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ch4rr0ch4rr0
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Merge branch 'bug_fixes'
2 parents da7b440 + 5a4d538 commit 73821b4

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‎.github/workflows/random_tests.yml

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name: Run bowtie random tests for all commits to master on Ubuntu and MacOS
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on:
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push:
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branches:
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- 'master'
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paths:
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- '**.c'
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- '**.h'
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- '**.cpp'
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- 'bowtie'
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- 'bowtie-build'
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- 'bowtie-inspect'
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- 'Makefile'
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- 'scripts/test/**'
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pull_request:
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branches:
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- 'master'
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paths:
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- '**.c'
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- '**.h'
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- '**.cpp'
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- 'bowtie'
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- 'bowtie-build'
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- 'bowtie-inspect'
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- 'Makefile'
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- 'scripts/test/**'
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jobs:
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setup:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository code
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uses: actions/checkout@v2
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- name: Install zlib development files
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run: |
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sudo apt-get update
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sudo apt-get install zlib1g-dev
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linux:
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runs-on: ubuntu-latest
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needs: setup
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steps:
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- uses: actions/checkout@v2
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- name: Run random tests
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run: |
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make allall
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make random-test
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macos:
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v2
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- name: Run random tests
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run: |
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make allall
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make random-test

‎.github/workflows/simple_tests.yml

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name: Run bowtie simple tests on Ubuntu and MacOS
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on:
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push:
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branches:
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- 'bug_fixes'
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- 'master'
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paths:
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- '**.c'
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- '**.h'
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- '**.cpp'
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- 'bowtie'
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- 'bowtie-build'
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- 'bowtie-inspect'
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- 'Makefile'
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- 'scripts/test/**'
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pull_request:
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branches:
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- 'master'
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paths:
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- '**.c'
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- '**.h'
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- '**.cpp'
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- 'bowtie'
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- 'bowtie-build'
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- 'bowtie-inspect'
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- 'Makefile'
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- 'scripts/test/**'
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jobs:
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setup:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository code
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uses: actions/checkout@v2
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- name: Install zlib development files
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run: |
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sudo apt-get update
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sudo apt-get install zlib1g-dev
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linux:
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runs-on: ubuntu-latest
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needs: setup
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steps:
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- uses: actions/checkout@v2
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- name: Run simple tests
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run: |
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make allall
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make simple-test
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macos:
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v2
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- name: Run simple tests
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run: |
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make allall
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make simple-test

‎.travis.yml

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@@ -7,46 +7,6 @@ branches:
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- bug_fixes
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matrix:
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include:
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# Linux (gcc4.9)
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- os: linux
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language: python
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python: "3.4"
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dist: xenial
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addons:
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apt:
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sources:
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- ubuntu-toolchain-r-test
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packages:
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- g++-4.9
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- zlib1g-dev
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env:
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- CC=gcc-4.9
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- CXX=g++-4.9
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# Linux (gcc8)
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- os: linux
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language: python
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python: "3.8"
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addons:
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apt:
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sources:
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- ubuntu-toolchain-r-test
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packages:
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- g++-8
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- zlib1g-dev
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env:
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- CC=gcc-8
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- CXX=g++-8
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- CXXFLAGS="-fuse-ld=gold"
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# MacOS
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- os: osx
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osx_image: xcode11.2
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compiler: clang
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env:
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- CC=clang
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- CXX=clang++
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- NPROC="$(sysctl -n hw.activecpu)"
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before_install:
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- brew unlink python@2
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# ARM 64-bit
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- os: linux
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arch: arm64

‎Makefile

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@@ -7,7 +7,7 @@ bindir = $(prefix)/bin
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ARCH = $(shell uname -m)
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INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) -I third_party
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LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
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LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz -lpthread
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HEADERS = $(wildcard *.h)
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BOWTIE_MM = 1
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BOWTIE_SHARED_MEM = 1
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ifeq (1,$(BOWTIE_SHARED_MEM))
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SHMEM_DEF = -DBOWTIE_SHARED_MEM
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endif
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PTHREAD_PKG =
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PTHREAD_LIB =
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PTHREAD_DEF =
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ifeq (1,$(MINGW))
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PTHREAD_LIB =
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override EXTRA_FLAGS += -static-libgcc -static-libstdc++
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else
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PTHREAD_LIB = -lpthread
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endif
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ifeq (1,$(NO_SPINLOCK))
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override EXTRA_FLAGS += -DNO_SPINLOCK
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endif
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LIBS += $(PTHREAD_LIB)
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ifeq (1, $(WITH_TBBMALLOC))
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LIBS += -ltbbmalloc
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endif
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POPCNT_CAPABILITY ?= 1
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endif
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ifeq (1, $(POPCNT_CAPABILITY))
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override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
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INC += -I third_party
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endif
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PREFETCH_LOCALITY = 2
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endif
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OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
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edit.cpp ebwt.cpp
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edit.cpp ebwt.cpp bt2_locks.cpp
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ifneq (1, $(NO_SPINLOCK))
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OTHER_CPPS += bt2_locks.cpp
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ifeq (1,$(WITH_QUEUELOCK))
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NO_SPINLOCK = 1
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override EXTRA_FLAGS += -DWITH_QUEUELOCK
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endif
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ifeq (1,$(WITH_QUEUELOCK))
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OTHER_CPPS += bt2_locks.cpp
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override EXTRA_FLAGS += -DWITH_QUEUELOCK=1
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ifeq (1,$(NO_SPINLOCK))
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$(info $(NO_SPINLOCK))
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override EXTRA_FLAGS += -DNO_SPINLOCK
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endif
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ifeq (1,$(WITH_FINE_TIMER))
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$(SHMEM_DEF)
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ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
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#
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# bowtie-build targets

‎NEWS

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Bowtie is now available for download. 0.9.0 is the first version to
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be released under the OSI Artistic License (see `LICENSE') and freely
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available to the public for download. The current version is 1.3.0.
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available to the public for download. The current version is 1.3.1.
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Reporting Issues
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================
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Version Release History
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=======================
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Version 1.3.1 - Sep 13, 2021
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* Fixed an overflow issue in `bowtie-build` that would sometimes
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yield corrupt "large" (64-bit) indexes; the resulting index
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would sometimes cause `bowtie` to hang. Note: `bowtie2-build`
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does not have this issue.
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* Fixed an issue in `bowtie` causing XM:i SAM optional field to
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sometimes be off by 1 when using the `-m/-M` flags.
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* Fixed an issue that would sometimes cause deadlocks in `bowtie`
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when running multithreaded.
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* Fixed an issue causing build errors when compiling against
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a pre-C++11 standard.
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Version 1.3.0 - Jul 22, 2020
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‎VERSION

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1.3.0
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1.3.1

‎bt2_locks.cpp

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#include "bt2_locks.h"
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#if (__cplusplus >= 201103L)
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5-
void mcs_lock::lock() {
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#include "bt2_locks.h"
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void mcs_lock::lock(mcs_node &node) {
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node.next = nullptr;
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node.unlocked = false;
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9-
mcs_node *pred = q.exchange(&node, std::memory_order_release);
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mcs_node *pred = q.exchange(&node, std::memory_order_acq_rel);
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if (pred) {
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pred->next = &node;
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node.unlocked = false;
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pred->next.store(&node, std::memory_order_release);
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spin_while_eq(node.unlocked, false);
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}
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node.unlocked.load(std::memory_order_acquire);
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}
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void mcs_lock::unlock() {
18-
if (!node.next) {
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void mcs_lock::unlock(mcs_node &node) {
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if (!node.next.load(std::memory_order_acquire)) {
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mcs_node *node_ptr = &node;
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if (q.compare_exchange_strong(node_ptr,
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(mcs_node *)nullptr,
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std::memory_order_release))
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return;
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spin_while_eq(node.next, (mcs_node *)nullptr);
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}
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node.next->unlocked.store(true, std::memory_order_release);
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node.next.load(std::memory_order_acquire)->unlocked.store(true, std::memory_order_release);
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}
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thread_local mcs_lock::mcs_node mcs_lock::node;
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void spin_lock::lock() {
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cpu_backoff backoff;
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void spin_lock::unlock() {
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flag.clear(std::memory_order_release);
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}
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#endif

‎bt2_locks.h

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public:
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mcs_lock(): q(nullptr) {}
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struct mcs_node {
51-
mcs_node *next;
51+
std::atomic<mcs_node *> next;
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std::atomic_bool unlocked;
5353
};
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55-
void lock();
56-
void unlock();
57-
typedef mcs_node* mcs_node_ptr;
55+
void lock(mcs_node &node);
56+
void unlock(mcs_node &node);
57+
typedef std::atomic<mcs_node *> mcs_node_ptr;
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private:
59-
void spin_while_eq(const volatile mcs_node_ptr& value, mcs_node *expected) {
59+
void spin_while_eq(const volatile mcs_node_ptr& value, const volatile mcs_node *expected) {
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cpu_backoff backoff;
61-
while (value == expected)
61+
while (value.load(std::memory_order_acquire) == expected)
6262
backoff.pause();
6363
}
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65-
void spin_while_eq(const volatile std::atomic_bool& value, bool expected) {
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void spin_while_eq(const volatile std::atomic_bool& value, const volatile bool expected) {
6666
cpu_backoff backoff;
6767
while (value.load(std::memory_order_acquire) == expected)
6868
backoff.pause();
6969
}
7070
std::atomic<mcs_node *> q;
71-
static thread_local mcs_node node;
7271
};
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#endif
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#endif // if (__cplusplus >= 201103L)
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#endif // __MCS_LOCK_H__

‎doc/website/manual.ssi

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<h1>Table of Contents</h1>
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<p>Bowtie 1.3.0</p>
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<p>Bowtie 1.3.1</p>
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<nav id="TOC" role="doc-toc">
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<ul>

‎doc/website/recent_news.ssi

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<h2>1.3.1 - 09/13/2021</h2>
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<ul>
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<li>Fixed an overflow issue in <code>bowtie-build</code> that would sometimes yield corrupt "large" (64-bit) indexes; the resulting index would sometimes cause <code>bowtie</code> to hang. Note: <code>bowtie2-build</code> does not have this issue.</li>
4+
<li>Fixed an issue in <code>bowtie</code> causing XM:i SAM optional field to sometimes be off by 1 when using the <code><a href="manual.shtml#bowtie-options-m">-m</a>/<a href="manual.shtml#bowtie-options-M">-M</a></code> flags.</li>
5+
<li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie</code> when running multithreaded.</li>
6+
<li>Fixed an issue causing build errors when compiling against a pre-C++11 standard.</li>
7+
</ul>
8+
19
<h2>1.3.0 - 07/22/2020</h2>
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<ul>
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<li>Fixed an issue causing <code>bowtie</code> to report incorrect results when using a Bowtie 2 index.</li>

‎doc/website/rhsidebar.ssi

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</tr>
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<tr>
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<td>
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<a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0">Bowtie 1.3.0</a>
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<a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1">Bowtie 1.3.1</a>
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</td>
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<td align="right">
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07/22/20
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09/13/21
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</td>
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</tr>
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<tr>

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