.gitignore

# 
# standard
# 
**/*.do_not_sync
**/*.do_not_sync.*
**/*.ignore
**/*.ignore.*
**/*.secret
**/*.secret.*

# Mac
.DS_STORE
.DS_Store
.env

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

# Env
.env

# C extensions
*.so

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

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

# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml

# Translations
*.mo

# Mr Developer
.mr.developer.cfg
.project
.pydevproject

# Rope
.ropeproject

# Django stuff:
*.log
*.pot

# Sphinx documentation
docs/_build/
**/doc/_build/

#Data files
/data/
*.wig
*.dat
*.png
*.out
*.prot_table

NOTES
*~

#Test output ignore
tests/testoutput.txt
tests/testoutput_genes.txt

#BWA generated files from fna
/src/pytransit/genomes/*.amb
/src/pytransit/genomes/*.ann
/src/pytransit/genomes/*.bwt
/src/pytransit/genomes/*.pac
/src/pytransit/genomes/*.sa
/tests/**/*.amb
/tests/**/*.ann
/tests/**/*.bwt
/tests/**/*.pac
/tests/**/*.sa
*.amb
*.ann
*.bwt
*.pac
*.sa