.gitignore

## fasta gtf
*.fa
*.FA
*.fasta
*.FASTA
*.gtf
*.GTF

## C files

# Prerequisites
*.d

# Object files
*.o
*.ko
*.obj
*.elf

# Linker output
*.ilk
*.map
*.exp

# Precompiled Headers
*.gch
*.pch

# Libraries
*.lib
*.a
*.la
*.lo

# Shared objects (inc. Windows DLLs)
*.dll
*.so
*.so.*
*.dylib

# Executables
*.exe
*.out
*.app
*.i*86
*.x86_64
*.hex

# Debug files
*.dSYM/
*.su
*.idb
*.pdb

# Kernel Module Compile Results
*.mod*
*.cmd
modules.order
Module.symvers
Mkfile.old
dkms.conf


## C++ files

# 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
*.out
*.app


## Perl files

/blib/
/.build/
_build/
cover_db/
inc/
Build
!Build/
Build.bat
.last_cover_stats
/Makefile
/Makefile.old
/MANIFEST.bak
/META.yml
/META.json
/MYMETA.*
nytprof.out
/pm_to_blib
*.o
*.bs
/_eumm/


## Python files

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
.hypothesis/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# dotenv
.env

# virtualenv
.venv/
venv/
ENV/

# Spyder project settings
.spyderproject

# Rope project settings
.ropeproject


## R files

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
/*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md


## Emacs files

# -*- 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


## Vim files

# swap
[._]*.s[a-w][a-z]
[._]s[a-w][a-z]
# session
Session.vim
# temporary
.netrwhist
*~
# auto-generated tag files
tags


## Linux files

*~

# 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*


## Windows files

# Windows image file caches
Thumbs.db
ehthumbs.db

# Folder config file
Desktop.ini

# Recycle Bin used on file shares
$RECYCLE.BIN/

# Windows Installer files
*.cab
*.msi
*.msm
*.msp

# Windows shortcuts
*.lnk


## macOS files

*.DS_Store
.AppleDouble
.LSOverride

# Icon must end with two \r
Icon


# 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



## Project Specific Files

data/*
data/raw/*
data/processed/*
tmp/*
code/bin/*

!data/
!data/raw/
!data/processed/
!code/bin/
!.gitignore
!code/bin/README.md
!data/processed/README.md
!data/README.md
!data/raw/README.md