[med-svn] [Git][med-team/flexbar][master] 2 commits: Fix Debian revision
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Feb 10 10:43:07 GMT 2023
Andreas Tille pushed to branch master at Debian Med / flexbar
Commits:
647bc2ed by Andreas Tille at 2023-02-10T11:40:57+01:00
Fix Debian revision
- - - - -
7ae4261f by Andreas Tille at 2023-02-10T11:42:39+01:00
Remove now unneeded not working onetbb patch
- - - - -
3 changed files:
- debian/changelog
- − debian/patches/onetbb.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-flexbar (1:3.5.0-6) unstable; urgency=medium
+flexbar (1:3.5.0-5) unstable; urgency=medium
[ Andreas Tille ]
* Set upstream metadata fields: Archive.
=====================================
debian/patches/onetbb.patch deleted
=====================================
@@ -1,183 +0,0 @@
-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>
-@@ -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;
-
-- 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 tbb::filter<TSeqStr, TString> {
-
- 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;
-
-@@ -47,7 +47,7 @@ public:
-
- 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),
---- 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 tbb::filter<TSeqStr, TString> {
-
- private:
-
-@@ -15,14 +15,14 @@ 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:
-
- 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),
---- 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 tbb::filter<TSeqStr, TString> {
-
- 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;
-
-@@ -41,7 +41,7 @@ public:
-
- 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),
---- 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
=====================================
@@ -1,5 +1,4 @@
no_march_native.patch
-# onetbb.patch
195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
1c872fa10d474f090633fc95d409aa60607a3f96.patch
19722f2743c96235ff57948eda82f963cf734131.patch
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/44a3340db8e08c6674c8d514371baa5207c44986...7ae4261f2b48ea40e753eea43e71797bf3f4bd34
--
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/44a3340db8e08c6674c8d514371baa5207c44986...7ae4261f2b48ea40e753eea43e71797bf3f4bd34
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