.coveragerc
.gitignore
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
.github/workflows/python-publish.yml
scbamtools/annotation.py
scbamtools/bctree.py
scbamtools/contrib.py
scbamtools/gene_model.py
scbamtools/quant.py
scbamtools/util.py
scbamtools.egg-info/PKG-INFO
scbamtools.egg-info/SOURCES.txt
scbamtools.egg-info/dependency_links.txt
scbamtools.egg-info/entry_points.txt
scbamtools.egg-info/not-zip-safe
scbamtools.egg-info/requires.txt
scbamtools.egg-info/top_level.txt
scbamtools/bin/BamTagHistogram.py
scbamtools/bin/ann.py
scbamtools/bin/count.py
scbamtools/bin/pa_scanner.py
scbamtools/bin/trim.py
scbamtools/bin/uBAM.py
scbamtools/config/__init__.py
scbamtools/config/default.yaml
scbamtools/config/__pycache__/__init__.cpython-310.pyc
scbamtools/config/__pycache__/__init__.cpython-311.pyc
scbamtools/cython/bctree.c
scbamtools/cython/bctree.pyx
scbamtools/cython/cigar.pyx
scbamtools/cython/kmers.c
scbamtools/cython/kmers.pyx
scbamtools/cython/types.pxd
test_data/adap_test.R1.fastq
test_data/adap_test.R2.fastq.gz
test_data/adap_test.bam
test_data/adap_test.ref.bam
test_data/simple_annotation.gtf
test_data/simple_chrom_sizes.csv
tests/fixtures.py
tests/make_test_genome_and_reads.py
tests/test_ann.py
tests/test_bctree.py
tests/test_quant.py
tests/test_trim.py
tests/test_uBAM.py