├── .gitignore ├── AUTHORS ├── LICENSE ├── MANUAL ├── MANUAL.markdown ├── Makefile ├── NEWS ├── README.md ├── TUTORIAL ├── VERSION ├── aligner_bt.cpp ├── aligner_bt.h ├── aligner_cache.cpp ├── aligner_cache.h ├── aligner_metrics.h ├── aligner_result.h ├── aligner_seed.cpp ├── aligner_seed.h ├── aligner_seed_policy.cpp ├── aligner_seed_policy.h ├── aligner_sw.cpp ├── aligner_sw.h ├── aligner_sw_common.h ├── aligner_sw_nuc.h ├── aligner_swsse.cpp ├── aligner_swsse.h ├── aligner_swsse_ee_i16.cpp ├── aligner_swsse_ee_u8.cpp ├── aligner_swsse_loc_i16.cpp ├── aligner_swsse_loc_u8.cpp ├── aln_sink.h ├── alphabet.cpp ├── alphabet.h ├── assert_helpers.h ├── binary_sa_search.h ├── bitpack.h ├── blockwise_sa.h ├── bt2_idx.cpp ├── bt2_idx.h ├── bt2_io.h ├── bt2_util.h ├── btypes.h ├── ccnt_lut.cpp ├── centrifuge ├── centrifuge-BuildSharedSequence.pl ├── centrifuge-RemoveEmptySequence.pl ├── centrifuge-RemoveN.pl ├── centrifuge-build ├── centrifuge-compress.pl ├── centrifuge-download ├── centrifuge-inspect ├── centrifuge-kreport ├── centrifuge-promote ├── centrifuge-sort-nt.pl ├── centrifuge.cpp ├── centrifuge.xcodeproj └── project.pbxproj ├── centrifuge_build.cpp ├── centrifuge_build_main.cpp ├── centrifuge_compress.cpp ├── centrifuge_inspect.cpp ├── centrifuge_main.cpp ├── centrifuge_report.cpp ├── classifier.h ├── diff_sample.cpp ├── diff_sample.h ├── doc ├── README ├── add.css ├── faq.shtml ├── footer.inc.html ├── index.shtml ├── manual.html ├── manual.inc.html ├── manual.inc.html.old ├── manual.shtml ├── sidebar.inc.shtml ├── strip_markdown.pl └── style.css ├── dp_framer.cpp ├── dp_framer.h ├── ds.cpp ├── ds.h ├── edit.cpp ├── edit.h ├── endian_swap.h ├── evaluation ├── centrifuge_evaluate.py ├── centrifuge_simulate_reads.py └── test │ ├── abundance.Rmd │ └── centrifuge_evaluate_mason.py ├── example ├── index │ ├── test.1.cf │ ├── test.2.cf │ ├── test.3.cf │ └── test.4.cf ├── reads │ └── input.fa └── reference │ ├── gi_to_tid.dmp │ ├── names.dmp │ ├── nodes.dmp │ └── test.fa ├── fast_mutex.h ├── filebuf.h ├── formats.h ├── functions.sh ├── group_walk.cpp ├── group_walk.h ├── hi_aligner.h ├── hier_idx.h ├── hier_idx_common.h ├── hyperloglogbias.h ├── hyperloglogplus.h ├── indices └── Makefile ├── limit.cpp ├── limit.h ├── ls.cpp ├── ls.h ├── mask.cpp ├── mask.h ├── mem_ids.h ├── mm.h ├── multikey_qsort.h ├── opts.h ├── outq.cpp ├── outq.h ├── pat.cpp ├── pat.h ├── pe.cpp ├── pe.h ├── presets.cpp ├── presets.h ├── processor_support.h ├── qual.cpp ├── qual.h ├── random_source.cpp ├── random_source.h ├── random_util.cpp ├── random_util.h ├── read.h ├── read_qseq.cpp ├── ref_coord.cpp ├── ref_coord.h ├── ref_read.cpp ├── ref_read.h ├── reference.cpp ├── reference.h ├── scoring.cpp ├── scoring.h ├── search_globals.h ├── sequence_io.h ├── shmem.cpp ├── shmem.h ├── simple_func.cpp ├── simple_func.h ├── sse_util.cpp ├── sse_util.h ├── sstring.cpp ├── sstring.h ├── str_util.h ├── taxonomy.h ├── third_party ├── MurmurHash3.cpp ├── MurmurHash3.h └── 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