MANIFEST.in
README.md
requirements.txt
setup.py
python/OBITools3.egg-info/PKG-INFO
python/OBITools3.egg-info/SOURCES.txt
python/OBITools3.egg-info/dependency_links.txt
python/OBITools3.egg-info/top_level.txt
python/obitools3/__init__.py
python/obitools3/utils.pxd
python/obitools3/utils.pyx
python/obitools3/version.py
python/obitools3/apps/__init__.py
python/obitools3/apps/arguments.pxd
python/obitools3/apps/arguments.pyx
python/obitools3/apps/command.pxd
python/obitools3/apps/command.pyx
python/obitools3/apps/config.pxd
python/obitools3/apps/config.pyx
python/obitools3/apps/logging.pxd
python/obitools3/apps/logging.pyx
python/obitools3/apps/progress.pxd
python/obitools3/apps/progress.pyx
python/obitools3/apps/temp.pxd
python/obitools3/apps/temp.pyx
python/obitools3/apps/optiongroups/__init__.py
python/obitools3/commands/__init__.py
python/obitools3/commands/align.pxd
python/obitools3/commands/align.pyx
python/obitools3/commands/alignpairedend.pxd
python/obitools3/commands/alignpairedend.pyx
python/obitools3/commands/annotate.pyx
python/obitools3/commands/build_ref_db.pyx
python/obitools3/commands/cat.pyx
python/obitools3/commands/clean.pyx
python/obitools3/commands/clean_dms.pyx
python/obitools3/commands/count.pyx
python/obitools3/commands/ecopcr.pyx
python/obitools3/commands/ecotag.pyx
python/obitools3/commands/export.pyx
python/obitools3/commands/grep.pyx
python/obitools3/commands/head.pyx
python/obitools3/commands/history.pyx
python/obitools3/commands/import.pyx
python/obitools3/commands/less.pyx
python/obitools3/commands/ls.pyx
python/obitools3/commands/ngsfilter.pyx
python/obitools3/commands/sort.pyx
python/obitools3/commands/stats.pyx
python/obitools3/commands/tail.pyx
python/obitools3/commands/test.pyx
python/obitools3/commands/uniq.pxd
python/obitools3/commands/uniq.pyx
python/obitools3/dms/__init__.py
python/obitools3/dms/dms.pxd
python/obitools3/dms/dms.pyx
python/obitools3/dms/obiseq.pxd
python/obitools3/dms/obiseq.pyx
python/obitools3/dms/object.pxd
python/obitools3/dms/object.pyx
python/obitools3/dms/capi/__init__.py
python/obitools3/dms/capi/apat.pxd
python/obitools3/dms/capi/build_reference_db.pxd
python/obitools3/dms/capi/kmer_similarity.pxd
python/obitools3/dms/capi/obiclean.pxd
python/obitools3/dms/capi/obidms.pxd
python/obitools3/dms/capi/obidmscolumn.pxd
python/obitools3/dms/capi/obiecopcr.pxd
python/obitools3/dms/capi/obiecotag.pxd
python/obitools3/dms/capi/obierrno.pxd
python/obitools3/dms/capi/obilcsalign.pxd
python/obitools3/dms/capi/obitaxonomy.pxd
python/obitools3/dms/capi/obitypes.pxd
python/obitools3/dms/capi/obiutils.pxd
python/obitools3/dms/capi/obiview.pxd
python/obitools3/dms/column/__init__.py
python/obitools3/dms/column/column.pxd
python/obitools3/dms/column/column.pyx
python/obitools3/dms/column/column_idx.pxd
python/obitools3/dms/column/column_idx.pyx
python/obitools3/dms/column/typed_column/__init__.py
python/obitools3/dms/column/typed_column/bool.pxd
python/obitools3/dms/column/typed_column/bool.pyx
python/obitools3/dms/column/typed_column/char.pxd
python/obitools3/dms/column/typed_column/char.pyx
python/obitools3/dms/column/typed_column/float.pxd
python/obitools3/dms/column/typed_column/float.pyx
python/obitools3/dms/column/typed_column/int.pxd
python/obitools3/dms/column/typed_column/int.pyx
python/obitools3/dms/column/typed_column/qual.pxd
python/obitools3/dms/column/typed_column/qual.pyx
python/obitools3/dms/column/typed_column/seq.pxd
python/obitools3/dms/column/typed_column/seq.pyx
python/obitools3/dms/column/typed_column/str.pxd
python/obitools3/dms/column/typed_column/str.pyx
python/obitools3/dms/taxo/__init__.py
python/obitools3/dms/taxo/taxo.pxd
python/obitools3/dms/taxo/taxo.pyx
python/obitools3/dms/view/__init__.py
python/obitools3/dms/view/view.pxd
python/obitools3/dms/view/view.pyx
python/obitools3/dms/view/typed_view/__init__.py
python/obitools3/dms/view/typed_view/view_NUC_SEQS.pxd
python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx
python/obitools3/files/__init__.py
python/obitools3/files/linebuffer.pxd
python/obitools3/files/linebuffer.pyx
python/obitools3/files/uncompress.pxd
python/obitools3/files/uncompress.pyx
python/obitools3/files/universalopener.pxd
python/obitools3/files/universalopener.pyx
python/obitools3/format/__init__.py
python/obitools3/format/fasta.pxd
python/obitools3/format/fasta.pyx
python/obitools3/format/fastq.pxd
python/obitools3/format/fastq.pyx
python/obitools3/format/header.pxd
python/obitools3/format/header.pyx
python/obitools3/format/tab.pxd
python/obitools3/format/tab.pyx
python/obitools3/libalign/__init__.py
python/obitools3/libalign/_assemble.pxd
python/obitools3/libalign/_assemble.pyx
python/obitools3/libalign/_dynamic.pxd
python/obitools3/libalign/_dynamic.pyx
python/obitools3/libalign/_freeendgap.pxd
python/obitools3/libalign/_freeendgap.pyx
python/obitools3/libalign/_freeendgapfm.pxd
python/obitools3/libalign/_freeendgapfm.pyx
python/obitools3/libalign/_nws.pxd
python/obitools3/libalign/_nws.pyx
python/obitools3/libalign/_qsassemble.pyx
python/obitools3/libalign/_qsrassemble.pyx
python/obitools3/libalign/_rassemble.pxd
python/obitools3/libalign/_rassemble.pyx
python/obitools3/libalign/_solexapairend.pyx
python/obitools3/libalign/apat_pattern.pxd
python/obitools3/libalign/apat_pattern.pyx
python/obitools3/libalign/shifted_ali.pxd
python/obitools3/libalign/shifted_ali.pyx
python/obitools3/libalign/solexapairend.py
python/obitools3/parsers/__init__.py
python/obitools3/parsers/embl.pxd
python/obitools3/parsers/embl.pyx
python/obitools3/parsers/embl_genbank_features.pxd
python/obitools3/parsers/embl_genbank_features.pyx
python/obitools3/parsers/fasta.pxd
python/obitools3/parsers/fasta.pyx
python/obitools3/parsers/fastq.pxd
python/obitools3/parsers/fastq.pyx
python/obitools3/parsers/genbank.pxd
python/obitools3/parsers/genbank.pyx
python/obitools3/parsers/header.pxd
python/obitools3/parsers/header.pyx
python/obitools3/parsers/ngsfilter.pxd
python/obitools3/parsers/ngsfilter.pyx
python/obitools3/parsers/tab.pxd
python/obitools3/parsers/tab.pyx
python/obitools3/parsers/universal.pxd
python/obitools3/parsers/universal.pyx
python/obitools3/uri/__init__.py
python/obitools3/uri/decode.pxd
python/obitools3/uri/decode.pyx
python/obitools3/writers/__init__.py
python/obitools3/writers/fasta.pxd
python/obitools3/writers/fasta.pyx
python/obitools3/writers/fastq.pxd
python/obitools3/writers/fastq.pyx
python/obitools3/writers/tab.pxd
python/obitools3/writers/tab.pyx
scripts/obi
src/CMakeLists.txt
src/_sse.h
src/array_indexer.c
src/array_indexer.h
src/bloom.c
src/bloom.h
src/build_reference_db.c
src/build_reference_db.h
src/char_str_indexer.c
src/char_str_indexer.h
src/crc64.c
src/crc64.h
src/dna_seq_indexer.c
src/dna_seq_indexer.h
src/encode.c
src/encode.h
src/hashtable.c
src/hashtable.h
src/kmer_similarity.c
src/kmer_similarity.h
src/linked_list.c
src/linked_list.h
src/murmurhash2.c
src/murmurhash2.h
src/obi_clean.c
src/obi_clean.h
src/obi_ecopcr.c
src/obi_ecopcr.h
src/obi_ecotag.c
src/obi_ecotag.h
src/obi_lcs.c
src/obi_lcs.h
src/obiavl.c
src/obiavl.h
src/obiblob.c
src/obiblob.h
src/obiblob_indexer.c
src/obiblob_indexer.h
src/obidebug.h
src/obidms.c
src/obidms.h
src/obidms_taxonomy.c
src/obidms_taxonomy.h
src/obidmscolumn.c
src/obidmscolumn.h
src/obidmscolumn_array.c
src/obidmscolumn_array.h
src/obidmscolumn_blob.c
src/obidmscolumn_blob.h
src/obidmscolumn_bool.c
src/obidmscolumn_bool.h
src/obidmscolumn_char.c
src/obidmscolumn_char.h
src/obidmscolumn_dict.c
src/obidmscolumn_dict.h
src/obidmscolumn_float.c
src/obidmscolumn_float.h
src/obidmscolumn_idx.c
src/obidmscolumn_idx.h
src/obidmscolumn_int.c
src/obidmscolumn_int.h
src/obidmscolumn_qual.c
src/obidmscolumn_qual.h
src/obidmscolumn_seq.c
src/obidmscolumn_seq.h
src/obidmscolumn_str.c
src/obidmscolumn_str.h
src/obidmscolumndir.c
src/obidmscolumndir.h
src/obierrno.c
src/obierrno.h
src/obilittlebigman.c
src/obilittlebigman.h
src/obisig.c
src/obisig.h
src/obitypes.c
src/obitypes.h
src/obiview.c
src/obiview.h
src/sse_banded_LCS_alignment.c
src/sse_banded_LCS_alignment.h
src/test_clean.c
src/uint8_indexer.c
src/uint8_indexer.h
src/upperband.c
src/upperband.h
src/utils.c
src/utils.h
src/libecoPCR/ecoError.c
src/libecoPCR/ecoMalloc.c
src/libecoPCR/ecoPCR.h
src/libecoPCR/ecoapat.c
src/libecoPCR/ecodna.c
src/libecoPCR/libapat/Gmach.h
src/libecoPCR/libapat/Gtypes.h
src/libecoPCR/libapat/apat.h
src/libecoPCR/libapat/apat_parse.c
src/libecoPCR/libapat/apat_search.c
src/libecoPCR/libapat/libstki.c
src/libecoPCR/libapat/libstki.h
src/libecoPCR/libapat/CODES/dft_code.h
src/libecoPCR/libapat/CODES/dna_code.h
src/libecoPCR/libapat/CODES/prot_code.h
src/libecoPCR/libthermo/nnparams.c
src/libecoPCR/libthermo/nnparams.h
src/libjson/cJSON.c
src/libjson/cJSON.h
src/libjson/json_utils.c
src/libjson/json_utils.h