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.gitignore
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.idea/
__pycache__/
kmers
kmerstest
kmercamel
kmercameltest
kmercamel-large
kmercameltest-large
kmercameltest-extra-large
src/version.h
🐫
bin/
####
# C/C++ devel .gitignore from https://gist.github.com/Yousha/3830712334ac30a90eb6041b932b68d7
####
##### Windows
# Windows thumbnail cache files
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db
# Dump file
*.stackdump
# Folder config file
[Dd]esktop.ini
# Recycle Bin used on file shares
$RECYCLE.BIN/
# Windows Installer files
*.cab
*.msi
*.msix
*.msm
*.msp
# Windows shortcuts
*.lnk
##### Linux
*~
# temporary files which can be created if a process still has a handle open of a deleted file
.fuse_hidden*
# KDE directory preferences
.directory
# Linux trash folder which might appear on any partition or disk
.Trash-*
# .nfs files are created when an open file is removed but is still being accessed
.nfs*
##### MacOS
# General
.DS_Store
.AppleDouble
.LSOverride
# Thumbnails
._*
# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent
# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk
##### Android
# Built application files
*.apk
*.ap_
*.aab
# Files for the ART/Dalvik VM
*.dex
# Java class files
*.class
# Generated files
bin/
gen/
out/
# Uncomment the following line in case you need and you don't have the release build type files in your app
# release/
# Gradle files
.gradle/
build/
# Local configuration file (sdk path, etc)
local.properties
# Proguard folder generated by Eclipse
proguard/
# Log Files
*.log
# Android Studio Navigation editor temp files
.navigation/
# Android Studio captures folder
captures/
# IntelliJ
*.iml
.idea/workspace.xml
.idea/tasks.xml
.idea/gradle.xml
.idea/assetWizardSettings.xml
.idea/dictionaries
.idea/libraries
# Android Studio 3 in .gitignore file.
.idea/caches
.idea/modules.xml
# Comment next line if keeping position of elements in Navigation Editor is relevant for you
.idea/navEditor.xml
# Keystore files
# Uncomment the following lines if you do not want to check your keystore files in.
#*.jks
#*.keystore
# External native build folder generated in Android Studio 2.2 and later
.externalNativeBuild
# Google Services (e.g. APIs or Firebase)
# google-services.json
# Freeline
freeline.py
freeline/
freeline_project_description.json
# fastlane
fastlane/report.xml
fastlane/Preview.html
fastlane/screenshots
fastlane/test_output
fastlane/readme.md
# Version control
vcs.xml
# lint
lint/intermediates/
lint/generated/
lint/outputs/
lint/tmp/
# lint/reports/
##### Backup
*.bak
*.gho
*.ori
*.orig
*.tmp
##### GPG
secring.*
##### Dropbox
# Dropbox settings and caches
.dropbox
.dropbox.attr
.dropbox.cache
##### SynopsysVCS
# Waveform formats
*.vcd
*.vpd
*.evcd
*.fsdb
# Default name of the simulation executable. A different name can be
# specified with this switch (the associated daidir database name is
# also taken from here): -o <path>/<filename>
simv
# Generated for Verilog and VHDL top configs
simv.daidir/
simv.db.dir/
# Infrastructure necessary to co-simulate SystemC models with
# Verilog/VHDL models. An alternate directory may be specified with this
# switch: -Mdir=<directory_path>
csrc/
# Log file - the following switch allows to specify the file that will be
# used to write all messages from simulation: -l <filename>
*.log
# Coverage results (generated with urg) and database location. The
# following switch can also be used: urg -dir <coverage_directory>.vdb
simv.vdb/
urgReport/
# DVE and UCLI related files.
DVEfiles/
ucli.key
# When the design is elaborated for DirectC, the following file is created
# with declarations for C/C++ functions.
vc_hdrs.h
##### SVN
.svn/
##### Mercurial
.hg/
.hgignore
.hgsigs
.hgsub
.hgsubstate
.hgtags
##### Bazaar
.bzr/
.bzrignore
##### CVS
/CVS/*
**/CVS/*
.cvsignore
*/.cvsignore
##### TortoiseGit
# Project-level settings
/.tgitconfig
##### PuTTY
# Private key
*.ppk
##### Vim
# Swap
[._]*.s[a-v][a-z]
!*.svg # comment out if you don't need vector files
[._]*.sw[a-p]
[._]s[a-rt-v][a-z]
[._]ss[a-gi-z]
[._]sw[a-p]
# Session
Session.vim
Sessionx.vim
# Temporary
.netrwhist
*~
# Auto-generated tag files
tags
# Persistent undo
[._]*.un~
##### Emacs
# -*- mode: gitignore; -*-
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*
# Org-mode
.org-id-locations
*_archive
# flymake-mode
*_flymake.*
# eshell files
/eshell/history
/eshell/lastdir
# elpa packages
/elpa/
# reftex files
*.rel
# AUCTeX auto folder
/auto/
# cask packages
.cask/
dist/
# Flycheck
flycheck_*.el
# server auth directory
/server/
# projectiles files
.projectile
# directory configuration
.dir-locals.el
# network security
/network-security.data
##### SublimeText
# Cache files for Sublime Text
*.tmlanguage.cache
*.tmPreferences.cache
*.stTheme.cache
# Workspace files are user-specific
*.sublime-workspace
# Project files should be checked into the repository, unless a significant
# proportion of contributors will probably not be using Sublime Text
# *.sublime-project
# SFTP configuration file
sftp-config.json
sftp-config-alt*.json
# Package control specific files
Package Control.last-run
Package Control.ca-list
Package Control.ca-bundle
Package Control.system-ca-bundle
Package Control.cache/
Package Control.ca-certs/
Package Control.merged-ca-bundle
Package Control.user-ca-bundle
oscrypto-ca-bundle.crt
bh_unicode_properties.cache
# Sublime-github package stores a github token in this file
# https://packagecontrol.io/packages/sublime-github
GitHub.sublime-settings
##### Notepad++
# Notepad++ backups #
*.bak
##### TextMate
*.tmproj
*.tmproject
tmtags
##### VisualStudioCode
.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json
*.code-workspace
# Local History for Visual Studio Code
.history/
##### NetBeans
**/nbproject/private/
**/nbproject/Makefile-*.mk
**/nbproject/Package-*.bash
build/
nbbuild/
dist/
nbdist/
.nb-gradle/
##### JetBrains
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
# User-specific stuff
.idea/**/workspace.xml
.idea/**/tasks.xml
.idea/**/usage.statistics.xml
.idea/**/dictionaries
.idea/**/shelf
# Generated files
.idea/**/contentModel.xml
# Sensitive or high-churn files
.idea/**/dataSources/
.idea/**/dataSources.ids
.idea/**/dataSources.local.xml
.idea/**/sqlDataSources.xml
.idea/**/dynamic.xml
.idea/**/uiDesigner.xml
.idea/**/dbnavigator.xml
# Gradle
.idea/**/gradle.xml
.idea/**/libraries
# Gradle and Maven with auto-import
# When using Gradle or Maven with auto-import, you should exclude module files,
# since they will be recreated, and may cause churn. Uncomment if using
# auto-import.
# .idea/artifacts
# .idea/compiler.xml
# .idea/jarRepositories.xml
# .idea/modules.xml
# .idea/*.iml
# .idea/modules
# *.iml
# *.ipr
# CMake
cmake-build-*/
# Mongo Explorer plugin
.idea/**/mongoSettings.xml
# File-based project format
*.iws
# IntelliJ
out/
# mpeltonen/sbt-idea plugin
.idea_modules/
# JIRA plugin
atlassian-ide-plugin.xml
# Cursive Clojure plugin
.idea/replstate.xml
# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
fabric.properties
# Editor-based Rest Client
.idea/httpRequests
# Android studio 3.1+ serialized cache file
.idea/caches/build_file_checksums.ser
##### Eclipse
.metadata
bin/
tmp/
*.tmp
*.bak
*.swp
*~.nib
local.properties
.settings/
.loadpath
.recommenders
# External tool builders
.externalToolBuilders/
# Locally stored "Eclipse launch configurations"
*.launch
# PyDev specific (Python IDE for Eclipse)
*.pydevproject
# CDT-specific (C/C++ Development Tooling)
.cproject
# CDT- autotools
.autotools
# Java annotation processor (APT)
.factorypath
# PDT-specific (PHP Development Tools)
.buildpath
# sbteclipse plugin
.target
# Tern plugin
.tern-project
# TeXlipse plugin
.texlipse
# STS (Spring Tool Suite)
.springBeans
# Code Recommenders
.recommenders/
# Annotation Processing
.apt_generated/
.apt_generated_test/
# Scala IDE specific (Scala & Java development for Eclipse)
.cache-main
.scala_dependencies
.worksheet
# Uncomment this line if you wish to ignore the project description file.
# Typically, this file would be tracked if it contains build/dependency configurations:
#.project
##### Qt
# C++ objects and libs
*.slo
*.lo
*.o
*.a
*.la
*.lai
*.so
*.so.*
*.dll
*.dylib
# Qt-es
object_script.*.Release
object_script.*.Debug
*_plugin_import.cpp
/.qmake.cache
/.qmake.stash
*.pro.user
*.pro.user.*
*.qbs.user
*.qbs.user.*
*.moc
moc_*.cpp
moc_*.h
qrc_*.cpp
ui_*.h
*.qmlc
*.jsc
Makefile*
*build-*
*.qm
*.prl
# Qt unit tests
target_wrapper.*
# QtCreator
*.autosave
# QtCreator Qml
*.qmlproject.user
*.qmlproject.user.*
# QtCreator CMake
CMakeLists.txt.user*
# QtCreator 4.8< compilation database
compile_commands.json
# QtCreator local machine specific files for imported projects
*creator.user*
##### VisualStudio
##### VisualStudio
## Ignore Visual Studio temporary files, build results, and
## files generated by popular Visual Studio add-ons.
##
## Get latest from https://github.com/github/gitignore/blob/master/VisualStudio.gitignore
# User-specific files
*.rsuser
*.suo
*.user
*.userosscache
*.sln.docstates
# User-specific files (MonoDevelop/Xamarin Studio)
*.userprefs
# Mono auto generated files
mono_crash.*
# Build results
[Dd]ebug/
[Dd]ebugPublic/
[Rr]elease/
[Rr]eleases/
x64/
x86/
[Ww][Ii][Nn]32/
[Aa][Rr][Mm]/
[Aa][Rr][Mm]64/
bld/
[Bb]in/
[Oo]bj/
[Ll]og/
[Ll]ogs/
# Visual Studio 2015/2017 cache/options directory
.vs/
# Uncomment if you have tasks that create the project's static files in wwwroot
#wwwroot/
# Visual Studio 2017 auto generated files
Generated\ Files/
# MSTest test Results
[Tt]est[Rr]esult*/
[Bb]uild[Ll]og.*
# NUnit
*.VisualState.xml
TestResult.xml
nunit-*.xml
# Build Results of an ATL Project
[Dd]ebugPS/
[Rr]eleasePS/
dlldata.c
# Benchmark Results
BenchmarkDotNet.Artifacts/
# .NET Core
project.lock.json
project.fragment.lock.json
artifacts/
# ASP.NET Scaffolding
ScaffoldingReadMe.txt
# StyleCop
StyleCopReport.xml
# Files built by Visual Studio
*_i.c
*_p.c
*_h.h
*.ilk
*.meta
*.obj
*.iobj
*.pch
*.pdb
*.ipdb
*.pgc
*.pgd
*.rsp
*.sbr
*.tlb
*.tli
*.tlh
*.tmp
*.tmp_proj
*_wpftmp.csproj
*.log
*.vspscc
*.vssscc
.builds
*.pidb
*.svclog
*.scc
# Chutzpah Test files
_Chutzpah*
# Visual C++ cache files
ipch/
*.aps
*.ncb
*.opendb
*.opensdf
*.sdf
*.cachefile
*.VC.db
*.VC.VC.opendb
# Visual Studio profiler
*.psess
*.vsp
*.vspx
*.sap
# Visual Studio Trace Files
*.e2e
# TFS 2012 Local Workspace
$tf/
# Guidance Automation Toolkit
*.gpState
# ReSharper is a .NET coding add-in
_ReSharper*/
*.[Rr]e[Ss]harper
*.DotSettings.user
# TeamCity is a build add-in
_TeamCity*
# DotCover is a Code Coverage Tool
*.dotCover
# AxoCover is a Code Coverage Tool
.axoCover/*
!.axoCover/settings.json
# Coverlet is a free, cross platform Code Coverage Tool
coverage*[.json, .xml, .info]
# Visual Studio code coverage results
*.coverage
*.coveragexml
# NCrunch
_NCrunch_*
.*crunch*.local.xml
nCrunchTemp_*
# MightyMoose
*.mm.*
AutoTest.Net/
# Web workbench (sass)
.sass-cache/
# Installshield output folder
[Ee]xpress/
# DocProject is a documentation generator add-in
DocProject/buildhelp/
DocProject/Help/*.HxT
DocProject/Help/*.HxC
DocProject/Help/*.hhc
DocProject/Help/*.hhk
DocProject/Help/*.hhp
DocProject/Help/Html2
DocProject/Help/html
# Click-Once directory
publish/
# Publish Web Output
*.[Pp]ublish.xml
*.azurePubxml
# Note: Comment the next line if you want to checkin your web deploy settings,
# but database connection strings (with potential passwords) will be unencrypted
*.pubxml
*.publishproj
# Microsoft Azure Web App publish settings. Comment the next line if you want to
# checkin your Azure Web App publish settings, but sensitive information contained
# in these scripts will be unencrypted
PublishScripts/
# NuGet Packages
*.nupkg
# NuGet Symbol Packages
*.snupkg
# The packages folder can be ignored because of Package Restore
**/[Pp]ackages/*
# except build/, which is used as an MSBuild target.
!**/[Pp]ackages/build/
# Uncomment if necessary however generally it will be regenerated when needed
#!**/[Pp]ackages/repositories.config
# NuGet v3's project.json files produces more ignorable files
*.nuget.props
*.nuget.targets
# Microsoft Azure Build Output
csx/
*.build.csdef
# Microsoft Azure Emulator
ecf/
rcf/
# Windows Store app package directories and files
AppPackages/
BundleArtifacts/
Package.StoreAssociation.xml
_pkginfo.txt
*.appx
*.appxbundle
*.appxupload
# Visual Studio cache files
# files ending in .cache can be ignored
*.[Cc]ache
# but keep track of directories ending in .cache
!?*.[Cc]ache/
# Others
ClientBin/
~$*
*~
*.dbmdl
*.dbproj.schemaview
*.jfm
*.pfx
*.publishsettings
orleans.codegen.cs
# Including strong name files can present a security risk
# (https://github.com/github/gitignore/pull/2483#issue-259490424)
#*.snk
# Since there are multiple workflows, uncomment next line to ignore bower_components
# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
#bower_components/
# RIA/Silverlight projects
Generated_Code/
# Backup & report files from converting an old project file
# to a newer Visual Studio version. Backup files are not needed,
# because we have git ;-)
_UpgradeReport_Files/
Backup*/
UpgradeLog*.XML
UpgradeLog*.htm
ServiceFabricBackup/
*.rptproj.bak
# SQL Server files
*.mdf
*.ldf
*.ndf
# Business Intelligence projects
*.rdl.data
*.bim.layout
*.bim_*.settings
*.rptproj.rsuser
*- [Bb]ackup.rdl
*- [Bb]ackup ([0-9]).rdl
*- [Bb]ackup ([0-9][0-9]).rdl
# Microsoft Fakes
FakesAssemblies/
# GhostDoc plugin setting file
*.GhostDoc.xml
# Node.js Tools for Visual Studio
.ntvs_analysis.dat
node_modules/
# Visual Studio 6 build log
*.plg
# Visual Studio 6 workspace options file
*.opt
# Visual Studio 6 auto-generated workspace file (contains which files were open etc.)
*.vbw
# Visual Studio LightSwitch build output
**/*.HTMLClient/GeneratedArtifacts
**/*.DesktopClient/GeneratedArtifacts
**/*.DesktopClient/ModelManifest.xml
**/*.Server/GeneratedArtifacts
**/*.Server/ModelManifest.xml
_Pvt_Extensions
# Paket dependency manager
.paket/paket.exe
paket-files/
# FAKE - F# Make
.fake/
# CodeRush personal settings
.cr/personal
# Python Tools for Visual Studio (PTVS)
__pycache__/
*.pyc
# Cake - Uncomment if you are using it
# tools/**
# !tools/packages.config
# Tabs Studio
*.tss
# Telerik's JustMock configuration file
*.jmconfig
# BizTalk build output
*.btp.cs
*.btm.cs
*.odx.cs
*.xsd.cs
# OpenCover UI analysis results
OpenCover/
# Azure Stream Analytics local run output
ASALocalRun/
# MSBuild Binary and Structured Log
*.binlog
# NVidia Nsight GPU debugger configuration file
*.nvuser
# MFractors (Xamarin productivity tool) working folder
.mfractor/
# Local History for Visual Studio
.localhistory/
# BeatPulse healthcheck temp database
healthchecksdb
# Backup folder for Package Reference Convert tool in Visual Studio 2017
MigrationBackup/
# Ionide (cross platform F# VS Code tools) working folder
.ionide/
# Fody - auto-generated XML schema
FodyWeavers.xsd
##### Gradle
.gradle
**/build/
!src/**/build/
# Ignore Gradle GUI config
gradle-app.setting
# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
!gradle-wrapper.jar
# Cache of project
.gradletasknamecache
# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
# gradle/wrapper/gradle-wrapper.properties
##### CMake
CMakeLists.txt.user
CMakeCache.txt
CMakeFiles
CMakeScripts
Testing
Makefile
cmake_install.cmake
install_manifest.txt
compile_commands.json
CTestTestfile.cmake
_deps
##### C++
# Prerequisites
*.d
# Compiled Object files
*.slo
*.lo
*.o
*.obj
# Precompiled Headers
*.gch
*.pch
# Compiled Dynamic libraries
*.so
*.dylib
*.dll
# Fortran module files
*.mod
*.smod
# Compiled Static libraries
*.lai
*.la
*.a
*.lib
# Executables
*.exe