├── COPYING ├── Makefile.am ├── Makefile.in ├── README.md ├── aclocal.m4 ├── blast └── hs-blastn-src │ ├── .DS_Store │ ├── COPYING │ ├── Makefile │ ├── README.md │ ├── VERSION │ ├── changeLog │ ├── edits.txt │ ├── how_to_verify_HS-BLASTN_produce_same_results_as_MegaBLAST.txt │ └── sources │ ├── QSufSort.c │ ├── QSufSort.h │ ├── align.h │ ├── buffer_line_iterator.cpp │ ├── buffer_line_iterator.h │ ├── bwt_gen.c │ ├── bwt_gen.h │ ├── commandline_options │ ├── arguments.cpp │ ├── arguments.h │ ├── options.cpp │ ├── options.h │ ├── parameters.cpp │ ├── parameters.h │ ├── stat.h │ ├── stat_functions.cpp │ └── stat_functions.h │ ├── dbinfo.cpp │ ├── dbinfo.h │ ├── def.h │ ├── gapalign.cpp │ ├── gapalign.h │ ├── greedy_align.cpp │ ├── greedy_align.h │ ├── greedy_align_impl.h │ ├── index.cpp │ ├── index.h │ ├── interval_tree.cpp │ ├── interval_tree.h │ ├── line_reader.cpp │ ├── line_reader.h │ ├── main.cpp │ ├── make_index.h │ ├── mask │ ├── include │ │ ├── dustmask │ │ │ ├── sdust.tex │ │ │ └── symdust.hpp │ │ └── winmask │ │ │ ├── README.API │ │ │ ├── seq_masker.hpp │ │ │ ├── seq_masker_cache_boost.hpp │ │ │ ├── seq_masker_istat.hpp │ │ │ ├── seq_masker_istat_ascii.hpp │ │ │ ├── seq_masker_istat_bin.hpp │ │ │ ├── seq_masker_istat_factory.hpp │ │ │ ├── seq_masker_istat_oascii.hpp │ │ │ ├── seq_masker_istat_obinary.hpp │ │ │ ├── seq_masker_ostat.hpp │ │ │ ├── seq_masker_ostat_ascii.hpp │ │ │ ├── seq_masker_ostat_bin.hpp │ │ │ ├── seq_masker_ostat_factory.hpp │ │ │ ├── seq_masker_ostat_opt.hpp │ │ │ ├── seq_masker_ostat_opt_ascii.hpp │ │ │ ├── seq_masker_ostat_opt_bin.hpp │ │ │ ├── seq_masker_score.hpp │ │ │ ├── seq_masker_score_mean.hpp │ │ │ ├── seq_masker_score_mean_glob.hpp │ │ │ ├── seq_masker_score_min.hpp │ │ │ ├── seq_masker_uset_array.hpp │ │ │ ├── seq_masker_uset_hash.hpp │ │ │ ├── seq_masker_uset_simple.hpp │ │ │ ├── seq_masker_util.hpp │ │ │ ├── seq_masker_version.hpp │ │ │ ├── seq_masker_window.hpp │ │ │ ├── seq_masker_window_ambig.hpp │ │ │ ├── seq_masker_window_pattern.hpp │ │ │ ├── seq_masker_window_pattern_ambig.hpp │ │ │ ├── win_mask_config.hpp │ │ │ ├── win_mask_counts_converter.hpp │ │ │ ├── win_mask_dup_table.hpp │ │ │ ├── win_mask_gen_counts.hpp │ │ │ └── win_mask_util.hpp │ ├── mask_common.cpp_ │ ├── mask_common.h_ │ ├── mask_macros.cpp │ ├── mask_macros.h │ ├── ncbi_limits.h │ ├── ncbi_pch.hpp │ ├── ncbimisc.hpp │ ├── src │ │ ├── dustmask │ │ │ ├── Makefile.in │ │ │ ├── Makefile.xalgodustmask.lib │ │ │ └── symdust.cpp │ │ └── winmask │ │ │ ├── Makefile.in │ │ │ ├── Makefile.xalgowinmask.lib │ │ │ ├── seq_masker.cpp │ │ │ ├── seq_masker_cache_boost.cpp │ │ │ ├── seq_masker_istat.cpp │ │ │ ├── seq_masker_istat_ascii.cpp │ │ │ ├── seq_masker_istat_bin.cpp │ │ │ ├── seq_masker_istat_factory.cpp │ │ │ ├── seq_masker_istat_oascii.cpp │ │ │ ├── seq_masker_istat_obinary.cpp │ │ │ ├── seq_masker_ostat.cpp │ │ │ ├── seq_masker_ostat_ascii.cpp │ │ │ ├── seq_masker_ostat_bin.cpp │ │ │ ├── seq_masker_ostat_factory.cpp │ │ │ ├── seq_masker_ostat_opt.cpp │ │ │ ├── seq_masker_ostat_opt_ascii.cpp │ │ │ ├── seq_masker_ostat_opt_bin.cpp │ │ │ ├── seq_masker_score_mean.cpp │ │ │ ├── seq_masker_score_mean_glob.cpp │ │ │ ├── seq_masker_score_min.cpp │ │ │ ├── seq_masker_uset_array.cpp │ │ │ ├── seq_masker_uset_hash.cpp │ │ │ ├── seq_masker_uset_simple.cpp │ │ │ ├── seq_masker_util.cpp │ │ │ ├── seq_masker_window.cpp │ │ │ ├── seq_masker_window_ambig.cpp │ │ │ ├── seq_masker_window_pattern.cpp │ │ │ ├── seq_masker_window_pattern_ambig.cpp │ │ │ ├── win_mask_config.cpp │ │ │ ├── win_mask_counts_converter.cpp │ │ │ ├── win_mask_dup_table.cpp │ │ │ ├── win_mask_gen_counts.cpp │ │ │ └── win_mask_util.cpp │ ├── string2int.cpp │ ├── version.cpp │ └── version.hpp │ ├── mask_misc.cpp │ ├── mask_misc.h │ ├── memallocator.cpp │ ├── memallocator.h │ ├── output_buffer.h │ ├── prelim_search.cpp │ ├── query_info.cpp │ ├── query_info.h │ ├── result_format.cpp │ ├── result_format.h │ ├── search_worker.cpp │ ├── search_worker.h │ ├── sequence.cpp │ ├── sequence.h │ ├── thread_structure.h │ ├── traceback.cpp │ ├── traceback.h │ ├── utility.cpp │ └── utility.h ├── blast_bin ├── makeblastdb-linux.gz ├── makeblastdb-mac.gz ├── windowmasker-linux.gz └── windowmasker-mac.gz ├── bootstrap ├── config.guess ├── config.sub ├── configure ├── configure.ac ├── genome_filter ├── hg19_filter.bed ├── hg38_filter.bed ├── mm10_filter.bed └── mm9_filter.bed ├── install-sh ├── missing ├── model └── ANN.E100B400L2N12-5D0.2SGDsee30_het_v5.h5 ├── requirement.txt ├── scripts ├── Makefile.am ├── Makefile.in ├── bowtie2_dummy.py ├── css │ ├── bootstrap.min.css │ ├── buttons.dataTables.min.css │ ├── font-awesome.min.css │ ├── jquery.dataTables.min.css │ └── mdb.min.css ├── js │ ├── bootstrap.min.js │ ├── buttons.flash.min.js │ ├── buttons.html5.min.js │ ├── dataTables.buttons.min.js │ ├── jquery-3.3.1.min.js │ ├── jquery.dataTables.min.js │ ├── jszip.min.js │ ├── mdb.min.js │ └── popper.min.js ├── keras_ANN_inference.py ├── nanovar.in ├── nv_bed_validator.py ├── nv_breakpoint_parser.py ├── nv_chrnum.py ├── nv_fasta_validator.py ├── nv_fastq-a_validator.py ├── nv_hsblast_SV_detector.py ├── nv_hsblast_parse.py ├── nv_hsblast_random_spliter.py ├── nv_lcov_outlier.py ├── nv_lr_overlap.py ├── nv_nanocorrector.py ├── nv_parser_VCF.py ├── nv_report.py ├── nv_scov.py ├── nv_test.py └── py_readlink.py ├── test ├── lread_test.fa.gz ├── pre-check-files │ ├── bed1.sort │ ├── bed2.sort │ ├── correct.fa │ ├── fastq1 │ ├── fastq2 │ ├── overlap.ANN0.6.tsv │ └── sam ├── ref_test.fa.gz ├── sread1.names_48k.fa.gz ├── sread2.names_48k.fa.gz └── valid_md5.txt └── virtualenv-15.2.0 ├── AUTHORS.txt ├── LICENSE.txt ├── MANIFEST.in ├── PKG-INFO ├── README.rst ├── bin └── rebuild-script.py ├── docs ├── Makefile ├── changes.rst ├── conf.py ├── development.rst ├── index.rst ├── installation.rst ├── make.bat ├── reference.rst └── userguide.rst ├── scripts └── virtualenv ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── test_activate.sh ├── 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