├── .github └── workflows │ ├── ibscpp.yml │ └── python-package.yml ├── .gitignore ├── IBScpp ├── CMakeLists.txt ├── KMC │ ├── .gitattributes │ ├── .gitignore │ ├── API.pdf │ ├── README.md │ ├── doc │ │ └── kmc_tools │ │ │ ├── complex.tex │ │ │ ├── filter_operation.tex │ │ │ ├── intro.tex │ │ │ ├── kmc_tools.tex │ │ │ ├── simple.tex │ │ │ ├── transform.tex │ │ │ └── usage.tex │ ├── kmc_api │ │ ├── kmc_file.cpp │ │ ├── kmc_file.h │ │ ├── kmer_api.cpp │ │ ├── kmer_api.h │ │ ├── kmer_defs.h │ │ ├── mmer.cpp │ │ ├── mmer.h │ │ └── stdafx.h │ ├── kmc_dump │ │ ├── kmc_dump.cpp │ │ ├── kmc_dump.vcxproj │ │ ├── nc_utils.cpp │ │ ├── nc_utils.h │ │ ├── stdafx.cpp │ │ ├── stdafx.h │ │ └── targetver.h │ ├── kmc_dump_sample │ │ ├── kmc_dump_sample.cpp │ │ ├── kmc_dump_sample.vcxproj │ │ ├── stdafx.cpp │ │ ├── stdafx.h │ │ └── targetver.h │ ├── kmc_tools.pdf │ ├── kmc_tools │ │ ├── bundle.h │ │ ├── check_kmer.h │ │ ├── config.h │ │ ├── defs.h │ │ ├── develop.h │ │ ├── dump_writer.h │ │ ├── expression_node.h │ │ ├── fastq_filter.cpp │ │ ├── fastq_filter.h │ │ ├── fastq_reader.cpp │ │ ├── fastq_reader.h │ │ ├── fastq_writer.cpp │ │ ├── fastq_writer.h │ │ ├── histogram_writer.h │ │ ├── kmc1_db_reader.h │ │ ├── kmc1_db_writer.h │ │ ├── kmc2_db_reader.h │ │ ├── kmc_header.cpp │ │ ├── kmc_header.h │ │ ├── kmc_tools.cpp │ │ ├── kmc_tools.vcxproj │ │ ├── kmc_tools.vcxproj.filters │ │ ├── kmer.h │ │ ├── libs │ │ │ ├── bzlib.h │ │ │ ├── bzlib_private.h │ │ │ ├── libbz2.1.0.5.dylib │ │ │ ├── libbz2.a │ │ │ ├── libbzip2.lib │ │ │ ├── libz.1.2.5.dylib │ │ │ ├── libz.a │ │ │ ├── zconf.h │ │ │ ├── zlib.h │ │ │ └── zlibstat.lib │ │ ├── meta_oper.h │ │ ├── nc_utils.cpp │ │ ├── nc_utils.h │ │ ├── operations.h │ │ ├── output_parser.h │ │ ├── parameters_parser.cpp │ │ ├── parameters_parser.h │ │ ├── parser.cpp │ │ ├── parser.h │ │ ├── percent_progress.cpp │ │ ├── percent_progress.h │ │ ├── queues.h │ │ ├── stdafx.cpp │ │ ├── stdafx.h │ │ ├── targetver.h │ │ ├── thread_watch.cpp │ │ ├── thread_watch.h │ │ ├── timer.h │ │ ├── tokenizer.cpp │ │ └── tokenizer.h │ ├── kmer_counter.sln │ ├── kmer_counter │ │ ├── bam_utils.h │ │ ├── binary_reader.h │ │ ├── bkb_merger.h │ │ ├── bkb_reader.cpp │ │ ├── bkb_reader.h │ │ ├── bkb_sorter.h │ │ ├── bkb_subbin.h │ │ ├── bkb_uncompactor.h │ │ ├── bkb_writer.cpp │ │ ├── bkb_writer.h │ │ ├── cpu_info.cpp │ │ ├── cpu_info.h │ │ ├── defs.h │ │ ├── develop.cpp │ │ ├── develop.h │ │ ├── fastq_reader.cpp │ │ ├── fastq_reader.h │ │ ├── first_dispatch.h │ │ ├── intr_copy.h │ │ ├── kb_collector.cpp │ │ ├── kb_collector.h │ │ ├── kb_completer.cpp │ │ ├── kb_completer.h │ │ ├── kb_reader.h │ │ ├── kb_sorter.h │ │ ├── kb_storer.cpp │ │ ├── kb_storer.h │ │ ├── kmc.h │ │ ├── kmer.cpp │ │ ├── kmer.h │ │ ├── kmer_counter.cpp │ │ ├── kmer_counter.vcxproj │ │ ├── kmer_counter.vcxproj.filters │ │ ├── kxmer_set.h │ │ ├── libs │ │ │ ├── bzlib.h │ │ │ ├── bzlib_private.h │ │ │ ├── libbz2.1.0.5.dylib │ │ │ ├── libbz2.a │ │ │ ├── libbzip2.lib │ │ │ ├── libz.1.2.5.dylib │ │ │ ├── libz.a │ │ │ ├── zconf.h │ │ │ ├── zlib.h │ │ │ └── zlibstat.lib │ │ ├── mem_disk_file.cpp │ │ ├── mem_disk_file.h │ │ ├── meta_oper.h │ │ ├── mmer.cpp │ │ ├── mmer.h │ │ ├── params.h │ │ ├── percent_progress.h │ │ ├── queues.h │ │ ├── radix.h │ │ ├── raduls.h │ │ ├── raduls_avx.cpp │ │ ├── raduls_avx2.cpp │ │ ├── raduls_impl.h │ │ ├── raduls_sse2.cpp │ │ ├── raduls_sse41.cpp │ │ ├── rev_byte.cpp │ │ ├── rev_byte.h │ │ ├── s_mapper.h │ │ ├── small_k_buf.h │ │ ├── small_sort.h │ │ ├── splitter.cpp │ │ ├── splitter.h │ │ ├── stdafx.cpp │ │ ├── stdafx.h │ │ ├── targetver.h │ │ ├── timer.cpp │ │ └── timer.h │ ├── makefile │ └── makefile_mac ├── README.md ├── cxxopts │ ├── .gitignore │ ├── .travis.yml │ ├── CHANGELOG.md │ ├── CMakeLists.txt │ ├── INSTALL │ ├── LICENSE │ ├── README.md │ ├── cxxopts-config.cmake.in │ ├── include │ │ └── cxxopts.hpp │ ├── src │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ └── example.cpp │ └── test │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── add-subdirectory-test │ │ └── CMakeLists.txt │ │ ├── catch.hpp │ │ ├── find-package-test │ │ └── CMakeLists.txt │ │ ├── link_a.cpp │ │ ├── link_b.cpp │ │ ├── main.cpp │ │ └── options.cpp ├── include │ ├── IBScpp.h │ ├── args.h │ ├── kmer_general.h │ ├── kmer_thread.h │ ├── kmerdb.h │ └── reference.h ├── sparsehash │ ├── dense_hash_map │ ├── dense_hash_set │ ├── internal │ │ ├── densehashtable.h │ │ ├── hashtable-common.h │ │ ├── libc_allocator_with_realloc.h │ │ ├── sparseconfig.h │ │ └── sparsehashtable.h │ ├── sparse_hash_map │ ├── sparse_hash_set │ ├── sparsetable │ ├── template_util.h │ └── type_traits.h └── src │ ├── IBScpp.cpp │ ├── args.cpp │ ├── kmer_general.cpp │ ├── kmer_thread.cpp │ ├── kmerdb.cpp │ └── reference.cpp ├── IBSpy ├── BlockMapping.py ├── IBSpy_options.py ├── IBSpy_plot.py ├── IBSpy_plot_window_results.py ├── IBSpy_result_set.py ├── IBSpy_results.py ├── IBSpy_values_matrix.py ├── IBSpy_window_count.py ├── __init__.py ├── build_score_matrix.py ├── call_haplotypes.py ├── extract_window.py ├── jellyfish_kmer_database.py ├── kmc3_kmer_database.py ├── kmerGWAS │ ├── kmer_db.c │ ├── kmer_db.h │ ├── kmer_general.c │ ├── kmer_general.h │ ├── kmer_gwas.pxd │ ├── kmer_gwas.pyx │ ├── nucleotide.c │ └── nucleotide.h ├── kmerGWAS_kmer.py ├── kmer_database.py └── window_affinity_propagation.py ├── LICENSE ├── MANIFEST.in ├── Pipfile ├── README.md ├── containers ├── singularity-IBSpy-0.3.1.def └── singularity-IBSpy-0.4.6.def ├── docs ├── Scoring.ipynb ├── classes.png └── packages.png ├── requirements.txt ├── setup.py ├── singularity └── IBSpy-0.4.0.def └── tests ├── data ├── affinity │ ├── bad_region_test.tsv │ ├── chi_jag_mapping.tsv │ ├── chr1A_variations_5000w.tsv │ ├── chr1A_variations_5000w_renamed.tsv │ ├── chr_lenghts_test.tsv │ ├── chromosome_lengths.tsv │ ├── good_region_test.tsv │ ├── jag_chi_test_merge.tsv │ ├── jag_chi_test_windows.tsv │ ├── jag_chi_test_windows_expected1.tsv │ ├── jag_chi_test_windows_expected2.tsv │ ├── kmeribs-Chinese_Spring-Agron.tsv │ ├── kmeribs-Chinese_Spring-WATDE0010.tsv │ ├── kmeribs-Chinese_Spring-WATDE0020.tsv │ ├── kmeribs-Chinese_Spring-ability.tsv │ ├── kmeribs-Wheat_Jagger-Agron.tsv │ ├── kmeribs-Wheat_Jagger-WATDE0010.tsv │ ├── kmeribs-Wheat_Jagger-WATDE0020.tsv │ ├── kmeribs-Wheat_Jagger-ability.tsv │ ├── mapped_window_1.tsv │ ├── mapped_window_2.tsv │ ├── mapped_window_3.tsv │ ├── predicted_bad.tsv │ ├── predicted_good.tsv │ ├── samples_metadata.tsv │ ├── unconverged_bad.tsv │ ├── unconverged_region_test.tsv │ ├── watseq_HC_test.tsv │ └── windows │ │ ├── 0.tsv │ │ ├── 1.tsv │ │ ├── 10.tsv │ │ ├── 11.tsv │ │ ├── 2.tsv │ │ ├── 3.tsv │ │ ├── 4.tsv │ │ ├── 5.tsv │ │ ├── 6.tsv │ │ ├── 7.tsv │ │ ├── 8.tsv │ │ └── 9.tsv ├── ibspy_integration_test.txt ├── jag_vs_sta.fa ├── jag_vs_sta_aln.fa ├── lines.txt ├── reference_suffix.tsv ├── short_test.fa ├── short_test.fa.fai ├── short_test_duplicate.fa ├── short_test_duplicate.fa.fai ├── 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