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.gitignore
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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# Literature
.literature/
.simulation
.notes
.test
test.*
.test/
.output
data/
# C extensions
*.so
# Distribution / packaging
.DS_Store
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib64/
parts/
sdist/
var/
*.tar.gz
#doc*
docs/build
giac/
*.tmp
input_other/
session.tex
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
.notes
.simulation
.data
data
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# mkdocs documentation
/site
# mypy
.mypy_cache/
gimble.bed
gimble.coverage_summary.csv
gimble.genomefile
gimble.log.txt
gimble.samples.csv
gimble.vcf.gz
gimble.heliconius.intergenic.testing_chr02_chr09_chr18.l_64.m_128.i_3.u_3.inter.blocks.tsv
gimble.model.s_A_B.n_1_1.M_A_B.ini
gimble.model.s_A_B.n_1_1.M_A_B.pdf
gimble.model.s_A_B.n_1_1.M_A_B.tsv
gimble.model.s_A_B.n_1_1.M_B_A.ini
gimble.model.s_A_B.n_1_1.M_B_A.pdf
gimble.model.s_A_B.n_1_1.M_B_A.tsv
dasktemp/global.lock
dasktemp/purge.lock
gimble.heliconius.intergenic.testing_chr02_chr09_chr18.windows.gridsearch.bed
gimble.heliconius.intergenic.testing_chr02_chr09_chr18.windows.gridsearch.bestfit.bed
gimble.model.s_A_B.n_1_1.M_A_B.J_A_B.ini
gimble.model.s_A_B.n_1_1.M_A_B.J_A_B.pdf
gimble.model.s_A_B.n_1_1.M_A_B.J_A_B.tsv
test_models/gimble.model.s_A_B.n_1_1.J_A_B.10_points.ini
test_models/gimble.model.s_A_B.n_1_1.J_A_B.50_points.ini
test_models/gimble.model.s_A_B.n_1_1.J_A_B.gridsearch_test.ini
test_models/gimble.model.s_A_B.n_1_1.J_A_B.ini
test_models/gimble.model.s_A_B.n_1_1.J_A_B.optimize.ini
notes.txt
log_ilt.txt
log_equation.txt
log_file.txt
log_ETPs.txt
gimble.heliconius.intergenic.testing_chr02_chr09_chr18.20200920.l_64.m_128.i_3.u_3.inter.blocks.tsv
gimble.heliconius.intergenic.testing_chr02_chr09_chr18.windows.bed
gimble.model.s_A_B.n_1_1.J_A_B.tsv
mergebed.sh
profile_bsfss.py
variation2bsfs.prof
windows2bsfs.prof
gimble.v0.7.1.master.parse.windows.popgen.bed
gimble.v0.7.1.master.toy.windows.popgen.bed
gimble.DIV.ini
gimble.DIV.no_sync.ini
gimble.MIG_AB.ini
gimble.test.master.parse.info.20210318_172725.txt
gimble.test.master.parse.info.txt
gimble.test.master.parse.l_64.m_128.i_3.u_3.kmax_3_3_3_3.tally.blocks.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.kmax_4_4_4_4.tally.blocks.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.kmax_None.tally.blocks.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.w_500.s_50.kmax_3_3_3_3.tally.windows_sum.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.w_500.s_50.kmax_None.tally.windows_sum.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.w_500.s_50.tally.windows_sum.tsv
gimble.test.master.parse.l_64.m_128.i_3.u_3.w_500.s_50.tally.windows.tsv
gimble.test.master.parse.windows.popgen.bed
gimble.test.master.parse.windows.popgen.bed.npunique_sample_sets
gimble.test.master.parse.windows.popgen.non_effective.bed
gimble.v0.7.1.master.parse.l_64.m_128.i_3.u_3.bsfs.blocks.tsv
gimble.v0.7.1.master.parse.l_64.m_128.i_3.u_3.kmax_2_2_2_2.tally.blocks.tsv
gimble.v0.7.1.master.parse.l_64.m_128.i_3.u_3.kmax_none.tally.blocks.tsv
gimble.v0.7.1.master.parse.l_64.m_128.i_3.u_3.tally.blocks.2_2_2_2.tsv
gimble.v0.7.1.master.parse.l_64.m_128.i_3.u_3.tally.blocks.tsv
log_single_ETP.txt
optimize_log_blocks_3797af1d905e281d74e97159b237e202_.tsv
optimize_log_blocks_d6d124216c56fe1cbdbdc399afb8fe47_.tsv
optimize_log_blocks_f1ccb61fa6a25da413f6dd207e65c4ef_.tsv
gimble.test.master.parse_var_fix.info.txt
gimble.test.master.parse.info.pre_count_var_fix.txt
test1.z/
test2.z/
test3.z/
test5.z/
test4.z/
.gimblelibjunk/
blessed_configs/
tests/output/
*.log
gimble.2chr_1M.optimize_maxk1_test_optimize_1.optimize.tsv
gimble.2chr_1M.optimize_maxk3_test_optimize_1.optimize.tsv
gimble.2chr_1M.optimize_simulate64_test_optimize_1.optimize.0.tsv
gimble.2chr_1M.optimize_simulate64_test_optimize_1.optimize.1.tsv
gimble.2chr_1M.optimize_simulate64_test_optimize_1.optimize.2.tsv
gimble.2chr_1M.tally_maxk1.tsv
gimble.2chr_1M.tally_maxk3.tsv
gimble.optimize.DIV.test_optimize_1.config.ini