.coveragerc
.gitattributes
.gitignore
.readthedocs.yml
.travis.yml
LICENSE
README.md
environment.yml
mkdocs.yml
setup.py
docs/examples.md
docs/index.md
docs/references.md
docs/API/cal_likelihood.md
docs/API/cal_pvalue.md
docs/API/cal_ref_match_pct.md
docs/API/cal_s_star.md
docs/API/cal_threshold.md
docs/API/utils.md
docs/userguide/likelihood.md
docs/userguide/overview.md
docs/userguide/pvalue.md
docs/userguide/rmatch.md
docs/userguide/score.md
docs/userguide/threshold.md
examples/data/ind_list/den.ind.list
examples/data/ind_list/nean.ind.list
examples/data/ind_list/ref.ind.list
examples/data/ind_list/src.ind.list
examples/data/ind_list/tgt.ind.list
examples/data/real_data/hum.windows.50k.10k.recomb.map
examples/data/real_data/sstar.example.biallelic.snps.vcf.gz
examples/data/real_data/sstar.example.biallelic.snps.vcf.gz.tbi
examples/data/simulated_data/gravel_asn_scale_60k.simulated.data
examples/data/simulated_data/sstar.example.simulated.alt1.src1.pval.txt
examples/data/simulated_data/sstar.example.simulated.alt1.src2.pval.txt
examples/data/simulated_data/sstar.example.simulated.alt2.src1.pval.txt
examples/data/simulated_data/sstar.example.simulated.alt2.src2.pval.txt
examples/data/simulated_data/sstar.example.simulated.null.src1.pval.txt
examples/data/simulated_data/sstar.example.simulated.null.src2.pval.txt
examples/results/sstar.example.match.den.filtered.pval.txt
examples/results/sstar.example.match.den.pval.txt
examples/results/sstar.example.match.nean.filtered.pval.txt
examples/results/sstar.example.match.nean.pval.txt
examples/results/sstar.example.posterior.prob.txt
examples/results/sstar.example.score.txt
examples/results/sstar.example.threshold.txt
examples/snakepipe/Snakefile
examples/snakepipe/conda-env.yaml
examples/snakepipe/config.yaml
examples/snakepipe/sstar-config.yaml
sstar/__init__.py
sstar/__main__.py
sstar/cal_likelihood.py
sstar/cal_pvalue.py
sstar/cal_ref_match_pct.py
sstar/cal_s_star.py
sstar/cal_threshold.py
sstar/conftest.py
sstar/utils.py
sstar.egg-info/PKG-INFO
sstar.egg-info/SOURCES.txt
sstar.egg-info/dependency_links.txt
sstar.egg-info/entry_points.txt
sstar.egg-info/requires.txt
sstar.egg-info/top_level.txt
tests/test_cal_likelihood.py
tests/test_cal_pvalue.py
tests/test_cal_ref_match.py
tests/test_cal_s_star.py
tests/test_cal_threshold.py
tests/test_utils.py
tests/data/test.anc.allele.bed
tests/data/test.data.vcf
tests/data/test.empty.anc.allele.bed
tests/data/test.empty.ind.list
tests/data/test.mapped.region.bed
tests/data/test.pvalue.data.vcf
tests/data/test.pvalue.ref.match.pct
tests/data/test.ref.ind.list
tests/data/test.tgt.ind.list
tests/results/test.posterior.prob.exp.results
tests/results/test.posterior.prob.results
tests/results/test.pvalue.data.pvalue.results
tests/results/test.pvalue.exp.results
tests/results/test.pvalue.results
tests/results/test.pvalue.score.exp.results
tests/results/test.ref.match.pct.exp.results
tests/results/test.ref.match.pct.results
tests/results/test.score.exp.results
tests/results/test.score.results
tests/results/test.threshold.exp.results
tests/results/test.threshold.results