Tree @upstream/latest (Download .tar.gz)
- centrifuge.xcodeproj
- doc
- evaluation
- example
- indices
- third_party
- .gitignore
- 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
- AUTHORS
- 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-build
- centrifuge-BuildSharedSequence.pl
- centrifuge-compress.pl
- centrifuge-download
- centrifuge-inspect
- centrifuge-kreport
- centrifuge-promote
- centrifuge-RemoveEmptySequence.pl
- centrifuge-RemoveN.pl
- centrifuge-sort-nt.pl
- centrifuge.cpp
- 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
- dp_framer.cpp
- dp_framer.h
- ds.cpp
- ds.h
- edit.cpp
- edit.h
- endian_swap.h
- 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
- LICENSE
- limit.cpp
- limit.h
- ls.cpp
- ls.h
- Makefile
- MANUAL
- MANUAL.markdown
- mask.cpp
- mask.h
- mem_ids.h
- mm.h
- multikey_qsort.h
- NEWS
- 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
- README.md
- 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
- threading.h
- timer.h
- tinythread.cpp
- tinythread.h
- tokenize.h
- TUTORIAL
- util.h
- VERSION
- word_io.h
- zbox.h