├── .gitmodules ├── .travis.yml ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── TODO.md ├── bin ├── bonsai.cpp ├── cmpshs.cpp ├── css2ss.cpp ├── errexp.cpp ├── fahist.cpp ├── genome2multiset.cpp ├── kmercnt.cpp ├── kmeridx.cpp ├── lca.cpp ├── rolling_multk.cpp ├── rolling_multk_sketch.cpp ├── setsketcher.cpp ├── setsketchindexer.cpp ├── setsketchroller.cpp ├── setsketchscreener.cpp ├── shs2sketch.cpp ├── stdin2ss.cpp └── taxmap.cpp ├── clhash ├── Makefile ├── benchmarks │ └── benchmark.c ├── cppexample.cpp ├── example.c ├── include │ └── clhash.h ├── src │ └── clhash.c └── tests │ ├── cppunit.cpp │ └── unit.c ├── doc └── tools.md ├── exp └── flat_concat.txt ├── include ├── bonsai │ ├── alphabet.h │ ├── bitcmp.h │ ├── bitmap.h │ ├── classifier.h │ ├── counter.h │ ├── database.h │ ├── diskarray.h │ ├── encoder.h │ ├── entropy.h │ ├── feature_min.h │ ├── flextree.h │ ├── gchunk.h │ ├── hash.h │ ├── kgset.h │ ├── khash64.h │ ├── khpp.h │ ├── kmer_counter.h │ ├── kmeridx.h │ ├── kmerutil.h │ ├── kseq_declare.h │ ├── logutil.h │ ├── popcnt.h │ ├── qmap.h │ ├── rhtraits.h │ ├── sample_gen.h │ ├── setcmp.h │ ├── spacer.h │ ├── ssi.h │ ├── tx.h │ └── util.h └── btree │ ├── btree.h │ ├── map.h │ └── set.h ├── klib ├── kbtree.h ├── khash.h ├── khashl.h ├── khmm.c ├── khmm.h ├── kseq.h ├── kstring.c ├── kstring.h ├── ksw.c ├── ksw.h ├── kthread.c └── kthread.h ├── kraken_benchmarks ├── HiSeq_accuracy.fa ├── HiSeq_class.txt ├── MiSeq_accuracy.fa └── MiSeq_class.txt ├── kspp ├── LICENSE ├── README.md ├── kb.h ├── kmp.h └── ks.h ├── lazy ├── LICENSE ├── README.md └── vector.h ├── lib └── .gitkeep ├── linear ├── LICENSE ├── README.md └── linear.h ├── pdqsort ├── pdqsort.h └── readme.md ├── python ├── Makefile ├── bns.cpp ├── distmat2np.py ├── download_genomes.py ├── download_genomes_subdir.py ├── gen_ent_table.py ├── gen_pc_table.py ├── load_data.py ├── load_shs.py ├── misc.py ├── old_refseq.py ├── parse_nodes.py ├── parse_sketch_results.py ├── run_dist.py └── setup.py ├── rollinghash ├── adler32.h ├── characterhash.h ├── cyclichash.h ├── generalhash.h ├── mersennetwister.h ├── rabinkarphash.h ├── threewisehash.h └── ztimer.h ├── save └── combined_nip.txt ├── sim ├── fa.py └── main.py ├── test ├── GCF_000302455.1_ASM30245v1_genomic.fna.gz ├── GCF_000762265.1_ASM76226v1_genomic.fna.gz ├── GCF_000953115.1_DSM1535_genomic.fna.gz ├── GCF_001723155.1_ASM172315v1_genomic.fna.gz ├── TODO.md ├── catch.hpp ├── cbuf.cpp ├── ec.k12.fa ├── ec │ ├── GCF_000005845.2_ASM584v2_genomic.fna.gz │ ├── GCF_000007445.1_ASM744v1_genomic.fna.gz │ ├── GCF_000008865.1_ASM886v1_genomic.fna.gz │ ├── GCF_000009565.1_ASM956v1_genomic.fna.gz │ └── GCF_000010245.2_ASM1024v1_genomic.fna.gz ├── encoding.cpp ├── hll.cpp ├── htest.cpp ├── linear.cpp ├── main.cpp ├── phix.fa ├── popcnt.cpp ├── small_genome.fa ├── tax.cpp ├── test_tx.cpp └── util.cpp └── tinythreadpp └── source └── fast_mutex.h /.gitmodules: -------------------------------------------------------------------------------- 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