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/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/include/jellyfish/
H A Djellyfish.hpp26 typedef jellyfish::cooperative::hash_counter<jellyfish::mer_dna> mer_hash;
28 typedef jellyfish::text_dumper<mer_array> text_dumper;
29 typedef jellyfish::text_reader<jellyfish::mer_dna, uint64_t> text_reader;
30 typedef jellyfish::binary_dumper<mer_array> binary_dumper;
31 typedef jellyfish::binary_reader<jellyfish::mer_dna, uint64_t> binary_reader;
32 typedef jellyfish::binary_query_base<jellyfish::mer_dna, uint64_t> binary_query;
33 typedef jellyfish::binary_writer<jellyfish::mer_dna, uint64_t> binary_writer;
34 typedef jellyfish::text_writer<jellyfish::mer_dna, uint64_t> text_writer;
/dports/biology/jellyfish/jellyfish-2.3.0/include/jellyfish/
H A Djellyfish.hpp18 typedef jellyfish::cooperative::hash_counter<jellyfish::mer_dna> mer_hash;
20 typedef jellyfish::text_dumper<mer_array> text_dumper;
21 typedef jellyfish::text_reader<jellyfish::mer_dna, uint64_t> text_reader;
22 typedef jellyfish::binary_dumper<mer_array> binary_dumper;
23 typedef jellyfish::binary_reader<jellyfish::mer_dna, uint64_t> binary_reader;
24 typedef jellyfish::binary_query_base<jellyfish::mer_dna, uint64_t> binary_query;
25 typedef jellyfish::binary_writer<jellyfish::mer_dna, uint64_t> binary_writer;
26 typedef jellyfish::text_writer<jellyfish::mer_dna, uint64_t> text_writer;
/dports/devel/py-jellyfish/jellyfish-0.8.9/
H A DREADME.rst2 jellyfish chapter
11 :target: https://pypi.python.org/pypi/jellyfish
51 >>> import jellyfish
52 >>> jellyfish.levenshtein_distance(u'jellyfish', u'smellyfish')
54 >>> jellyfish.jaro_distance(u'jellyfish', u'smellyfish')
56 >>> jellyfish.damerau_levenshtein_distance(u'jellyfish', u'jellyfihs')
59 >>> jellyfish.metaphone(u'Jellyfish')
61 >>> jellyfish.soundex(u'Jellyfish')
63 >>> jellyfish.nysiis(u'Jellyfish')
65 >>> jellyfish.match_rating_codex(u'Jellyfish')
[all …]
H A DPKG-INFO2 Name: jellyfish
5 Home-page: http://github.com/jamesturk/jellyfish
22 jellyfish
71 >>> import jellyfish
72 >>> jellyfish.levenshtein_distance(u'jellyfish', u'smellyfish')
74 >>> jellyfish.jaro_distance(u'jellyfish', u'smellyfish')
76 >>> jellyfish.damerau_levenshtein_distance(u'jellyfish', u'jellyfihs')
79 >>> jellyfish.metaphone(u'Jellyfish')
81 >>> jellyfish.soundex(u'Jellyfish')
83 >>> jellyfish.nysiis(u'Jellyfish')
[all …]
/dports/devel/py-jellyfish/jellyfish-0.8.9/jellyfish.egg-info/
H A DPKG-INFO2 Name: jellyfish
5 Home-page: http://github.com/jamesturk/jellyfish
22 jellyfish
71 >>> import jellyfish
72 >>> jellyfish.levenshtein_distance(u'jellyfish', u'smellyfish')
74 >>> jellyfish.jaro_distance(u'jellyfish', u'smellyfish')
76 >>> jellyfish.damerau_levenshtein_distance(u'jellyfish', u'jellyfihs')
79 >>> jellyfish.metaphone(u'Jellyfish')
81 >>> jellyfish.soundex(u'Jellyfish')
83 >>> jellyfish.nysiis(u'Jellyfish')
[all …]
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/quorum/src/
H A Dkmer.hpp12 jellyfish::mer_dna _fmer, _rmer;
16 int x = jellyfish::mer_dna::code(c); in shift_left()
30 int x = jellyfish::mer_dna::code(c); in shift_right()
44 const jellyfish::mer_dna& fmer() const { return _fmer; } in fmer()
45 const jellyfish::mer_dna& rmer() const { return _rmer; } in rmer()
49 _rmer.base(jellyfish::mer_dna::k() - i - 1) = jellyfish::mer_dna::complement(x); in replace()
52 char base(int i) const { return jellyfish::mer_dna::rev_code(code(i)); } in base()
79 const jellyfish::mer_dna& canonical() const { return _m.canonical(); } in canonical()
83 const jellyfish::mer_dna& rmer() const { return _m.rmer(); } in rmer()
100 const jellyfish::mer_dna& canonical() const { return _m.canonical(); } in canonical()
[all …]
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/sub_commands/
H A Dbc_main.cc34 namespace err = jellyfish::err;
45 using jellyfish::mer_dna;
46 using jellyfish::mer_dna_bloom_counter;
47 typedef jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<file_vector::const_iterato…
48 typedef jellyfish::mer_iterator<sequence_parser, jellyfish::mer_dna> mer_iterator;
51 class mer_bloom_counter : public jellyfish::thread_exec {
54 jellyfish::stream_manager<PathIterator> streams_;
88 jellyfish::file_header header; in bc_main()
95 std::unique_ptr<jellyfish::generator_manager> generator_manager; in bc_main()
98 new jellyfish::generator_manager(args.generator_arg, args.Generators_arg, in bc_main()
[all …]
H A Dcount_main.cc48 namespace err = jellyfish::err;
57 using jellyfish::mer_dna;
58 using jellyfish::mer_dna_bloom_counter;
59 using jellyfish::mer_dna_bloom_filter;
63 typedef jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<file_vector::const_iterato…
69 public jellyfish::whole_sequence_parser<jellyfish::stream_manager<file_vector::const_iterator> >
127 class mer_counter_base : public jellyfish::thread_exec {
130 jellyfish::stream_manager<PathIterator> streams_;
189 jellyfish::file_header header(in); in load_bloom_filter()
218 jellyfish::file_header header; in count_main()
[all …]
H A Dinfo_main.cc10 namespace err = jellyfish::err;
14 std::string get_command(const jellyfish::generic_file_header& h) { in get_command()
18 (cmd += " ") += jellyfish::quote_arg(*it); in get_command()
23 std::string get_where(const jellyfish::generic_file_header& h) { in get_where()
24 std::string res(jellyfish::quote_arg(h["hostname"])); in get_where()
27 res += jellyfish::quote_arg(h["pwd"]); in get_where()
38 jellyfish::file_header header; in info_main()
H A Dquery_main.cc30 namespace err = jellyfish::err;
32 using jellyfish::mer_dna;
33 using jellyfish::mer_dna_bloom_counter;
35 typedef jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<file_vector::iterator> > s…
36 typedef jellyfish::mer_iterator<sequence_parser, mer_dna> mer_iterator;
47 jellyfish::stream_manager<PathIterator> streams(file_begin, file_end); in query_from_sequence()
95 jellyfish::file_header header(in); in query_main()
100 jellyfish::hash_pair<mer_dna> fns(header.matrix(1), header.matrix(2)); in query_main()
109 jellyfish::mapped_file binary_map(args.file_arg); in query_main()
/dports/biology/jellyfish/jellyfish-2.3.0/sub_commands/
H A Dbc_main.cc34 namespace err = jellyfish::err;
45 using jellyfish::mer_dna;
46 using jellyfish::mer_dna_bloom_counter;
47 typedef jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<file_vector::const_iterato…
48 typedef jellyfish::mer_iterator<sequence_parser, jellyfish::mer_dna> mer_iterator;
51 class mer_bloom_counter : public jellyfish::thread_exec {
54 jellyfish::stream_manager<PathIterator> streams_;
88 jellyfish::file_header header; in bc_main()
95 std::unique_ptr<jellyfish::generator_manager> generator_manager; in bc_main()
98 new jellyfish::generator_manager(args.generator_arg, args.Generators_arg, in bc_main()
[all …]
H A Dcount_main.cc53 namespace err = jellyfish::err;
62 using jellyfish::mer_dna;
63 using jellyfish::mer_dna_bloom_counter;
64 using jellyfish::mer_dna_bloom_filter;
75 public jellyfish::whole_sequence_parser<jellyfish::stream_manager<file_vector::const_iterator> >
78 typedef jellyfish::whole_sequence_parser<StreamIterator> super;
135 class mer_counter_base : public jellyfish::thread_exec {
193 jellyfish::file_header header(in); in load_bloom_filter()
222 jellyfish::file_header header; in count_main()
260 std::unique_ptr<jellyfish::generator_manager> generator_manager; in count_main()
[all …]
H A Dinfo_main.cc10 namespace err = jellyfish::err;
14 std::string get_command(const jellyfish::generic_file_header& h) { in get_command()
18 (cmd += " ") += jellyfish::quote_arg(*it); in get_command()
23 std::string get_where(const jellyfish::generic_file_header& h) { in get_where()
24 std::string res(jellyfish::quote_arg(h["hostname"])); in get_where()
27 res += jellyfish::quote_arg(h["pwd"]); in get_where()
38 jellyfish::file_header header; in info_main()
H A Dquery_main.cc30 namespace err = jellyfish::err;
32 using jellyfish::mer_dna;
33 using jellyfish::mer_dna_bloom_counter;
35 typedef jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<file_vector::iterator> > s…
36 typedef jellyfish::mer_iterator<sequence_parser, mer_dna> mer_iterator;
47 jellyfish::stream_manager<PathIterator> streams(file_begin, file_end); in query_from_sequence()
95 jellyfish::file_header header(in); in query_main()
100 jellyfish::hash_pair<mer_dna> fns(header.matrix(1), header.matrix(2)); in query_main()
109 jellyfish::mapped_file binary_map(args.file_arg); in query_main()
/dports/biology/jellyfish/jellyfish-2.3.0/
H A DMakefile.am4 EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE-BSD-3-Clause LICENSE-GPL-3.0 # jell…
5 man1_MANS = doc/jellyfish.man
8 pkgconfig_DATA = jellyfish-2.0.pc
33 bin_PROGRAMS += bin/jellyfish
52 jellyfish/merge_files.cc
78 library_includedir=$(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
79 JFI = include/jellyfish
125 noinst_HEADERS += jellyfish/fstream_default.hpp jellyfish/dbg.hpp \
126 jellyfish/randomc.h jellyfish/merge_files.hpp
137 bin_fastq2sam_SOURCES = jellyfish/fastq2sam.cc
[all …]
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/
H A DMakefile.am3 EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE # jellyfish.spec
4 man1_MANS = doc/jellyfish.man
7 pkgconfig_DATA = jellyfish-2.0.pc
31 bin_PROGRAMS += bin/jellyfish
39 bin_jellyfish_SOURCES = sub_commands/jellyfish.cc \
50 jellyfish/merge_files.cc
77 library_includedir=$(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
78 JFI = include/jellyfish
122 noinst_HEADERS += jellyfish/fstream_default.hpp jellyfish/dbg.hpp \
123 jellyfish/randomc.h jellyfish/merge_files.hpp
[all …]
/dports/biology/jellyfish/jellyfish-2.3.0/unit_tests/
H A Dtest_misc.cc28 ASSERT_EQ(i, jellyfish::floorLog2(this->x << i)); in TYPED_TEST()
29 ASSERT_EQ(i, jellyfish::floorLog2((this->x << i) | ((this->x << i) - 1))); in TYPED_TEST()
33 using jellyfish::bitsize;
57 m += jellyfish::random_bits(41); in TEST()
72 …EXPECT_EQ(i, *jellyfish::binary_search_first_false(jellyfish::pointer_integer<int>(0), jellyfish::… in TEST()
87 std::pair<unsigned int, unsigned int> b = jellyfish::slice(i, nb_slices, size); in TEST()
99 EXPECT_EQ(arg, jellyfish::quote_arg(arg)); in TEST()
103 EXPECT_EQ("'" + arg + "'", jellyfish::quote_arg(arg)); in TEST()
107 EXPECT_EQ("'coucou_'\\''voila'", jellyfish::quote_arg(arg)); in TEST()
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/unit_tests/
H A Dtest_misc.cc28 ASSERT_EQ(i, jellyfish::floorLog2(this->x << i)); in TYPED_TEST()
29 ASSERT_EQ(i, jellyfish::floorLog2((this->x << i) | ((this->x << i) - 1))); in TYPED_TEST()
33 using jellyfish::bitsize;
57 m += jellyfish::random_bits(41); in TEST()
73 …EXPECT_EQ(i, *jellyfish::binary_search_first_false(jellyfish::pointer_integer<int>(0), jellyfish::… in TEST()
88 std::pair<unsigned int, unsigned int> b = jellyfish::slice(i, nb_slices, size); in TEST()
100 EXPECT_EQ(arg, jellyfish::quote_arg(arg)); in TEST()
104 EXPECT_EQ("'" + arg + "'", jellyfish::quote_arg(arg)); in TEST()
108 EXPECT_EQ("'coucou_'\\''voila'", jellyfish::quote_arg(arg)); in TEST()
/dports/devel/py-jellyfish/jellyfish-0.8.9/docs/
H A Dindex.rst1 jellyfish |release|
7 jellyfish is a library of functions for approximate and phonetic matching of strings.
10 <https://github.com/jamesturk/jellyfish>`_
33 import jellyfish._jellyfish as pyjellyfish
34 import jellyfish.cjellyfish as cjellyfish
36 If you've already imported jellyfish and are not sure what implementation you
37 are using, you can check by querying ``jellyfish.library``::
39 if jellyfish.library == 'Python':
41 elif jellyfish.library == 'C':
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/swig/
H A DMakefile.am2 SWIG_SRC = swig/jellyfish.i swig/hash_counter.i swig/hash_set.i \
19 PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/jellyfish.py
22 pythonextdir = $(PYTHON_SITE_PKG)/jellyfish
33 %/__init__.pyc: %/jellyfish.py
35 swig/python/jellyfish.py: swig/python/swig_wrap.cpp
44 rubyext_LTLIBRARIES = swig/ruby/jellyfish.la
54 PERL_BUILT = swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
57 perlext_SCRIPTS = swig/perl5/jellyfish.pm
58 perlext_LTLIBRARIES = swig/perl5/jellyfish.la
64 swig/perl5/jellyfish.pm: swig/perl5/swig_wrap.cpp
/dports/math/gap/gap-4.11.0/pkg/recog-1.3.2/gap/
H A Dsnksetswrsr.gi207 jellyfish := Difference( jellyfish, deltagamma );
218 return [ jellyfish, Set(idjf) ];
227 ## The following function takes a jellyfish <jellyfish> and constructs
228 ## n*r jellyfish by building up the <G>-orbit of <jellyfish>, since <G>
229 ## is transitive on jellyfish. The order in which the jellyfish are
247 # jellyfish, then the two jellyfish are equal
249 HaveSeen := function( jellyfish )
263 for i in jellyfish do
310 HaveSeen := function( jellyfish )
322 for i in jellyfish do
[all …]
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/lib/
H A Drectangular_binary_matrix.cc24 uint64_t *jellyfish::RectangularBinaryMatrix::alloc(unsigned int r, unsigned int c) { in alloc()
40 void jellyfish::RectangularBinaryMatrix::init_low_identity() { in init_low_identity()
49 bool jellyfish::RectangularBinaryMatrix::is_low_identity() { in is_low_identity()
64 jellyfish::RectangularBinaryMatrix jellyfish::RectangularBinaryMatrix::pseudo_multiplication(const … in pseudo_multiplication()
104 unsigned int jellyfish::RectangularBinaryMatrix::pseudo_rank() const { in pseudo_rank()
138 jellyfish::RectangularBinaryMatrix jellyfish::RectangularBinaryMatrix::pseudo_inverse() const { in pseudo_inverse()
188 void jellyfish::RectangularBinaryMatrix::print(std::ostream &os) const { in print()
199 void jellyfish::RectangularBinaryMatrix::print_vector(std::ostream &os, const T &v) const { in print_vector()
209 jellyfish::RectangularBinaryMatrix jellyfish::RectangularBinaryMatrix::randomize_pseudo_inverse(uin… in randomize_pseudo_inverse()
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/SuperReadsR/src/
H A Dbloom_query.cc10 void operator()(const jellyfish::mer_dna& m, uint64_t *hashes) const { in operator ()()
14 typedef bloom_counter2<jellyfish::mer_dna, mer_dna_hash> mer_bloom_counter2;
20 jellyfish::mer_dna::k(args.mer_arg); in main()
22 jellyfish::mapped_file dbf(args.input_arg); in main()
27 jellyfish::mer_dna m; in main()
28 jellyfish::mer_dna mq; in main()
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/swig/perl5/
H A Djellyfish.pm7 package jellyfish; package
11 bootstrap jellyfish;
12 package jellyfish; package
17 package jellyfish; package
50 package jellyfish; package
57 package jellyfish::MerDNA;
160 package jellyfish::ReadMerFile;
201 package jellyfish::HashCounter;
243 package jellyfish::HashSet;
283 package jellyfish::StringMers;
[all …]
/dports/biology/jellyfish/jellyfish-2.3.0/swig/perl5/
H A Djellyfish.pm7 package jellyfish; package
11 bootstrap jellyfish;
12 package jellyfish; package
17 package jellyfish; package
50 package jellyfish; package
57 package jellyfish::MerDNA;
160 package jellyfish::ReadMerFile;
201 package jellyfish::HashCounter;
243 package jellyfish::HashSet;
283 package jellyfish::StringMers;
[all …]

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