[med-svn] [Git][med-team/flexbar][master] 2 commits: Attempt to port to onetbb
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jan 19 08:51:47 GMT 2023
Andreas Tille pushed to branch master at Debian Med / flexbar
Commits:
52fb2df9 by Andreas Tille at 2023-01-19T09:50:46+01:00
Attempt to port to onetbb
- - - - -
88f07f5e by Andreas Tille at 2023-01-19T09:51:17+01:00
Fix watch file
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/onetbb.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,11 @@
-flexbar (1:3.5.0-5) UNRELEASED; urgency=medium
+flexbar (1:3.5.0-6) UNRELEASED; urgency=medium
* Set upstream metadata fields: Archive.
+ * Attempt to port to onetbb
+ Closes: #1008220, #1011656
+ * Fix watch file
- -- Andreas Tille <tille at debian.org> Fri, 25 Mar 2022 08:13:45 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 19 Jan 2023 09:47:44 +0100
flexbar (1:3.5.0-4) unstable; urgency=medium
=====================================
debian/patches/onetbb.patch
=====================================
@@ -0,0 +1,146 @@
+Description: Attempt to port to onetbb
+FIXME: Does not work yet
+Bug-Debian: https://bugs.debian.org/1008220
+ https://bugs.debian.org/1011656
+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
+@@ -12,8 +12,8 @@
+ #include <iostream>
+ #include <vector>
+
+-#include <tbb/pipeline.h>
+-#include <tbb/task_scheduler_init.h>
++#include <tbb/parallel_pipeline.h>
++#include <tbb/task_scheduler_observer.h>
+ #include <tbb/concurrent_vector.h>
+
+ #include <seqan/basic.h>
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -126,7 +126,7 @@ namespace flexbar{
+ FSeqStr seq;
+ bool rcAdapter;
+
+- tbb::atomic<unsigned long> rmOverlap, rmFull;
++ std::atomic<unsigned long> rmOverlap, rmFull;
+
+ TBar() :
+ rmOverlap(0),
+--- a/src/PairedAlign.h
++++ b/src/PairedAlign.h
+@@ -9,7 +9,7 @@
+
+
+ template <typename TSeqStr, typename TString>
+-class PairedAlign : public tbb::filter {
++class PairedAlign : public oneapi::tbb::filter {
+
+ private:
+
+@@ -31,7 +31,7 @@ private:
+ const flexbar::TrimEnd m_aTrimEnd, m_arcTrimEnd, m_bTrimEnd;
+ const flexbar::PairOverlap m_poMode;
+
+- tbb::atomic<unsigned long> m_unassigned;
++ std::atomic<unsigned long> m_unassigned;
+ 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
+@@ -7,7 +7,7 @@
+
+
+ template <typename TSeqStr, typename TString>
+-class PairedInput : public tbb::filter {
++class PairedInput : public oneapi::tbb::filter {
+
+ private:
+
+@@ -15,7 +15,7 @@ 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;
++ std::atomic<unsigned long> m_uncalled, m_uncalledPairs, m_tagCounter, m_nBundles;
+ SeqInput<TSeqStr, TString> *m_f1, *m_f2, *m_b;
+
+ public:
+--- a/src/PairedOutput.h
++++ b/src/PairedOutput.h
+@@ -9,7 +9,7 @@
+
+
+ template <typename TSeqStr, typename TString>
+-class PairedOutput : public tbb::filter {
++class PairedOutput : public oneapi::tbb::filter {
+
+ private:
+
+@@ -18,7 +18,7 @@ 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;
++ std::atomic<unsigned long> m_nSingleReads, m_nLowPhred;
+
+ const std::string m_target;
+
+--- a/src/SeqAlign.h
++++ b/src/SeqAlign.h
+@@ -20,7 +20,7 @@ private:
+ const float m_errorRate;
+ const unsigned int m_bundleSize;
+
+- tbb::atomic<unsigned long> m_nPreShortReads, m_modified;
++ std::atomic<unsigned long> m_nPreShortReads, m_modified;
+ 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:
+ const float m_errorRate;
+ const unsigned int m_bundleSize;
+
+- tbb::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified;
++ std::atomic<unsigned long> m_nPreShortReads, m_overlaps, m_modified;
+ tbb::concurrent_vector<unsigned long> m_overlapLengths;
+
+ std::ostream *m_out;
+--- 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
+@@ -18,7 +18,7 @@ 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;
++ std::atomic<unsigned long> m_countGood, m_countGoodChars;
+ tbb::concurrent_vector<unsigned long> m_lengthDist;
+
+ public:
+--- 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/series
=====================================
@@ -1 +1,2 @@
no_march_native.patch
+onetbb.patch
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-https://github.com/seqan/flexbar/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+https://github.com/seqan/flexbar/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/aea46b2c86641a00aa8d6f8eac05ffc2577173fa...88f07f5e707f3c891586902a2896b050e72fe4bd
--
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/aea46b2c86641a00aa8d6f8eac05ffc2577173fa...88f07f5e707f3c891586902a2896b050e72fe4bd
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