.coveragerc
.gitignore
.pylintrc
.travis.yml
LICENSE
MANIFEST.in
README.rst
readthedocs.yml
requirements.txt
setup.cfg
setup.py
tox.ini
docs/index.rst
sam_alignment_reconstructor/__init__.py
sam_alignment_reconstructor/cli.py
sam_alignment_reconstructor/pairwise.py
sam_alignment_reconstructor.egg-info/PKG-INFO
sam_alignment_reconstructor.egg-info/SOURCES.txt
sam_alignment_reconstructor.egg-info/dependency_links.txt
sam_alignment_reconstructor.egg-info/entry_points.txt
sam_alignment_reconstructor.egg-info/requires.txt
sam_alignment_reconstructor.egg-info/top_level.txt
tests/__init__.py
tests/test_commandline.py
tests/test_pairwise.py
tests/sam_files/test_DS.out
tests/sam_files/test_DS.sam
tests/sam_files/test_D_noMD.sam
tests/sam_files/test_Hend.out
tests/sam_files/test_Hend.sam
tests/sam_files/test_Hstart.out
tests/sam_files/test_Hstart.sam
tests/sam_files/test_MD0end.out
tests/sam_files/test_MD0end.sam
tests/sam_files/test_N.out
tests/sam_files/test_N.sam
tests/sam_files/test_SI.out
tests/sam_files/test_SI.sam
tests/sam_files/test_SPI.out
tests/sam_files/test_SPI.sam
tests/sam_files/test_X=.out
tests/sam_files/test_X=.sam
tests/sam_files/test_charstartCIGAR.sam
tests/sam_files/test_invalidCIGAR.sam
tests/sam_files/test_starcigar.out
tests/sam_files/test_starcigar.sam