LICENSE
MANIFEST.in
README.md
setup.py
IBSPy/BlockMapping.py
IBSPy/IBSPy_results.py
IBSPy/IBSpy_options.py
IBSPy/IBSpy_plot.py
IBSPy/IBSpy_plot_window_results.py
IBSPy/IBSpy_result_set.py
IBSPy/IBSpy_results.py
IBSPy/IBSpy_values_matrix.py
IBSPy/IBSpy_window_count.py
IBSPy/__init__.py
IBSPy/build_score_matrix.py
IBSPy/jellyfish_kmer_database.py
IBSPy/kmc3_kmer_database.py
IBSPy/kmerGWAS_kmer.py
IBSPy/kmer_database.py
IBSPy/window_affinity_propagation.py
IBSPy.egg-info/PKG-INFO
IBSPy.egg-info/SOURCES.txt
IBSPy.egg-info/dependency_links.txt
IBSPy.egg-info/top_level.txt
IBSpy/BlockMapping.py
IBSpy/IBSPy_results.py
IBSpy/IBSpy_options.py
IBSpy/IBSpy_plot.py
IBSpy/IBSpy_plot_window_results.py
IBSpy/IBSpy_result_set.py
IBSpy/IBSpy_results.py
IBSpy/IBSpy_values_matrix.py
IBSpy/IBSpy_window_count.py
IBSpy/__init__.py
IBSpy/build_score_matrix.py
IBSpy/jellyfish_kmer_database.py
IBSpy/kmc3_kmer_database.py
IBSpy/kmerGWAS_kmer.py
IBSpy/kmer_database.py
IBSpy/window_affinity_propagation.py
IBSpy.egg-info/PKG-INFO
IBSpy.egg-info/SOURCES.txt
IBSpy.egg-info/dependency_links.txt
IBSpy.egg-info/entry_points.txt
IBSpy.egg-info/top_level.txt
IBSpy/kmerGWAS/kmer_db.c
IBSpy/kmerGWAS/kmer_db.h
IBSpy/kmerGWAS/kmer_general.c
IBSpy/kmerGWAS/kmer_general.h
IBSpy/kmerGWAS/kmer_gwas.c
IBSpy/kmerGWAS/kmer_gwas.pxd
IBSpy/kmerGWAS/kmer_gwas.pyx
IBSpy/kmerGWAS/nucleotide.c
IBSpy/kmerGWAS/nucleotide.h
tests/ibspy_out.txt
tests/integration_cpp.sh
tests/integration_python.sh
tests/test_affinity_propagation.py
tests/test_block_mapping.py
tests/test_fasta.py
tests/test_jellyfish.py
tests/test_kmc3.py
tests/test_kmerGWAS.py
tests/test_result_set.py
tests/test_results.py
tests/test_run.ini
tests/data/ibspy_integration_test.txt
tests/data/jag_vs_sta.fa
tests/data/jag_vs_sta_aln.fa
tests/data/short_example.fa
tests/data/short_test.fa
tests/data/short_test.fa.fai
tests/data/short_test_duplicate.fa
tests/data/short_test_duplicate.fa.fai
tests/data/test4B.arinalrfor.fa
tests/data/test4B.arinalrfor.fa.fai
tests/data/test4B.jagger.fa
tests/data/test4B.jagger.fa.fai
tests/data/test4B.jagger.fa.k31.jf
tests/data/test4B.jagger.kmc_k31.kmc_pre
tests/data/test4B.jagger.kmc_k31.kmc_suf
tests/data/test4B.jagger.kmerGWAS_k31
tests/data/test4B.jagger.temp.kmerGWAS_k31
tests/data/test4B.julius.fa
tests/data/test4B.julius.fa.fai
tests/data/test4B.lancer.fa
tests/data/test4B.lancer.fa.fai
tests/data/test4B.landmark.fa
tests/data/test4B.landmark.fa.fai
tests/data/test4B.mace.fa
tests/data/test4B.mace.fa.fai
tests/data/test4B.norin61.fa
tests/data/test4B.norin61.fa.fai
tests/data/test4B.spelta.fa
tests/data/test4B.spelta.fa.fai
tests/data/test4B.stanley.fa
tests/data/test4B.stanley.fa.fai
tests/data/test4B.stanley.rev.fa
tests/data/test4B.stanley.rev.fa.fai
tests/data/test4B.sy_mattis.fa
tests/data/test4B.sy_mattis.fa.fai
tests/data/affinity/bad_region_test.tsv
tests/data/affinity/chi_jag_mapping.tsv
tests/data/affinity/chr1A_variations_5000w.tsv
tests/data/affinity/chr1A_variations_5000w_renamed.tsv
tests/data/affinity/chr_lenghts_test.tsv
tests/data/affinity/good_region_test.tsv
tests/data/affinity/jag_chi_test_merge.tsv
tests/data/affinity/jag_chi_test_windows.tsv
tests/data/affinity/jag_chi_test_windows_expected1.tsv
tests/data/affinity/jag_chi_test_windows_expected2.tsv
tests/data/affinity/kmeribs-Chinese_Spring-Agron.tsv
tests/data/affinity/kmeribs-Chinese_Spring-WATDE0010.tsv
tests/data/affinity/kmeribs-Chinese_Spring-WATDE0020.tsv
tests/data/affinity/kmeribs-Chinese_Spring-ability.tsv
tests/data/affinity/kmeribs-Wheat_Jagger-Agron.tsv
tests/data/affinity/kmeribs-Wheat_Jagger-WATDE0010.tsv
tests/data/affinity/kmeribs-Wheat_Jagger-WATDE0020.tsv
tests/data/affinity/kmeribs-Wheat_Jagger-ability.tsv
tests/data/affinity/mapped_window_1.tsv
tests/data/affinity/mapped_window_2.tsv
tests/data/affinity/predicted_bad.tsv
tests/data/affinity/predicted_good.tsv
tests/data/affinity/samples_metadata.tsv
tests/data/affinity/unconverged_bad.tsv
tests/data/affinity/unconverged_region_test.tsv
tests/data/affinity/watseq_HC_test.tsv
tests/data/affinity/out/chr1A_variations_5000w_renamed.tsv
tests/data/affinity/windows/0.tsv
tests/data/affinity/windows/1.tsv
tests/data/affinity/windows/10.tsv
tests/data/affinity/windows/11.tsv
tests/data/affinity/windows/2.tsv
tests/data/affinity/windows/3.tsv
tests/data/affinity/windows/4.tsv
tests/data/affinity/windows/5.tsv
tests/data/affinity/windows/6.tsv
tests/data/affinity/windows/7.tsv
tests/data/affinity/windows/8.tsv
tests/data/affinity/windows/9.tsv
tests/plots_data/kmeribs-Wheat_Jagger-Flame.tsv.gz
tests/plots_data/test_chr_sizes_jagger.tsv
tests/plots_data/test_kmeribs-Wheat_Jagger-Flame.tsv
tests/plots_data/test_run_arguments.sh
tests/plots_data/expected_output/gmm_ibs.tsv.gz
tests/plots_data/expected_output/gmm_plots.pdf