AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/api.rst
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/usage.rst
src/pyim/__init__.py
src/pyim/model.py
src/pyim.egg-info/PKG-INFO
src/pyim.egg-info/SOURCES.txt
src/pyim.egg-info/dependency_links.txt
src/pyim.egg-info/entry_points.txt
src/pyim.egg-info/not-zip-safe
src/pyim.egg-info/requires.txt
src/pyim.egg-info/top_level.txt
src/pyim/align/__init__.py
src/pyim/align/util.py
src/pyim/align/pipelines/__init__.py
src/pyim/align/pipelines/base.py
src/pyim/align/pipelines/nextera.py
src/pyim/align/pipelines/shear_splink.py
src/pyim/annotate/__init__.py
src/pyim/annotate/filter_.py
src/pyim/annotate/metadata.py
src/pyim/annotate/util.py
src/pyim/annotate/annotators/__init__.py
src/pyim/annotate/annotators/base.py
src/pyim/annotate/annotators/rbm.py
src/pyim/annotate/annotators/window.py
src/pyim/cis/__init__.py
src/pyim/cis/util.py
src/pyim/cis/callers/__init__.py
src/pyim/cis/callers/base.py
src/pyim/cis/callers/cimpl.py
src/pyim/external/__init__.py
src/pyim/external/bowtie2.py
src/pyim/external/cutadapt.py
src/pyim/external/util.py
src/pyim/main/__init__.py
src/pyim/main/pyim_align.py
src/pyim/main/pyim_annotate.py
src/pyim/main/pyim_bed.py
src/pyim/main/pyim_cis.py
src/pyim/main/pyim_demultiplex.py
src/pyim/main/pyim_merge.py
src/pyim/main/pyim_split.py
src/pyim/util/__init__.py
src/pyim/util/frozendict.py
src/pyim/util/path.py
src/pyim/util/rpy2.py
src/pyim/util/tabix.py
tests/conftest.py
tests/data/reference.gtf
tests/data/reference.gtf.gz
tests/data/reference.gtf.gz.tbi
tests/pyim/annotate/annotators/conftest.py
tests/pyim/annotate/annotators/test_rbm.py
tests/pyim/annotate/annotators/test_window.py
tests/pyim/external/test_bowtie2.py
tests/pyim/external/test_cutadapt.py
tests/pyim/external/test_util.py
tests/pyim/util/test_path.py