diff -Nru bowtie-1.3.0+dfsg1/bowtie-inspect bowtie-1.3.1/bowtie-inspect --- bowtie-1.3.0+dfsg1/bowtie-inspect 2020-07-23 02:52:57.000000000 +0000 +++ bowtie-1.3.1/bowtie-inspect 2021-09-14 01:38:24.000000000 +0000 @@ -21,7 +21,6 @@ import os -import imp import inspect from importlib.machinery import SourceFileLoader import logging diff -Nru bowtie-1.3.0+dfsg1/bt2_locks.cpp bowtie-1.3.1/bt2_locks.cpp --- bowtie-1.3.0+dfsg1/bt2_locks.cpp 2020-07-23 02:52:57.000000000 +0000 +++ bowtie-1.3.1/bt2_locks.cpp 2021-09-14 01:38:24.000000000 +0000 @@ -1,21 +1,21 @@ -#include "bt2_locks.h" - #if (__cplusplus >= 201103L) -void mcs_lock::lock() { +#include "bt2_locks.h" + +void mcs_lock::lock(mcs_node &node) { node.next = nullptr; - node.unlocked = false; - mcs_node *pred = q.exchange(&node, std::memory_order_release); + mcs_node *pred = q.exchange(&node, std::memory_order_acq_rel); if (pred) { - pred->next = &node; + node.unlocked = false; + pred->next.store(&node, std::memory_order_release); spin_while_eq(node.unlocked, false); } node.unlocked.load(std::memory_order_acquire); } -void mcs_lock::unlock() { - if (!node.next) { +void mcs_lock::unlock(mcs_node &node) { + if (!node.next.load(std::memory_order_acquire)) { mcs_node *node_ptr = &node; if (q.compare_exchange_strong(node_ptr, (mcs_node *)nullptr, @@ -23,10 +23,9 @@ return; spin_while_eq(node.next, (mcs_node *)nullptr); } - node.next->unlocked.store(true, std::memory_order_release); + node.next.load(std::memory_order_acquire)->unlocked.store(true, std::memory_order_release); } -thread_local mcs_lock::mcs_node mcs_lock::node; void spin_lock::lock() { cpu_backoff backoff; @@ -37,4 +36,5 @@ void spin_lock::unlock() { flag.clear(std::memory_order_release); } + #endif diff -Nru bowtie-1.3.0+dfsg1/bt2_locks.h bowtie-1.3.1/bt2_locks.h --- bowtie-1.3.0+dfsg1/bt2_locks.h 2020-07-23 02:52:57.000000000 +0000 +++ bowtie-1.3.1/bt2_locks.h 2021-09-14 01:38:24.000000000 +0000 @@ -12,13 +12,17 @@ class cpu_backoff { public: cpu_backoff(): count(1) {} - void pause() { + inline void pause() { if (count <= LOOPS_BEFORE_YIELD) { for (int32_t i = 0; i < count; i++) { #ifdef __aarch64__ __asm__ __volatile__("yield" ::: "memory"); -#else +#elif __ppc__ + __asm__ __volatile__("or 27,27,27" ::: "memory"); +#elif __x86_64__ __asm__ __volatile__("pause;"); +#else + // do nothing #endif } count *= 2; @@ -44,27 +48,27 @@ public: mcs_lock(): q(nullptr) {} struct mcs_node { - mcs_node *next; + std::atomic next; std::atomic_bool unlocked; }; - void lock(); - void unlock(); - typedef mcs_node* mcs_node_ptr; + void lock(mcs_node &node); + void unlock(mcs_node &node); + typedef std::atomic mcs_node_ptr; private: - void spin_while_eq(const volatile mcs_node_ptr& value, mcs_node *expected) { + void spin_while_eq(const volatile mcs_node_ptr& value, const volatile mcs_node *expected) { cpu_backoff backoff; - while (value == expected) + while (value.load(std::memory_order_acquire) == expected) backoff.pause(); } - void spin_while_eq(const volatile std::atomic_bool& value, bool expected) { + void spin_while_eq(const volatile std::atomic_bool& value, const volatile bool expected) { cpu_backoff backoff; while (value.load(std::memory_order_acquire) == expected) backoff.pause(); } std::atomic q; - static thread_local mcs_node node; }; -#endif + +#endif // if (__cplusplus >= 201103L) #endif // __MCS_LOCK_H__ diff -Nru bowtie-1.3.0+dfsg1/debian/bowtie.lintian-overrides bowtie-1.3.1/debian/bowtie.lintian-overrides --- bowtie-1.3.0+dfsg1/debian/bowtie.lintian-overrides 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/bowtie.lintian-overrides 2021-09-14 05:01:35.000000000 +0000 @@ -1,12 +1,12 @@ -bowtie: binary-without-manpage usr/bin/bowtie-align-l -bowtie: binary-without-manpage usr/bin/bowtie-align-s -bowtie: binary-without-manpage usr/bin/bowtie-build-l -bowtie: binary-without-manpage usr/bin/bowtie-build-s -bowtie: binary-without-manpage usr/bin/bowtie-inspect-l -bowtie: binary-without-manpage usr/bin/bowtie-inspect-s -bowtie: binary-without-manpage usr/bin/bowtie-align-l-debug -bowtie: binary-without-manpage usr/bin/bowtie-align-s-debug -bowtie: binary-without-manpage usr/bin/bowtie-build-l-debug -bowtie: binary-without-manpage usr/bin/bowtie-build-s-debug -bowtie: binary-without-manpage usr/bin/bowtie-inspect-l-debug -bowtie: binary-without-manpage usr/bin/bowtie-inspect-s-debug +bowtie: no-manual-page usr/bin/bowtie-align-l +bowtie: no-manual-page usr/bin/bowtie-align-s +bowtie: no-manual-page usr/bin/bowtie-build-l +bowtie: no-manual-page usr/bin/bowtie-build-s +bowtie: no-manual-page usr/bin/bowtie-inspect-l +bowtie: no-manual-page usr/bin/bowtie-inspect-s +bowtie: no-manual-page usr/bin/bowtie-align-l-debug +bowtie: no-manual-page usr/bin/bowtie-align-s-debug +bowtie: no-manual-page usr/bin/bowtie-build-l-debug +bowtie: no-manual-page usr/bin/bowtie-build-s-debug +bowtie: no-manual-page usr/bin/bowtie-inspect-l-debug +bowtie: no-manual-page usr/bin/bowtie-inspect-s-debug diff -Nru bowtie-1.3.0+dfsg1/debian/changelog bowtie-1.3.1/debian/changelog --- bowtie-1.3.0+dfsg1/debian/changelog 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/changelog 2021-09-14 05:01:35.000000000 +0000 @@ -1,3 +1,15 @@ +bowtie (1.3.1-1) unstable; urgency=medium + + * New upstream version + * Fix watchfile to detect new versions on github (routine-update) + * Standards-Version: 4.6.0 (routine-update) + * Update renamed lintian tag names in lintian overrides. + * Apply multi-arch hints. + + bowtie-examples: Add Multi-Arch: foreign. + * No need to exclude files from upstream tarball any more + + -- Andreas Tille Tue, 14 Sep 2021 07:01:35 +0200 + bowtie (1.3.0+dfsg1-1) unstable; urgency=medium [ Andreas Tille ] diff -Nru bowtie-1.3.0+dfsg1/debian/control bowtie-1.3.1/debian/control --- bowtie-1.3.0+dfsg1/debian/control 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/control 2021-09-14 05:01:35.000000000 +0000 @@ -15,7 +15,7 @@ libclone-perl, libtest-deep-perl, libsys-info-perl -Standards-Version: 4.5.0 +Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/bowtie Vcs-Git: https://salsa.debian.org/med-team/bowtie.git Homepage: http://bowtie-bio.sourceforge.net/ @@ -45,6 +45,7 @@ Depends: ${misc:Depends} Recommends: bowtie Enhances: bowtie +Multi-Arch: foreign Description: Examples for bowtie, the ultrafast memory-efficient short read aligner This package addresses the problem to interpret the results from the latest (2010) DNA sequencing technologies. Those will yield fairly diff -Nru bowtie-1.3.0+dfsg1/debian/copyright bowtie-1.3.1/debian/copyright --- bowtie-1.3.0+dfsg1/debian/copyright 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/copyright 2021-09-14 05:01:35.000000000 +0000 @@ -2,9 +2,6 @@ Upstream-Name: Bowtie Upstream-Contact: Ben Langmead Source: https://github.com/BenLangmead/bowtie/ -Files-Excluded: SeqAn* - genomes/.cvsignore - third_party/ Files: * Copyright: © 2009-2014 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg diff -Nru bowtie-1.3.0+dfsg1/debian/patches/popcnt_capability.patch bowtie-1.3.1/debian/patches/popcnt_capability.patch --- bowtie-1.3.0+dfsg1/debian/patches/popcnt_capability.patch 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/patches/popcnt_capability.patch 2021-09-14 05:01:35.000000000 +0000 @@ -6,7 +6,7 @@ --- a/Makefile +++ b/Makefile -@@ -89,7 +89,7 @@ ifeq (1, $(WITH_TBBMALLOC)) +@@ -73,7 +73,7 @@ ifeq (1,$(MINGW)) endif POPCNT_CAPABILITY ?= 1 diff -Nru bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch bowtie-1.3.1/debian/patches/reproducible.patch --- bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/patches/reproducible.patch 2021-09-14 05:01:35.000000000 +0000 @@ -2,7 +2,7 @@ Author: Sascha Steinbiss --- a/Makefile +++ b/Makefile -@@ -234,9 +234,9 @@ else +@@ -218,9 +218,9 @@ else endif DEFS=-fno-strict-aliasing \ -DBOWTIE_VERSION="\"`cat VERSION`\"" \ @@ -15,12 +15,12 @@ $(FILE_FLAGS) \ $(PTHREAD_DEF) \ $(PREF_DEF) \ -@@ -244,8 +244,8 @@ DEFS=-fno-strict-aliasing \ +@@ -228,8 +228,8 @@ DEFS=-fno-strict-aliasing \ $(SHMEM_DEF) ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) --DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" --RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" +-DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" +-RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" +DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\"" +RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\"" diff -Nru bowtie-1.3.0+dfsg1/debian/patches/simple-test bowtie-1.3.1/debian/patches/simple-test --- bowtie-1.3.0+dfsg1/debian/patches/simple-test 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/patches/simple-test 2021-09-14 05:01:35.000000000 +0000 @@ -22,7 +22,7 @@ last unless defined($c); --- a/Makefile +++ b/Makefile -@@ -429,12 +429,11 @@ install: all +@@ -413,12 +413,11 @@ install: all done .PHONY: simple-test diff -Nru bowtie-1.3.0+dfsg1/debian/patches/use-dpkg-buildflags.patch bowtie-1.3.1/debian/patches/use-dpkg-buildflags.patch --- bowtie-1.3.0+dfsg1/debian/patches/use-dpkg-buildflags.patch 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/patches/use-dpkg-buildflags.patch 2021-09-14 05:01:35.000000000 +0000 @@ -6,12 +6,12 @@ --- a/Makefile +++ b/Makefile -@@ -243,7 +243,7 @@ DEFS=-fno-strict-aliasing \ +@@ -227,7 +227,7 @@ DEFS=-fno-strict-aliasing \ $(MM_DEF) \ $(SHMEM_DEF) -ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS) +ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\"" - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\"" + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\"" diff -Nru bowtie-1.3.0+dfsg1/debian/upstream/metadata bowtie-1.3.1/debian/upstream/metadata --- bowtie-1.3.0+dfsg1/debian/upstream/metadata 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/upstream/metadata 2021-09-14 05:01:35.000000000 +0000 @@ -1,24 +1,28 @@ Bug-Database: https://github.com/BenLangmead/bowtie/issues Bug-Submit: https://github.com/BenLangmead/bowtie/issues/new Reference: - author: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n" - title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\ - \ genome\n" - journal: Genome Biology - volume: 10 - pages: R25 - year: 2009 - DOI: 10.1186/gb-2009-10-3-r25 - URL: http://genomebiology.com/2009/10/3/R25 - eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf + - Author: > + Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg + Title: > + Ultrafast and memory-efficient alignment of short DNA sequences to the + human genome + Journal: Genome Biology + Volume: 10 + Pages: R25 + Year: 2009 + DOI: 10.1186/gb-2009-10-3-r25 + URL: http://genomebiology.com/2009/10/3/R25 + eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf Registry: -- Name: SciCrunch - Entry: SCR_005476 -- Name: OMICtools - Entry: OMICS_00653 -- Name: bio.tools - Entry: bowtie -- Name: conda:bioconda - Entry: bowtie + - Name: SciCrunch + Entry: SCR_005476 + - Name: OMICtools + Entry: OMICS_00653 + - Name: bio.tools + Entry: bowtie + - Name: conda:bioconda + Entry: bowtie + - Name: guix + Entry: bowtie1 Repository: https://github.com/BenLangmead/bowtie.git Repository-Browse: https://github.com/BenLangmead/bowtie diff -Nru bowtie-1.3.0+dfsg1/debian/watch bowtie-1.3.1/debian/watch --- bowtie-1.3.0+dfsg1/debian/watch 2020-10-13 11:16:39.000000000 +0000 +++ bowtie-1.3.1/debian/watch 2021-09-14 05:01:35.000000000 +0000 @@ -1,4 +1,4 @@ version=4 -opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/BenLangmead/bowtie/releases .*/archive/v(\d[-.\d]+)@ARCHIVE_EXT@ +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ + https://github.com/BenLangmead/bowtie/tags (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@ diff -Nru bowtie-1.3.0+dfsg1/doc/website/manual.ssi bowtie-1.3.1/doc/website/manual.ssi --- bowtie-1.3.0+dfsg1/doc/website/manual.ssi 2020-07-23 02:52:57.000000000 +0000 +++ bowtie-1.3.1/doc/website/manual.ssi 2021-09-14 01:38:24.000000000 +0000 @@ -1,5 +1,5 @@

Table of Contents

-

Bowtie 1.3.0

+

Bowtie 1.3.1