[med-svn] [Git][med-team/flexbar][master] onetbb.patch: port Paired* classes.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Fri Jan 27 22:06:49 GMT 2023 


Étienne Mollier pushed to branch master at Debian Med / flexbar


Commits:
5d634955 by Étienne Mollier at 2023-01-27T23:06:27+01:00
onetbb.patch: port Paired* classes.

- - - - -


2 changed files:

- debian/changelog
- debian/patches/onetbb.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,15 @@
 flexbar (1:3.5.0-6) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Set upstream metadata fields: Archive.
   * Attempt to port to onetbb
     Closes: #1008220, #1011656
   * Fix watch file
 
- -- Andreas Tille <tille at debian.org>  Thu, 19 Jan 2023 09:47:44 +0100
+  [ Étienne Mollier ]
+  * onetbb.patch: port Paired* classes.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 27 Jan 2023 23:05:13 +0100
 
 flexbar (1:3.5.0-4) unstable; urgency=medium
 


=====================================
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
 
---- a/src/Flexbar.h
-+++ b/src/Flexbar.h
+--- flexbar.orig/src/Flexbar.h
++++ flexbar/src/Flexbar.h
 @@ -12,8 +12,8 @@
  #include <iostream>
  #include <vector>
@@ -18,9 +18,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  #include <tbb/concurrent_vector.h>
  
  #include <seqan/basic.h>
---- a/src/FlexbarTypes.h
-+++ b/src/FlexbarTypes.h
-@@ -126,7 +126,7 @@ namespace flexbar{
+--- flexbar.orig/src/FlexbarTypes.h
++++ flexbar/src/FlexbarTypes.h
+@@ -126,7 +126,7 @@
  		FSeqStr seq;
  		bool rcAdapter;
  		
@@ -29,18 +29,18 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  		
  		TBar() :
  			rmOverlap(0),
---- a/src/PairedAlign.h
-+++ b/src/PairedAlign.h
+--- flexbar.orig/src/PairedAlign.h
++++ flexbar/src/PairedAlign.h
 @@ -9,7 +9,7 @@
  
  
  template <typename TSeqStr, typename TString>
 -class PairedAlign : public tbb::filter {
-+class PairedAlign : public oneapi::tbb::filter {
++class PairedAlign : public tbb::filter<TSeqStr, TString> {
  
  private:
  	
-@@ -31,7 +31,7 @@ private:
+@@ -31,7 +31,7 @@
  	const flexbar::TrimEnd        m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
  	const flexbar::PairOverlap    m_poMode;
  	
@@ -49,18 +49,27 @@ 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;
  	
---- a/src/PairedInput.h
-+++ b/src/PairedInput.h
+@@ -47,7 +47,7 @@
+ 	
+ 	PairedAlign(Options &o) :
+ 		
+-		filter(parallel),
++		tbb::filter<TSeqStr, TString>(tbb::filter_mode::parallel),
+ 		m_format(o.format),
+ 		m_log(o.logAlign),
+ 		m_runType(o.runType),
+--- flexbar.orig/src/PairedInput.h
++++ flexbar/src/PairedInput.h
 @@ -7,7 +7,7 @@
  
  
  template <typename TSeqStr, typename TString>
 -class PairedInput : public tbb::filter {
-+class PairedInput : public oneapi::tbb::filter {
++class PairedInput : public tbb::filter<TSeqStr, TString> {
  
  private:
  	
-@@ -15,7 +15,7 @@ private:
+@@ -15,14 +15,14 @@
  	const bool m_isPaired, m_useBarRead, m_useNumberTag, m_interleaved;
  	const unsigned int m_bundleSize;
  	
@@ -69,18 +78,26 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b;
  	
  public:
---- a/src/PairedOutput.h
-+++ b/src/PairedOutput.h
+ 	
+ 	PairedInput(const Options &o) :
+ 		
+-		filter(serial_in_order),
++		tbb::filter<TSeqStr, TString>(tbb::filter_mode::serial_in_order),
+ 		m_format(o.format),
+ 		m_useNumberTag(o.useNumberTag),
+ 		m_interleaved(o.interleavedInput),
+--- flexbar.orig/src/PairedOutput.h
++++ flexbar/src/PairedOutput.h
 @@ -9,7 +9,7 @@
  
  
  template <typename TSeqStr, typename TString>
 -class PairedOutput : public tbb::filter {
-+class PairedOutput : public oneapi::tbb::filter {
++class PairedOutput : public tbb::filter<TSeqStr, TString> {
  
  private:
  	
-@@ -18,7 +18,7 @@ private:
+@@ -18,7 +18,7 @@
  	const bool m_isPaired, m_writeUnassigned, m_writeSingleReads, m_writeSingleReadsP;
  	const bool m_twoBarcodes, m_qtrimPostRm;
  	
@@ -89,9 +106,18 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	
  	const std::string m_target;
  	
---- a/src/SeqAlign.h
-+++ b/src/SeqAlign.h
-@@ -20,7 +20,7 @@ private:
+@@ -41,7 +41,7 @@
+ 	
+ 	PairedOutput(Options &o) :
+ 		
+-		filter(serial_in_order),
++		tbb::filter<TSeqStr, TString>(tbb::filter_mode::serial_in_order),
+ 		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 @@
  	const float m_errorRate;
  	const unsigned int m_bundleSize;
  	
@@ -100,9 +126,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	tbb::concurrent_vector<flexbar::TBar> *m_queries;
  	tbb::concurrent_vector<unsigned long> m_rmOverlaps;
  	
---- a/src/SeqAlignPair.h
-+++ b/src/SeqAlignPair.h
-@@ -20,7 +20,7 @@ private:
+--- flexbar.orig/src/SeqAlignPair.h
++++ flexbar/src/SeqAlignPair.h
+@@ -20,7 +20,7 @@
  	const float m_errorRate;
  	const unsigned int m_bundleSize;
  	
@@ -111,9 +137,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	tbb::concurrent_vector<unsigned long> m_overlapLengths;
  	
  	std::ostream *m_out;
---- a/src/SeqInput.h
-+++ b/src/SeqInput.h
-@@ -18,7 +18,7 @@ private:
+--- flexbar.orig/src/SeqInput.h
++++ flexbar/src/SeqInput.h
+@@ -18,7 +18,7 @@
  	
  	const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput;
  	const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
@@ -122,9 +148,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	
  public:
  	
---- a/src/SeqOutput.h
-+++ b/src/SeqOutput.h
-@@ -18,7 +18,7 @@ private:
+--- flexbar.orig/src/SeqOutput.h
++++ flexbar/src/SeqOutput.h
+@@ -18,7 +18,7 @@
  	const bool m_switch2Fasta, m_writeLenDist, m_useStdout;
  	const unsigned int m_minLength, m_cutLen_read;
  	
@@ -133,9 +159,9 @@ Last-Update: Thu, 19 Jan 2023 09:47:44 +0100
  	tbb::concurrent_vector<unsigned long> m_lengthDist;
  	
  public:
---- a/src/SeqOutputFiles.h
-+++ b/src/SeqOutputFiles.h
-@@ -14,7 +14,7 @@ public:
+--- flexbar.orig/src/SeqOutputFiles.h
++++ flexbar/src/SeqOutputFiles.h
+@@ -14,7 +14,7 @@
  	typedef SeqOutput<TSeqStr, TString> TSeqOutput;
  	
  	TSeqOutput *f1, *f2, *single1, *single2;



View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/commit/5d634955412b9a48d6c244a1d1de58a15b395ab9

-- 
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/commit/5d634955412b9a48d6c244a1d1de58a15b395ab9
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