Searched refs:postnuc (Results 1 – 13 of 13) sorted by relevance
| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/include/mummer/ |
| H A D | nucmer.hpp | 145 const postnuc::merge_syntenys merger;
168 std::vector<postnuc::Alignment> alignments; in align()
176 std::vector<postnuc::Alignment>& alignments, in align_sequences()
400 typedef postnuc::Synteny<FastaRecordPtr> synteny_type; in thread_align_file()
414 postnuc::Cluster cl(cluster_dir); in thread_align_file()
470 cluster_dir = postnuc::FORWARD_CHAR; in thread_align_file()
485 cluster_dir = postnuc::REVERSE_CHAR; in thread_align_file()
496 typedef postnuc::Synteny<FastaRecordPtr> synteny_type; in align_long_sequences()
513 postnuc::Cluster cl(cluster_dir); in align_long_sequences()
550 cluster_dir = postnuc::FORWARD_CHAR; in align_long_sequences()
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| H A D | postnuc.hh | 18 namespace postnuc { namespace
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/umd/ |
| H A D | nucmer.cc | 16 typedef postnuc::Synteny<FastaRecordSeq> synteny_type;
44 void SequenceAligner::align(const char* query, size_t query_len, std::vector<postnuc::Alignment>& a… in align()
54 postnuc::Cluster cl(cluster_dir); in align()
69 cluster_dir = postnuc::FORWARD_CHAR; in align()
82 cluster_dir = postnuc::REVERSE_CHAR; in align()
87 [&](std::vector<postnuc::Alignment>&& als, const FastaRecordSeq& Af, in align()
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| H A D | nucmer_main.cc | 32 auto print_function = [&](std::vector<mummer::postnuc::Alignment>&& als, in query_thread()
37 …mummer::postnuc::printDeltaAlignments(als, Af.Id(), Af.len(), Bf.Id(), Bf.len(), *output_it, args-… in query_thread()
39 …mummer::postnuc::printSAMAlignments(als, Af, Bf, *output_it, args->sam_long_given, args->minalign_… in query_thread()
50 auto print_function = [&](std::vector<mummer::postnuc::Alignment>&& als, in query_long()
52 …mummer::postnuc::printDeltaAlignments(als, Af.Id(), Af.len(), Bf.Id(), Bf.len(), *output_it, args-… in query_long()
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/swig/ |
| H A D | nucmer.i | 12 namespace postnuc {
32 %template(AlignmentVector) ::std::vector<mummer::postnuc::Alignment>;
80 ::std::vector<mummer::postnuc::Alignment> align_sequences(const char* reference, size_t reference_l…
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
| H A D | Makefile | 19 postnuc postpro prenuc prepro repeat-match \
68 postnuc: postnuc.cc tigrinc.o sw_align.o target
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| H A D | postnuc_main.cc | 51 using namespace mummer::postnuc;
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| H A D | postnuc.cc | 19 namespace postnuc { namespace
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/unittests/ |
| H A D | test_nucmer.cc | 68 …const auto al = std::find_if(a.cbegin(), a.cend(), [](const mummer::postnuc::Alignment& al) { retu… in TEST()
93 auto append_matches = [&](std::vector<mummer::postnuc::Alignment>&& al, in TEST()
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/ |
| H A D | Makefile.am | 54 libumdmummer_la_SOURCES += src/tigr/mgaps.cc src/tigr/postnuc.cc src/tigr/sw_align.cc src/tigr/tigr…
62 include/mummer/postnuc.hh \
112 pkglibexec_PROGRAMS += mgaps postnuc prepro postpro program
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/tests/ |
| H A D | test_sequence_align.cc | 43 …mummer::postnuc::printDeltaAlignments(aligner.align(qry_sequences[i].c_str(), qry_sequences[i].siz… in main()
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/docs/ |
| H A D | nucmer.README | 263 using the -d switch for the 'postnuc' program.
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| H A D | promer.README | 260 using the -d switch for the 'postnuc' program.
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