeRecord(seqFileOut, seqRead.id, seqRead.seq, seqRead.qual);
+ }
+ }
+- catch(seqan::Exception const &e){
++ catch(seqan2::Exception const &e){
+ cerr << "\nERROR: " << e.what() << "\nProgram execution aborted.\n" << endl;
+ close(seqFileOut);
+ exit(1);
=====================================
debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
=====================================
@@ -1,4 +1,3 @@
-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
@@ -20,7 +19,7 @@ Subject: [PATCH] Migrate from tbb to onetbb
- add find_package for TBB to CMakeLists.txt
---
src/CMakeLists.txt | 9 ++-------
- src/Flexbar.h | 27 +++++++++++++++------------
+ src/Flexbar.h | 26 +++++++++++++++-----------
src/FlexbarTypes.h | 16 +++++++++++++++-
src/LoadAdapters.h | 4 ++--
src/LoadFasta.h | 6 +++---
@@ -28,13 +27,15 @@ Subject: [PATCH] Migrate from tbb to onetbb
src/PairedAlign.h | 23 ++++++++++-------------
src/PairedInput.h | 10 ++++------
src/PairedOutput.h | 29 ++++++++++++-----------------
- src/SeqAlign.h | 12 ++++++------
+ src/SeqAlign.h | 10 +++++-----
src/SeqAlignPair.h | 6 +++---
src/SeqInput.h | 2 +-
src/SeqOutput.h | 6 +++---
src/SeqOutputFiles.h | 2 +-
- 14 files changed, 78 insertions(+), 76 deletions(-)
+ 14 files changed, 77 insertions(+), 74 deletions(-)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index ede581f..db9b8df 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -30,9 +30,9 @@ else()
@@ -59,6 +60,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
-# endif()
-
set( SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} flexbar CACHE INTERNAL "" )
+diff --git a/src/Flexbar.h b/src/Flexbar.h
+index 2f82f18..d1a8f31 100644
--- a/src/Flexbar.h
+++ b/src/Flexbar.h
@@ -12,9 +12,9 @@
@@ -101,6 +104,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@
@@ -133,6 +138,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 {
@@ -153,6 +160,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 {
@@ -179,6 +188,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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{
@@ -190,6 +201,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@
@@ -274,6 +287,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@
@@ -320,6 +335,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@
@@ -422,6 +439,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
const unsigned int maxSpaceLen = 20;
int startLen = 8;
+diff --git a/src/SeqAlign.h b/src/SeqAlign.h
+index 979d05f..dc7a032 100644
--- a/src/SeqAlign.h
+++ b/src/SeqAlign.h
@@ -20,16 +20,16 @@ private:
@@ -454,6 +473,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
};
+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 @@ private:
@@ -476,6 +497,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
};
+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 @@ private:
@@ -487,6 +510,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@ private:
@@ -509,6 +534,8 @@ Subject: [PATCH] Migrate from tbb to onetbb
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 @@ public:
=====================================
debian/patches/19722f2743c96235ff57948eda82f963cf734131.patch
=====================================
@@ -1,4 +1,3 @@
-From 19722f2743c96235ff57948eda82f963cf734131 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
Date: Fri, 10 Feb 2023 10:21:22 +0100
Subject: [PATCH] revert accidental removal of pthread linking in
@@ -8,6 +7,8 @@ Subject: [PATCH] revert accidental removal of pthread linking in
src/CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index db9b8df..f8df09b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -30,6 +30,7 @@ else()
=====================================
debian/patches/1c872fa10d474f090633fc95d409aa60607a3f96.patch
=====================================
@@ -1,4 +1,3 @@
-From 1c872fa10d474f090633fc95d409aa60607a3f96 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
Date: Fri, 10 Feb 2023 09:55:58 +0100
Subject: [PATCH] Fix parallel_pipeline issues
@@ -41,7 +40,7 @@ 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 {
+@@ -221,9 +221,14 @@ public:
prBundle = static_cast< TPairedReadBundle* >(loadPairedReadBundle());
=====================================
debian/patches/a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
=====================================
@@ -1,4 +1,3 @@
-From a9b0eb87a391aeaf760f8116dca777749c8b4f96 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
Date: Fri, 10 Feb 2023 10:52:35 +0100
Subject: [PATCH] use `std::atomic` instead of `FlexbarAtomic` in filters as
@@ -28,7 +27,7 @@ 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 {
+@@ -31,7 +31,7 @@ private:
const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
const flexbar::PairOverlap m_poMode;
@@ -41,7 +40,7 @@ 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 {
+@@ -15,7 +15,7 @@ private:
const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved;
const unsigned int m_bundleSize;
@@ -54,7 +53,7 @@ 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 {
+@@ -18,7 +18,7 @@ private:
const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP;
const bool m_twoBarcodes, m_qtrimPostRm;
=====================================
debian/patches/no_march_native.patch
=====================================
@@ -1,11 +1,19 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
+Date: Sun, 27 Aug 2017 22:07:28 +0200
+Subject: Do not build with -march=native
+
Last-Update: Sun, 27 Aug 2017 22:04:31 +0200
Bug-Debian: https://bugs.debian.org/873429
Forwarded: no
-Description: Do not build with -march=native
+---
+ src/CMakeLists.txt | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index a5643ca..ede581f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -11,8 +11,6 @@
+@@ -11,8 +11,6 @@ else()
endif()
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ no_march_native.patch
1c872fa10d474f090633fc95d409aa60607a3f96.patch
19722f2743c96235ff57948eda82f963cf734131.patch
a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
+0006-Upgrade-to-SeqAn-2.5.0.patch
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/0c69a1e23bb3607443f9f650f8a530bfb447f68e...8a5d0ee46628c91a1879106d74f595ea4c3f4619
--
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/0c69a1e23bb3607443f9f650f8a530bfb447f68e...8a5d0ee46628c91a1879106d74f595ea4c3f4619
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