[med-svn] [Git][med-team/spades][upstream] New upstream version 4.0.0+really3.15.5+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sat Apr 12 10:59:27 BST 2025
Pierre Gruet pushed to branch upstream at Debian Med / spades
Commits:
76c0d6c9 by Pierre Gruet at 2025-04-12T09:53:44+02:00
New upstream version 4.0.0+really3.15.5+dfsg
- - - - -
10961 changed files:
- .github/ISSUE_TEMPLATE/config.yml
- − .github/workflows/basic.yml
- + .github/workflows/basic.yml.disabled
- − .github/workflows/docs.yml
- − .github/workflows/full_runs.yml
- − .github/workflows/gcc.yml
- − .github/workflows/iontorrent.yml
- − .github/workflows/isolated.yml
- − .github/workflows/long_reads.yml
- − .github/workflows/mate_pairs.yml
- − .github/workflows/meta.yml
- − .github/workflows/release.yml
- − .github/workflows/rna.yml
- − .github/workflows/single_cell.yml
- + .github/workflows/spades-test.yml.disabled
- − .github/workflows/sra.yml
- − .github/workflows/update_saves.yml
- − .github/workflows/usecases.yml
- − LICENSE
- README.md
- − VERSION
- .clang-format → assembler/.clang-format
- + assembler/.gitignore
- GPLv2.txt → assembler/GPLv2.txt
- + assembler/LICENSE
- + assembler/VERSION
- src/projects/spades/biosynthetic_spades_hmms/AMP.hmm.gz → assembler/biosynthetic_spades_hmms/AMP.hmm.gz
- src/projects/spades/biosynthetic_spades_hmms/AT.hmm.gz → assembler/biosynthetic_spades_hmms/AT.hmm.gz
- src/projects/spades/biosynthetic_spades_hmms/CStart.hmm.gz → assembler/biosynthetic_spades_hmms/CStart.hmm.gz
- src/projects/spades/biosynthetic_spades_hmms/KR.hmm.gz → assembler/biosynthetic_spades_hmms/KR.hmm.gz
- src/projects/spades/biosynthetic_spades_hmms/KS.hmm.gz → assembler/biosynthetic_spades_hmms/KS.hmm.gz
- src/projects/spades/biosynthetic_spades_hmms/TE.hmm.gz → assembler/biosynthetic_spades_hmms/TE.hmm.gz
- + assembler/changelog.html
- + assembler/changer_of_K.py
- + assembler/compare_saves.sh
- + assembler/configs/.gitignore
- src/projects/corrector/configs/corrector.info → assembler/configs/corrector/corrector.info
- src/projects/corrector/configs/log.properties → assembler/configs/corrector/log.properties
- src/projects/spades/configs/careful_mda_mode.info → assembler/configs/debruijn/careful_mda_mode.info
- src/projects/spades/configs/careful_mode.info → assembler/configs/debruijn/careful_mode.info
- src/projects/spades/configs/config.info → assembler/configs/debruijn/config.info
- src/projects/spades/configs/construction.info → assembler/configs/debruijn/construction.info
- src/projects/spades/configs/detail_info_printer.info → assembler/configs/debruijn/detail_info_printer.info
- src/projects/spades/configs/distance_estimation.info → assembler/configs/debruijn/distance_estimation.info
- src/projects/spades/configs/hmm_mode.info → assembler/configs/debruijn/hmm_mode.info
- src/projects/spades/configs/isolate_mode.info → assembler/configs/debruijn/isolate_mode.info
- src/projects/spades/configs/large_genome_mode.info → assembler/configs/debruijn/large_genome_mode.info
- src/projects/spades/configs/log.properties → assembler/configs/debruijn/log.properties
- src/projects/spades/configs/mda_mode.info → assembler/configs/debruijn/mda_mode.info
- src/projects/spades/configs/meta_mode.info → assembler/configs/debruijn/meta_mode.info
- src/projects/spades/configs/metaplasmid_mode.info → assembler/configs/debruijn/metaplasmid_mode.info
- src/projects/spades/configs/metaviral_mode.info → assembler/configs/debruijn/metaviral_mode.info
- + assembler/configs/debruijn/moleculo_mode.info
- src/projects/spades/configs/pe_params.info → assembler/configs/debruijn/pe_params.info
- src/projects/spades/configs/plasmid_mode.info → assembler/configs/debruijn/plasmid_mode.info
- src/projects/spades/configs/rna_mode.info → assembler/configs/debruijn/rna_mode.info
- src/projects/spades/configs/rnaviral_mode.info → assembler/configs/debruijn/rnaviral_mode.info
- src/projects/spades/configs/simplification.info → assembler/configs/debruijn/simplification.info
- src/projects/spades/configs/toy.info → assembler/configs/debruijn/toy.info
- src/projects/spades/configs/toy.yaml → assembler/configs/debruijn/toy.yaml
- + assembler/configs/debruijn/tsa.info
- src/projects/hammer/configs/config.info → assembler/configs/hammer/config.info
- src/projects/ionhammer/configs/ionhammer.cfg → assembler/configs/ionhammer/ionhammer.cfg
- src/projects/spades/pipeline/coronaspades.py → assembler/coronaspades.py
- src/projects/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz → assembler/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz
- src/projects/spades/coronaspades_hmms/Phan-CoV.hmm.gz → assembler/coronaspades_hmms/Phan-CoV.hmm.gz
- + assembler/editcfg
- + assembler/ext/include/ConsensusCore/AffineAlignment.hpp
- + assembler/ext/include/ConsensusCore/Coverage.hpp
- + assembler/ext/include/ConsensusCore/LFloat.hpp
- + assembler/ext/include/ConsensusCore/Matrix/DenseMatrix-inl.hpp
- + assembler/ext/include/ConsensusCore/Matrix/DenseMatrix.hpp
- + assembler/ext/include/ConsensusCore/Matrix/SparseMatrix-inl.hpp
- + assembler/ext/include/ConsensusCore/Matrix/SparseMatrix.hpp
- + assembler/ext/include/ConsensusCore/Matrix/SparseVector-inl.hpp
- + assembler/ext/include/ConsensusCore/Matrix/SparseVector.hpp
- + assembler/ext/include/ConsensusCore/Mutation-inl.hpp
- + assembler/ext/include/ConsensusCore/Mutation.hpp
- + assembler/ext/include/ConsensusCore/PairwiseAlignment.hpp
- + assembler/ext/include/ConsensusCore/Poa/PoaConfig.hpp
- + assembler/ext/include/ConsensusCore/Poa/PoaConsensus.hpp
- + assembler/ext/include/ConsensusCore/Poa/PoaGraph.hpp
- + assembler/ext/include/ConsensusCore/Sequence.hpp
- + assembler/ext/include/ConsensusCore/Types.hpp
- + assembler/ext/include/ConsensusCore/Utils.hpp
- + assembler/ext/include/ConsensusCore/Version.hpp
- + assembler/ext/include/bamtools/api/BamAlgorithms.h
- + assembler/ext/include/bamtools/api/BamAlignment.h
- + assembler/ext/include/bamtools/api/BamAux.h
- + assembler/ext/include/bamtools/api/BamConstants.h
- + assembler/ext/include/bamtools/api/BamIndex.h
- + assembler/ext/include/bamtools/api/BamMultiReader.h
- + assembler/ext/include/bamtools/api/BamReader.h
- + assembler/ext/include/bamtools/api/BamWriter.h
- + assembler/ext/include/bamtools/api/IBamIODevice.h
- + assembler/ext/include/bamtools/api/SamConstants.h
- + assembler/ext/include/bamtools/api/SamHeader.h
- + assembler/ext/include/bamtools/api/SamProgram.h
- + assembler/ext/include/bamtools/api/SamProgramChain.h
- + assembler/ext/include/bamtools/api/SamReadGroup.h
- + assembler/ext/include/bamtools/api/SamReadGroupDictionary.h
- + assembler/ext/include/bamtools/api/SamSequence.h
- + assembler/ext/include/bamtools/api/SamSequenceDictionary.h
- + assembler/ext/include/bamtools/api/algorithms/Sort.h
- + assembler/ext/include/bamtools/api/api_global.h
- + assembler/ext/include/bamtools/shared/bamtools_global.h
- ext/include/boomphf/BooPHF.h → assembler/ext/include/boomphf/BooPHF.h
- + assembler/ext/include/boost/algorithm/algorithm.hpp
- + assembler/ext/include/boost/algorithm/clamp.hpp
- + assembler/ext/include/boost/algorithm/cxx11/all_of.hpp
- + assembler/ext/include/boost/algorithm/cxx11/any_of.hpp
- + assembler/ext/include/boost/algorithm/cxx11/copy_if.hpp
- + assembler/ext/include/boost/algorithm/cxx11/copy_n.hpp
- + assembler/ext/include/boost/algorithm/cxx11/find_if_not.hpp
- + assembler/ext/include/boost/algorithm/cxx11/iota.hpp
- + assembler/ext/include/boost/algorithm/cxx11/is_partitioned.hpp
- + assembler/ext/include/boost/algorithm/cxx11/is_permutation.hpp
- + assembler/ext/include/boost/algorithm/cxx11/is_sorted.hpp
- + assembler/ext/include/boost/algorithm/cxx11/none_of.hpp
- + assembler/ext/include/boost/algorithm/cxx11/one_of.hpp
- + assembler/ext/include/boost/algorithm/cxx11/partition_copy.hpp
- + assembler/ext/include/boost/algorithm/cxx11/partition_point.hpp
- + assembler/ext/include/boost/algorithm/cxx14/equal.hpp
- + assembler/ext/include/boost/algorithm/cxx14/is_permutation.hpp
- + assembler/ext/include/boost/algorithm/cxx14/mismatch.hpp
- + assembler/ext/include/boost/algorithm/gather.hpp
- + assembler/ext/include/boost/algorithm/hex.hpp
- + assembler/ext/include/boost/algorithm/is_palindrome.hpp
- + assembler/ext/include/boost/algorithm/minmax.hpp
- + assembler/ext/include/boost/algorithm/minmax_element.hpp
- + assembler/ext/include/boost/algorithm/searching/boyer_moore.hpp
- + assembler/ext/include/boost/algorithm/searching/boyer_moore_horspool.hpp
- + assembler/ext/include/boost/algorithm/searching/detail/bm_traits.hpp
- + assembler/ext/include/boost/algorithm/searching/detail/debugging.hpp
- + assembler/ext/include/boost/algorithm/searching/knuth_morris_pratt.hpp
- + assembler/ext/include/boost/algorithm/sort_subrange.hpp
- + assembler/ext/include/boost/algorithm/string.hpp
- + assembler/ext/include/boost/algorithm/string/case_conv.hpp
- + assembler/ext/include/boost/algorithm/string/classification.hpp
- + assembler/ext/include/boost/algorithm/string/compare.hpp
- + assembler/ext/include/boost/algorithm/string/concept.hpp
- + assembler/ext/include/boost/algorithm/string/config.hpp
- + assembler/ext/include/boost/algorithm/string/constants.hpp
- + assembler/ext/include/boost/algorithm/string/detail/case_conv.hpp
- + assembler/ext/include/boost/algorithm/string/detail/classification.hpp
- + assembler/ext/include/boost/algorithm/string/detail/find_format.hpp
- + assembler/ext/include/boost/algorithm/string/detail/find_format_all.hpp
- + assembler/ext/include/boost/algorithm/string/detail/find_format_store.hpp
- + assembler/ext/include/boost/algorithm/string/detail/find_iterator.hpp
- + assembler/ext/include/boost/algorithm/string/detail/finder.hpp
- + assembler/ext/include/boost/algorithm/string/detail/finder_regex.hpp
- + assembler/ext/include/boost/algorithm/string/detail/formatter.hpp
- + assembler/ext/include/boost/algorithm/string/detail/formatter_regex.hpp
- + assembler/ext/include/boost/algorithm/string/detail/predicate.hpp
- + assembler/ext/include/boost/algorithm/string/detail/replace_storage.hpp
- + assembler/ext/include/boost/algorithm/string/detail/sequence.hpp
- + assembler/ext/include/boost/algorithm/string/detail/trim.hpp
- + assembler/ext/include/boost/algorithm/string/detail/util.hpp
- + assembler/ext/include/boost/algorithm/string/erase.hpp
- + assembler/ext/include/boost/algorithm/string/find.hpp
- + assembler/ext/include/boost/algorithm/string/find_format.hpp
- + assembler/ext/include/boost/algorithm/string/find_iterator.hpp
- + assembler/ext/include/boost/algorithm/string/finder.hpp
- + assembler/ext/include/boost/algorithm/string/formatter.hpp
- + assembler/ext/include/boost/algorithm/string/iter_find.hpp
- + assembler/ext/include/boost/algorithm/string/join.hpp
- + assembler/ext/include/boost/algorithm/string/predicate.hpp
- + assembler/ext/include/boost/algorithm/string/predicate_facade.hpp
- + assembler/ext/include/boost/algorithm/string/regex.hpp
- + assembler/ext/include/boost/algorithm/string/regex_find_format.hpp
- + assembler/ext/include/boost/algorithm/string/replace.hpp
- + assembler/ext/include/boost/algorithm/string/sequence_traits.hpp
- + assembler/ext/include/boost/algorithm/string/split.hpp
- + assembler/ext/include/boost/algorithm/string/std/list_traits.hpp
- + assembler/ext/include/boost/algorithm/string/std/rope_traits.hpp
- + assembler/ext/include/boost/algorithm/string/std/slist_traits.hpp
- + assembler/ext/include/boost/algorithm/string/std/string_traits.hpp
- + assembler/ext/include/boost/algorithm/string/std_containers_traits.hpp
- + assembler/ext/include/boost/algorithm/string/trim.hpp
- + assembler/ext/include/boost/algorithm/string/trim_all.hpp
- + assembler/ext/include/boost/algorithm/string/yes_no_type.hpp
- + assembler/ext/include/boost/algorithm/string_regex.hpp
- + assembler/ext/include/boost/align/align.hpp
- + assembler/ext/include/boost/align/align_down.hpp
- + assembler/ext/include/boost/align/align_down_forward.hpp
- + assembler/ext/include/boost/align/align_up.hpp
- + assembler/ext/include/boost/align/align_up_forward.hpp
- + assembler/ext/include/boost/align/aligned_alloc.hpp
- + assembler/ext/include/boost/align/aligned_allocator.hpp
- + assembler/ext/include/boost/align/aligned_allocator_adaptor.hpp
- + assembler/ext/include/boost/align/aligned_allocator_adaptor_forward.hpp
- + assembler/ext/include/boost/align/aligned_allocator_forward.hpp
- + assembler/ext/include/boost/align/aligned_delete.hpp
- + assembler/ext/include/boost/align/aligned_delete_forward.hpp
- + assembler/ext/include/boost/align/alignment_of.hpp
- + assembler/ext/include/boost/align/alignment_of_forward.hpp
- + assembler/ext/include/boost/align/assume_aligned.hpp
- + assembler/ext/include/boost/align/detail/addressof.hpp
- + assembler/ext/include/boost/align/detail/align.hpp
- + assembler/ext/include/boost/align/detail/align_cxx11.hpp
- + assembler/ext/include/boost/align/detail/align_down.hpp
- + assembler/ext/include/boost/align/detail/align_up.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc_android.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc_macos.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc_msvc.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc_posix.hpp
- + assembler/ext/include/boost/align/detail/aligned_alloc_sunos.hpp
- + assembler/ext/include/boost/align/detail/alignment_of.hpp
- + assembler/ext/include/boost/align/detail/alignment_of_clang.hpp
- + assembler/ext/include/boost/align/detail/alignment_of_codegear.hpp
- + assembler/ext/include/boost/align/detail/alignment_of_cxx11.hpp
- + assembler/ext/include/boost/align/detail/alignment_of_gcc.hpp
- + assembler/ext/include/boost/align/detail/alignment_of_msvc.hpp
- + assembler/ext/include/boost/align/detail/assume_aligned.hpp
- + assembler/ext/include/boost/align/detail/assume_aligned_clang.hpp
- + assembler/ext/include/boost/align/detail/assume_aligned_gcc.hpp
- + assembler/ext/include/boost/align/detail/assume_aligned_intel.hpp
- + assembler/ext/include/boost/align/detail/assume_aligned_msvc.hpp
- + assembler/ext/include/boost/align/detail/element_type.hpp
- + assembler/ext/include/boost/align/detail/integral_constant.hpp
- + assembler/ext/include/boost/align/detail/is_aligned.hpp
- + assembler/ext/include/boost/align/detail/is_alignment.hpp
- + assembler/ext/include/boost/align/detail/is_alignment_constant.hpp
- + assembler/ext/include/boost/align/detail/max_align.hpp
- + assembler/ext/include/boost/align/detail/max_objects.hpp
- + assembler/ext/include/boost/align/detail/max_size.hpp
- + assembler/ext/include/boost/align/detail/min_size.hpp
- + assembler/ext/include/boost/align/is_aligned.hpp
- + assembler/ext/include/boost/align/is_aligned_forward.hpp
- + assembler/ext/include/boost/aligned_storage.hpp
- + assembler/ext/include/boost/any.hpp
- + assembler/ext/include/boost/array.hpp
- + assembler/ext/include/boost/assert.hpp
- + assembler/ext/include/boost/bimap.hpp
- + assembler/ext/include/boost/bimap/bimap.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/associative_container_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/container_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/detail/comparison_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/detail/functor_bag.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/detail/identity_converters.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/detail/key_extractor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/detail/non_unique_container_helper.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/list_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/list_map_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/map_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/multimap_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/multiset_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/ordered_associative_container_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/sequence_container_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/set_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/support/iterator_facade_converters.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/unordered_associative_container_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/unordered_map_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/unordered_multimap_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/unordered_multiset_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/unordered_set_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/vector_adaptor.hpp
- + assembler/ext/include/boost/bimap/container_adaptor/vector_map_adaptor.hpp
- + assembler/ext/include/boost/bimap/detail/bimap_core.hpp
- + assembler/ext/include/boost/bimap/detail/concept_tags.hpp
- + assembler/ext/include/boost/bimap/detail/debug/static_error.hpp
- + assembler/ext/include/boost/bimap/detail/generate_index_binder.hpp
- + assembler/ext/include/boost/bimap/detail/generate_relation_binder.hpp
- + assembler/ext/include/boost/bimap/detail/generate_view_binder.hpp
- + assembler/ext/include/boost/bimap/detail/is_set_type_of.hpp
- + assembler/ext/include/boost/bimap/detail/manage_additional_parameters.hpp
- + assembler/ext/include/boost/bimap/detail/manage_bimap_key.hpp
- + assembler/ext/include/boost/bimap/detail/map_view_base.hpp
- + assembler/ext/include/boost/bimap/detail/map_view_iterator.hpp
- + assembler/ext/include/boost/bimap/detail/modifier_adaptor.hpp
- + assembler/ext/include/boost/bimap/detail/non_unique_views_helper.hpp
- + assembler/ext/include/boost/bimap/detail/set_view_base.hpp
- + assembler/ext/include/boost/bimap/detail/set_view_iterator.hpp
- + assembler/ext/include/boost/bimap/detail/test/check_metadata.hpp
- + assembler/ext/include/boost/bimap/detail/user_interface_config.hpp
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- + assembler/ext/include/boost/bimap/property_map/set_support.hpp
- + assembler/ext/include/boost/bimap/property_map/unordered_set_support.hpp
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- + assembler/ext/include/boost/bimap/relation/detail/metadata_access_builder.hpp
- + assembler/ext/include/boost/bimap/relation/detail/mutant.hpp
- + assembler/ext/include/boost/bimap/relation/detail/static_access_builder.hpp
- + assembler/ext/include/boost/bimap/relation/detail/to_mutable_relation_functor.hpp
- + assembler/ext/include/boost/bimap/relation/member_at.hpp
- + assembler/ext/include/boost/bimap/relation/mutant_relation.hpp
- + assembler/ext/include/boost/bimap/relation/pair_layout.hpp
- + assembler/ext/include/boost/bimap/relation/structured_pair.hpp
- + assembler/ext/include/boost/bimap/relation/support/data_extractor.hpp
- + assembler/ext/include/boost/bimap/relation/support/get.hpp
- + assembler/ext/include/boost/bimap/relation/support/get_pair_functor.hpp
- + assembler/ext/include/boost/bimap/relation/support/is_tag_of_member_at.hpp
- + assembler/ext/include/boost/bimap/relation/support/member_with_tag.hpp
- + assembler/ext/include/boost/bimap/relation/support/opposite_tag.hpp
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- + assembler/ext/include/boost/bimap/relation/support/value_type_of.hpp
- + assembler/ext/include/boost/bimap/relation/symmetrical_base.hpp
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- + assembler/ext/include/boost/bimap/support/key_type_by.hpp
- + assembler/ext/include/boost/bimap/support/lambda.hpp
- + assembler/ext/include/boost/bimap/support/map_by.hpp
- + assembler/ext/include/boost/bimap/support/map_type_by.hpp
- + assembler/ext/include/boost/bimap/support/value_type_by.hpp
- + assembler/ext/include/boost/bimap/tags/support/apply_to_value_type.hpp
- + assembler/ext/include/boost/bimap/tags/support/default_tagged.hpp
- + assembler/ext/include/boost/bimap/tags/support/is_tagged.hpp
- + assembler/ext/include/boost/bimap/tags/support/overwrite_tagged.hpp
- + assembler/ext/include/boost/bimap/tags/support/tag_of.hpp
- + assembler/ext/include/boost/bimap/tags/support/value_type_of.hpp
- + assembler/ext/include/boost/bimap/tags/tagged.hpp
- + assembler/ext/include/boost/bimap/unconstrained_set_of.hpp
- + assembler/ext/include/boost/bimap/unordered_multiset_of.hpp
- + assembler/ext/include/boost/bimap/unordered_set_of.hpp
- + assembler/ext/include/boost/bimap/vector_of.hpp
- + assembler/ext/include/boost/bimap/views/list_map_view.hpp
- + assembler/ext/include/boost/bimap/views/list_set_view.hpp
- + assembler/ext/include/boost/bimap/views/map_view.hpp
- + assembler/ext/include/boost/bimap/views/multimap_view.hpp
- + assembler/ext/include/boost/bimap/views/multiset_view.hpp
- + assembler/ext/include/boost/bimap/views/set_view.hpp
- + assembler/ext/include/boost/bimap/views/unconstrained_map_view.hpp
- + assembler/ext/include/boost/bimap/views/unconstrained_set_view.hpp
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- + assembler/ext/include/boost/xpressive/detail/utility/chset/chset.hpp
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- + assembler/ext/include/boost/xpressive/traits/cpp_regex_traits.hpp
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- + assembler/ext/include/btree/COPYING
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- + assembler/ext/include/btree/btree_container.h
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- ext/include/bwa/bntseq.h → assembler/ext/include/bwa/bntseq.h
- ext/include/bwa/bwa.h → assembler/ext/include/bwa/bwa.h
- ext/include/bwa/bwamem.h → assembler/ext/include/bwa/bwamem.h
- ext/include/bwa/bwt.h → assembler/ext/include/bwa/bwt.h
- ext/include/bwa/rle.h → assembler/ext/include/bwa/rle.h
- ext/include/bwa/rope.h → assembler/ext/include/bwa/rope.h
- ext/include/bwa/utils.h → assembler/ext/include/bwa/utils.h
- ext/include/clipp/clipp.h → assembler/ext/include/clipp/clipp.h
- ext/include/cppformat/format.h → assembler/ext/include/cppformat/format.h
- ext/include/cppformat/posix.h → assembler/ext/include/cppformat/posix.h
- + assembler/ext/include/cuckoo/LICENSE
- + assembler/ext/include/cuckoo/city_hasher.hh
- + assembler/ext/include/cuckoo/cuckoohash_config.hh
- + assembler/ext/include/cuckoo/cuckoohash_map.hh
- + assembler/ext/include/cuckoo/cuckoohash_util.hh
- + assembler/ext/include/cuckoo/libcuckoo_lazy_array.hh
- + assembler/ext/include/cxxopts/cxxopts.hpp
- ext/include/edlib/edlib.h → assembler/ext/include/edlib/edlib.h
- ext/include/folly/PackedSyncPtr.h → assembler/ext/include/folly/PackedSyncPtr.h
- + assembler/ext/include/folly/Portability.h
- + assembler/ext/include/folly/SmallLocks.h
- src/projects/mts/getopt_pp/CHANGELOG → assembler/ext/include/getopt_pp/CHANGELOG
- src/projects/mts/getopt_pp/README → assembler/ext/include/getopt_pp/README
- src/projects/mts/getopt_pp/getopt_pp.h → assembler/ext/include/getopt_pp/getopt_pp.h
- src/projects/mts/getopt_pp/getopt_pp_standalone.h → assembler/ext/include/getopt_pp/getopt_pp_standalone.h
- + assembler/ext/include/gfa1/gfa.h
- ext/include/gqf/gqf.h → assembler/ext/include/gqf/gqf.h
- + assembler/ext/include/kseq/kseq.h
- + assembler/ext/include/libcxx/sort.hpp
- ext/include/llvm/ADT/APFloat.h → assembler/ext/include/llvm/ADT/APFloat.h
- ext/include/llvm/ADT/APInt.h → assembler/ext/include/llvm/ADT/APInt.h
- ext/include/llvm/ADT/APSInt.h → assembler/ext/include/llvm/ADT/APSInt.h
- ext/include/llvm/ADT/AllocatorList.h → assembler/ext/include/llvm/ADT/AllocatorList.h
- ext/include/llvm/ADT/ArrayRef.h → assembler/ext/include/llvm/ADT/ArrayRef.h
- ext/include/llvm/ADT/BitVector.h → assembler/ext/include/llvm/ADT/BitVector.h
- ext/include/llvm/ADT/BitmaskEnum.h → assembler/ext/include/llvm/ADT/BitmaskEnum.h
- ext/include/llvm/ADT/DenseMap.h → assembler/ext/include/llvm/ADT/DenseMap.h
- ext/include/llvm/ADT/DenseMapInfo.h → assembler/ext/include/llvm/ADT/DenseMapInfo.h
- ext/include/llvm/ADT/DenseSet.h → assembler/ext/include/llvm/ADT/DenseSet.h
- ext/include/llvm/ADT/EpochTracker.h → assembler/ext/include/llvm/ADT/EpochTracker.h
- ext/include/llvm/ADT/FloatingPointMode.h → assembler/ext/include/llvm/ADT/FloatingPointMode.h
- ext/include/llvm/ADT/FoldingSet.h → assembler/ext/include/llvm/ADT/FoldingSet.h
- ext/include/llvm/ADT/FunctionExtras.h → assembler/ext/include/llvm/ADT/FunctionExtras.h
- ext/include/llvm/ADT/Hashing.h → assembler/ext/include/llvm/ADT/Hashing.h
- ext/include/llvm/ADT/IntrusiveRefCntPtr.h → assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h
- ext/include/llvm/ADT/None.h → assembler/ext/include/llvm/ADT/None.h
- ext/include/llvm/ADT/Optional.h → assembler/ext/include/llvm/ADT/Optional.h
- ext/include/llvm/ADT/PackedVector.h → assembler/ext/include/llvm/ADT/PackedVector.h
- ext/include/llvm/ADT/PointerEmbeddedInt.h → assembler/ext/include/llvm/ADT/PointerEmbeddedInt.h
- ext/include/llvm/ADT/PointerIntPair.h → assembler/ext/include/llvm/ADT/PointerIntPair.h
- ext/include/llvm/ADT/PointerSumType.h → assembler/ext/include/llvm/ADT/PointerSumType.h
- ext/include/llvm/ADT/PointerUnion.h → assembler/ext/include/llvm/ADT/PointerUnion.h
- ext/include/llvm/ADT/STLExtras.h → assembler/ext/include/llvm/ADT/STLExtras.h
- ext/include/llvm/ADT/ScopeExit.h → assembler/ext/include/llvm/ADT/ScopeExit.h
- ext/include/llvm/ADT/SmallBitVector.h → assembler/ext/include/llvm/ADT/SmallBitVector.h
- ext/include/llvm/ADT/SmallPtrSet.h → assembler/ext/include/llvm/ADT/SmallPtrSet.h
- ext/include/llvm/ADT/SmallSet.h → assembler/ext/include/llvm/ADT/SmallSet.h
- ext/include/llvm/ADT/SmallString.h → assembler/ext/include/llvm/ADT/SmallString.h
- ext/include/llvm/ADT/SmallVector.h → assembler/ext/include/llvm/ADT/SmallVector.h
- ext/include/llvm/ADT/SparseBitVector.h → assembler/ext/include/llvm/ADT/SparseBitVector.h
- ext/include/llvm/ADT/SparseMultiSet.h → assembler/ext/include/llvm/ADT/SparseMultiSet.h
- ext/include/llvm/ADT/StringExtras.h → assembler/ext/include/llvm/ADT/StringExtras.h
- ext/include/llvm/ADT/StringMap.h → assembler/ext/include/llvm/ADT/StringMap.h
- ext/include/llvm/ADT/StringMapEntry.h → assembler/ext/include/llvm/ADT/StringMapEntry.h
- ext/include/llvm/ADT/StringRef.h → assembler/ext/include/llvm/ADT/StringRef.h
- ext/include/llvm/ADT/StringSwitch.h → assembler/ext/include/llvm/ADT/StringSwitch.h
- ext/include/llvm/ADT/Twine.h → assembler/ext/include/llvm/ADT/Twine.h
- ext/include/llvm/ADT/bit.h → assembler/ext/include/llvm/ADT/bit.h
- ext/include/llvm/ADT/edit_distance.h → assembler/ext/include/llvm/ADT/edit_distance.h
- ext/include/llvm/ADT/ilist.h → assembler/ext/include/llvm/ADT/ilist.h
- ext/include/llvm/ADT/ilist_base.h → assembler/ext/include/llvm/ADT/ilist_base.h
- ext/include/llvm/ADT/ilist_iterator.h → assembler/ext/include/llvm/ADT/ilist_iterator.h
- ext/include/llvm/ADT/ilist_node.h → assembler/ext/include/llvm/ADT/ilist_node.h
- ext/include/llvm/ADT/ilist_node_base.h → assembler/ext/include/llvm/ADT/ilist_node_base.h
- ext/include/llvm/ADT/ilist_node_options.h → assembler/ext/include/llvm/ADT/ilist_node_options.h
- ext/include/llvm/ADT/iterator.h → assembler/ext/include/llvm/ADT/iterator.h
- ext/include/llvm/ADT/iterator_range.h → assembler/ext/include/llvm/ADT/iterator_range.h
- ext/include/llvm/ADT/simple_ilist.h → assembler/ext/include/llvm/ADT/simple_ilist.h
- ext/include/llvm/Config.h.in → assembler/ext/include/llvm/Config.h.in
- ext/include/llvm/Support/AlignOf.h → assembler/ext/include/llvm/Support/AlignOf.h
- ext/include/llvm/Support/Alignment.h → assembler/ext/include/llvm/Support/Alignment.h
- ext/include/llvm/Support/Allocator.h → assembler/ext/include/llvm/Support/Allocator.h
- ext/include/llvm/Support/AllocatorBase.h → assembler/ext/include/llvm/Support/AllocatorBase.h
- ext/include/llvm/Support/Atomic.h → assembler/ext/include/llvm/Support/Atomic.h
- ext/include/llvm/Support/Casting.h → assembler/ext/include/llvm/Support/Casting.h
- ext/include/llvm/Support/Chrono.h → assembler/ext/include/llvm/Support/Chrono.h
- ext/include/llvm/Support/Compiler.h → assembler/ext/include/llvm/Support/Compiler.h
- + assembler/ext/include/llvm/Support/ConvertUTF.h
- ext/include/llvm/Support/CrashRecoveryContext.h → assembler/ext/include/llvm/Support/CrashRecoveryContext.h
- ext/include/llvm/Support/DJB.h → assembler/ext/include/llvm/Support/DJB.h
- ext/include/llvm/Support/DataTypes.h → assembler/ext/include/llvm/Support/DataTypes.h
- ext/include/llvm/Support/Debug.h → assembler/ext/include/llvm/Support/Debug.h
- ext/include/llvm/Support/Endian.h → assembler/ext/include/llvm/Support/Endian.h
- ext/include/llvm/Support/Errc.h → assembler/ext/include/llvm/Support/Errc.h
- ext/include/llvm/Support/Errno.h → assembler/ext/include/llvm/Support/Errno.h
- ext/include/llvm/Support/Error.h → assembler/ext/include/llvm/Support/Error.h
- ext/include/llvm/Support/ErrorHandling.h → assembler/ext/include/llvm/Support/ErrorHandling.h
- ext/include/llvm/Support/ErrorOr.h → assembler/ext/include/llvm/Support/ErrorOr.h
- ext/include/llvm/Support/FileOutputBuffer.h → assembler/ext/include/llvm/Support/FileOutputBuffer.h
- ext/include/llvm/Support/FileSystem.h → assembler/ext/include/llvm/Support/FileSystem.h
- ext/include/llvm/Support/FileUtilities.h → assembler/ext/include/llvm/Support/FileUtilities.h
- ext/include/llvm/Support/Format.h → assembler/ext/include/llvm/Support/Format.h
- ext/include/llvm/Support/FormatAdapters.h → assembler/ext/include/llvm/Support/FormatAdapters.h
- ext/include/llvm/Support/FormatCommon.h → assembler/ext/include/llvm/Support/FormatCommon.h
- ext/include/llvm/Support/FormatProviders.h → assembler/ext/include/llvm/Support/FormatProviders.h
- ext/include/llvm/Support/FormatVariadic.h → assembler/ext/include/llvm/Support/FormatVariadic.h
- ext/include/llvm/Support/FormatVariadicDetails.h → assembler/ext/include/llvm/Support/FormatVariadicDetails.h
- ext/include/llvm/Support/Host.h → assembler/ext/include/llvm/Support/Host.h
- ext/include/llvm/Support/JSON.h → assembler/ext/include/llvm/Support/JSON.h
- ext/include/llvm/Support/LEB128.h → assembler/ext/include/llvm/Support/LEB128.h
- ext/include/llvm/Support/LineIterator.h → assembler/ext/include/llvm/Support/LineIterator.h
- ext/include/llvm/Support/Locale.h → assembler/ext/include/llvm/Support/Locale.h
- ext/include/llvm/Support/MD5.h → assembler/ext/include/llvm/Support/MD5.h
- ext/include/llvm/Support/ManagedStatic.h → assembler/ext/include/llvm/Support/ManagedStatic.h
- ext/include/llvm/Support/MathExtras.h → assembler/ext/include/llvm/Support/MathExtras.h
- ext/include/llvm/Support/MemAlloc.h → assembler/ext/include/llvm/Support/MemAlloc.h
- ext/include/llvm/Support/Memory.h → assembler/ext/include/llvm/Support/Memory.h
- ext/include/llvm/Support/MemoryBuffer.h → assembler/ext/include/llvm/Support/MemoryBuffer.h
- ext/include/llvm/Support/Mutex.h → assembler/ext/include/llvm/Support/Mutex.h
- ext/include/llvm/Support/NativeFormatting.h → assembler/ext/include/llvm/Support/NativeFormatting.h
- ext/include/llvm/Support/Path.h → assembler/ext/include/llvm/Support/Path.h
- ext/include/llvm/Support/PointerLikeTypeTraits.h → assembler/ext/include/llvm/Support/PointerLikeTypeTraits.h
- ext/include/llvm/Support/Process.h → assembler/ext/include/llvm/Support/Process.h
- ext/include/llvm/Support/Program.h → assembler/ext/include/llvm/Support/Program.h
- ext/include/llvm/Support/Regex.h → assembler/ext/include/llvm/Support/Regex.h
- ext/include/llvm/Support/ReverseIteration.h → assembler/ext/include/llvm/Support/ReverseIteration.h
- ext/include/llvm/Support/SMLoc.h → assembler/ext/include/llvm/Support/SMLoc.h
- ext/include/llvm/Support/SaveAndRestore.h → assembler/ext/include/llvm/Support/SaveAndRestore.h
- ext/include/llvm/Support/Signals.h → assembler/ext/include/llvm/Support/Signals.h
- ext/include/llvm/Support/SmallVectorMemoryBuffer.h → assembler/ext/include/llvm/Support/SmallVectorMemoryBuffer.h
- ext/include/llvm/Support/SourceMgr.h → assembler/ext/include/llvm/Support/SourceMgr.h
- ext/include/llvm/Support/StringSaver.h → assembler/ext/include/llvm/Support/StringSaver.h
- ext/include/llvm/Support/SwapByteOrder.h → assembler/ext/include/llvm/Support/SwapByteOrder.h
- ext/include/llvm/Support/ThreadLocal.h → assembler/ext/include/llvm/Support/ThreadLocal.h
- ext/include/llvm/Support/Threading.h → assembler/ext/include/llvm/Support/Threading.h
- ext/include/llvm/Support/TimeProfiler.h → assembler/ext/include/llvm/Support/TimeProfiler.h
- ext/include/llvm/Support/TrailingObjects.h → assembler/ext/include/llvm/Support/TrailingObjects.h
- ext/include/llvm/Support/Unicode.h → assembler/ext/include/llvm/Support/Unicode.h
- ext/include/llvm/Support/UnicodeCharRanges.h → assembler/ext/include/llvm/Support/UnicodeCharRanges.h
- ext/include/llvm/Support/WindowsError.h → assembler/ext/include/llvm/Support/WindowsError.h
- ext/include/llvm/Support/WithColor.h → assembler/ext/include/llvm/Support/WithColor.h
- ext/include/llvm/Support/YAMLParser.h → assembler/ext/include/llvm/Support/YAMLParser.h
- ext/include/llvm/Support/YAMLTraits.h → assembler/ext/include/llvm/Support/YAMLTraits.h
- ext/include/llvm/Support/raw_os_ostream.h → assembler/ext/include/llvm/Support/raw_os_ostream.h
- ext/include/llvm/Support/raw_ostream.h → assembler/ext/include/llvm/Support/raw_ostream.h
- ext/include/llvm/Support/thread.h → assembler/ext/include/llvm/Support/thread.h
- ext/include/llvm/Support/type_traits.h → assembler/ext/include/llvm/Support/type_traits.h
- + assembler/ext/include/parallel_hashmap/meminfo.h
- + assembler/ext/include/parallel_hashmap/phmap.h
- + assembler/ext/include/parallel_hashmap/phmap_base.h
- + assembler/ext/include/parallel_hashmap/phmap_bits.h
- + assembler/ext/include/parallel_hashmap/phmap_config.h
- + assembler/ext/include/parallel_hashmap/phmap_fwd_decl.h
- + assembler/ext/include/parallel_hashmap/phmap_utils.h
- + assembler/ext/include/sparsehash/dense_hash_map
- + assembler/ext/include/sparsehash/dense_hash_set
- + assembler/ext/include/sparsehash/internal/densehashtable.h
- + assembler/ext/include/sparsehash/internal/hashtable-common.h
- + assembler/ext/include/sparsehash/internal/libc_allocator_with_realloc.h
- + assembler/ext/include/sparsehash/internal/sparseconfig.h
- + assembler/ext/include/sparsehash/internal/sparsehashtable.h
- + assembler/ext/include/sparsehash/sparse_hash_map
- + assembler/ext/include/sparsehash/sparse_hash_set
- + assembler/ext/include/sparsehash/sparsetable
- + assembler/ext/include/sparsehash/template_util.h
- + assembler/ext/include/sparsehash/type_traits.h
- ext/include/teamcity_gtest/teamcity_gtest.h → assembler/ext/include/teamcity_gtest/teamcity_gtest.h
- ext/include/teamcity_gtest/teamcity_messages.h → assembler/ext/include/teamcity_gtest/teamcity_messages.h
- ext/include/threadpool/LICENSE → assembler/ext/include/threadpool/LICENSE
- ext/include/threadpool/hooks.hpp → assembler/ext/include/threadpool/hooks.hpp
- ext/include/threadpool/threadpool.hpp → assembler/ext/include/threadpool/threadpool.hpp
- + assembler/ext/include/tsl/array-hash/array_growth_policy.h
- + assembler/ext/include/tsl/array-hash/array_hash.h
- + assembler/ext/include/tsl/array-hash/array_map.h
- + assembler/ext/include/tsl/array-hash/array_set.h
- + assembler/ext/include/tsl/htrie_hash.h
- + assembler/ext/include/tsl/htrie_map.h
- + assembler/ext/include/tsl/htrie_set.h
- + assembler/ext/include/xxh/xxhash.h
- ext/src/.gitignore → assembler/ext/src/.gitignore
- + assembler/ext/src/CMakeLists.txt
- + assembler/ext/src/ConsensusCore/AffineAlignment.cpp
- + assembler/ext/src/ConsensusCore/CMakeLists.txt
- + assembler/ext/src/ConsensusCore/Coverage.cpp
- + assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp
- + assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp
- + assembler/ext/src/ConsensusCore/Mutation.cpp
- + assembler/ext/src/ConsensusCore/PairwiseAlignment.cpp
- + assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp
- + assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp
- + assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp
- + assembler/ext/src/ConsensusCore/Sequence.cpp
- + assembler/ext/src/ConsensusCore/Utils.cpp
- + assembler/ext/src/ConsensusCore/Version.cpp
- + assembler/ext/src/bamtools/CMakeLists.txt
- + assembler/ext/src/bamtools/api/BamAlignment.cpp
- + assembler/ext/src/bamtools/api/BamMultiReader.cpp
- + assembler/ext/src/bamtools/api/BamReader.cpp
- + assembler/ext/src/bamtools/api/BamWriter.cpp
- + assembler/ext/src/bamtools/api/CMakeLists.txt
- + assembler/ext/src/bamtools/api/SamHeader.cpp
- + assembler/ext/src/bamtools/api/SamProgram.cpp
- + assembler/ext/src/bamtools/api/SamProgramChain.cpp
- + assembler/ext/src/bamtools/api/SamReadGroup.cpp
- + assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp
- + assembler/ext/src/bamtools/api/SamSequence.cpp
- + assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp
- + assembler/ext/src/bamtools/api/internal/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp
- + assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.h
- + assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h
- + assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp
- + assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.h
- + assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp
- + assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.h
- + assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp
- + assembler/ext/src/bamtools/api/internal/bam/BamReader_p.h
- + assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp
- + assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.h
- + assembler/ext/src/bamtools/api/internal/bam/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp
- + assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.h
- + assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp
- + assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.h
- + assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp
- + assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.h
- + assembler/ext/src/bamtools/api/internal/index/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.h
- + assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/BamFile_p.h
- + assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.h
- + assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/ByteArray_p.h
- + assembler/ext/src/bamtools/api/internal/io/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.h
- + assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.h
- + assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.h
- + assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp
- + assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c
- ext/src/samtools/bgzf.h → assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/block.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.h
- ext/src/samtools/knetfile.c → assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c
- ext/include/samtools/knetfile.h → assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c
- + assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.h
- + assembler/ext/src/bamtools/api/internal/sam/CMakeLists.txt
- + assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp
- + assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.h
- + assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp
- + assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.h
- + assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp
- + assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.h
- + assembler/ext/src/bamtools/api/internal/sam/SamHeaderVersion_p.h
- + assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp
- + assembler/ext/src/bamtools/api/internal/utils/BamException_p.h
- + assembler/ext/src/bamtools/api/internal/utils/CMakeLists.txt
- ext/src/cppformat/CMakeLists.txt → assembler/ext/src/cppformat/CMakeLists.txt
- ext/src/cppformat/format.cc → assembler/ext/src/cppformat/format.cc
- ext/src/cppformat/posix.cc → assembler/ext/src/cppformat/posix.cc
- + assembler/ext/src/easel/CMakeLists.txt
- + assembler/ext/src/easel/INSTALL
- + assembler/ext/src/easel/LICENSE
- + assembler/ext/src/easel/LICENSE.sh.in
- + assembler/ext/src/easel/LICENSE.tag
- ext/src/easel/easel.c → assembler/ext/src/easel/easel.c
- ext/src/easel/easel.h → assembler/ext/src/easel/easel.h
- ext/src/easel/esl_alphabet.c → assembler/ext/src/easel/esl_alphabet.c
- ext/src/easel/esl_alphabet.h → assembler/ext/src/easel/esl_alphabet.h
- + assembler/ext/src/easel/esl_avx.c
- + assembler/ext/src/easel/esl_avx.h
- ext/src/easel/esl_buffer.c → assembler/ext/src/easel/esl_buffer.c
- ext/src/easel/esl_buffer.h → assembler/ext/src/easel/esl_buffer.h
- ext/src/easel/esl_cluster.c → assembler/ext/src/easel/esl_cluster.c
- + assembler/ext/src/easel/esl_cluster.h
- ext/src/easel/esl_composition.c → assembler/ext/src/easel/esl_composition.c
- ext/src/easel/esl_composition.h → assembler/ext/src/easel/esl_composition.h
- + assembler/ext/src/easel/esl_config.h.cmake
- + assembler/ext/src/easel/esl_config.h.in
- + assembler/ext/src/easel/esl_dirichlet.c
- + assembler/ext/src/easel/esl_dirichlet.h
- + assembler/ext/src/easel/esl_distance.c
- + assembler/ext/src/easel/esl_distance.h
- ext/src/easel/esl_dmatrix.c → assembler/ext/src/easel/esl_dmatrix.c
- ext/src/easel/esl_dmatrix.h → assembler/ext/src/easel/esl_dmatrix.h
- ext/src/easel/esl_dsqdata.c → assembler/ext/src/easel/esl_dsqdata.c
- + assembler/ext/src/easel/esl_dsqdata.h
- ext/src/easel/esl_exponential.c → assembler/ext/src/easel/esl_exponential.c
- ext/src/easel/esl_exponential.h → assembler/ext/src/easel/esl_exponential.h
- ext/src/easel/esl_fileparser.c → assembler/ext/src/easel/esl_fileparser.c
- ext/src/easel/esl_fileparser.h → assembler/ext/src/easel/esl_fileparser.h
- + assembler/ext/src/easel/esl_gamma.c
- ext/src/easel/esl_gamma.h → assembler/ext/src/easel/esl_gamma.h
- ext/src/easel/esl_gencode.c → assembler/ext/src/easel/esl_gencode.c
- ext/src/easel/esl_gencode.h → assembler/ext/src/easel/esl_gencode.h
- ext/src/easel/esl_getopts.c → assembler/ext/src/easel/esl_getopts.c
- ext/src/easel/esl_getopts.h → assembler/ext/src/easel/esl_getopts.h
- ext/src/easel/esl_gev.c → assembler/ext/src/easel/esl_gev.c
- ext/src/easel/esl_gev.h → assembler/ext/src/easel/esl_gev.h
- ext/src/easel/esl_gumbel.c → assembler/ext/src/easel/esl_gumbel.c
- ext/src/easel/esl_gumbel.h → assembler/ext/src/easel/esl_gumbel.h
- ext/src/easel/esl_heap.c → assembler/ext/src/easel/esl_heap.c
- ext/src/easel/esl_heap.h → assembler/ext/src/easel/esl_heap.h
- ext/src/easel/esl_histogram.c → assembler/ext/src/easel/esl_histogram.c
- ext/src/easel/esl_histogram.h → assembler/ext/src/easel/esl_histogram.h
- ext/src/easel/esl_hmm.c → assembler/ext/src/easel/esl_hmm.c
- ext/src/easel/esl_hmm.h → assembler/ext/src/easel/esl_hmm.h
- ext/src/easel/esl_hyperexp.c → assembler/ext/src/easel/esl_hyperexp.c
- ext/src/easel/esl_hyperexp.h → assembler/ext/src/easel/esl_hyperexp.h
- ext/src/easel/esl_keyhash.c → assembler/ext/src/easel/esl_keyhash.c
- ext/src/easel/esl_keyhash.h → assembler/ext/src/easel/esl_keyhash.h
- + assembler/ext/src/easel/esl_mem.c
- ext/src/easel/esl_mem.h → assembler/ext/src/easel/esl_mem.h
- + assembler/ext/src/easel/esl_minimizer.c
- + assembler/ext/src/easel/esl_minimizer.h
- ext/src/easel/esl_mixgev.c → assembler/ext/src/easel/esl_mixgev.c
- ext/src/easel/esl_mixgev.h → assembler/ext/src/easel/esl_mixgev.h
- ext/src/easel/esl_mpi.c → assembler/ext/src/easel/esl_mpi.c
- ext/src/easel/esl_mpi.h → assembler/ext/src/easel/esl_mpi.h
- ext/src/easel/esl_msa.c → assembler/ext/src/easel/esl_msa.c
- ext/src/easel/esl_msa.h → assembler/ext/src/easel/esl_msa.h
- ext/src/easel/esl_msacluster.c → assembler/ext/src/easel/esl_msacluster.c
- + assembler/ext/src/easel/esl_msacluster.h
- ext/src/easel/esl_msafile.c → assembler/ext/src/easel/esl_msafile.c
- ext/src/easel/esl_msafile.h → assembler/ext/src/easel/esl_msafile.h
- + assembler/ext/src/easel/esl_msafile.md
- ext/src/easel/esl_msafile2.c → assembler/ext/src/easel/esl_msafile2.c
- ext/src/easel/esl_msafile2.h → assembler/ext/src/easel/esl_msafile2.h
- ext/src/easel/esl_msafile_a2m.c → assembler/ext/src/easel/esl_msafile_a2m.c
- ext/src/easel/esl_msafile_a2m.h → assembler/ext/src/easel/esl_msafile_a2m.h
- ext/src/easel/esl_msafile_afa.c → assembler/ext/src/easel/esl_msafile_afa.c
- ext/src/easel/esl_msafile_afa.h → assembler/ext/src/easel/esl_msafile_afa.h
- ext/src/easel/esl_msafile_clustal.c → assembler/ext/src/easel/esl_msafile_clustal.c
- ext/src/easel/esl_msafile_clustal.h → assembler/ext/src/easel/esl_msafile_clustal.h
- ext/src/easel/esl_msafile_phylip.c → assembler/ext/src/easel/esl_msafile_phylip.c
- ext/src/easel/esl_msafile_phylip.h → assembler/ext/src/easel/esl_msafile_phylip.h
- ext/src/easel/esl_msafile_psiblast.c → assembler/ext/src/easel/esl_msafile_psiblast.c
- ext/src/easel/esl_msafile_psiblast.h → assembler/ext/src/easel/esl_msafile_psiblast.h
- ext/src/easel/esl_msafile_selex.c → assembler/ext/src/easel/esl_msafile_selex.c
- ext/src/easel/esl_msafile_selex.h → assembler/ext/src/easel/esl_msafile_selex.h
- ext/src/easel/esl_msafile_stockholm.c → assembler/ext/src/easel/esl_msafile_stockholm.c
- ext/src/easel/esl_msafile_stockholm.h → assembler/ext/src/easel/esl_msafile_stockholm.h
- ext/src/easel/esl_msashuffle.c → assembler/ext/src/easel/esl_msashuffle.c
- ext/src/easel/esl_msashuffle.h → assembler/ext/src/easel/esl_msashuffle.h
- + assembler/ext/src/easel/esl_msaweight.c
- + assembler/ext/src/easel/esl_msaweight.h
- ext/src/easel/esl_normal.c → assembler/ext/src/easel/esl_normal.c
- ext/src/easel/esl_normal.h → assembler/ext/src/easel/esl_normal.h
- ext/src/easel/esl_paml.c → assembler/ext/src/easel/esl_paml.c
- ext/src/easel/esl_paml.h → assembler/ext/src/easel/esl_paml.h
- ext/src/easel/esl_random.c → assembler/ext/src/easel/esl_random.c
- ext/src/easel/esl_random.h → assembler/ext/src/easel/esl_random.h
- ext/src/easel/esl_randomseq.c → assembler/ext/src/easel/esl_randomseq.c
- ext/src/easel/esl_randomseq.h → assembler/ext/src/easel/esl_randomseq.h
- ext/src/easel/esl_ratematrix.c → assembler/ext/src/easel/esl_ratematrix.c
- ext/src/easel/esl_ratematrix.h → assembler/ext/src/easel/esl_ratematrix.h
- ext/src/easel/esl_recorder.c → assembler/ext/src/easel/esl_recorder.c
- ext/src/easel/esl_recorder.h → assembler/ext/src/easel/esl_recorder.h
- ext/src/easel/esl_regexp.c → assembler/ext/src/easel/esl_regexp.c
- ext/src/easel/esl_regexp.h → assembler/ext/src/easel/esl_regexp.h
- ext/src/easel/esl_rootfinder.c → assembler/ext/src/easel/esl_rootfinder.c
- ext/src/easel/esl_rootfinder.h → assembler/ext/src/easel/esl_rootfinder.h
- ext/src/easel/esl_scorematrix.c → assembler/ext/src/easel/esl_scorematrix.c
- ext/src/easel/esl_scorematrix.h → assembler/ext/src/easel/esl_scorematrix.h
- ext/src/easel/esl_sq.c → assembler/ext/src/easel/esl_sq.c
- ext/src/easel/esl_sq.h → assembler/ext/src/easel/esl_sq.h
- ext/src/easel/esl_sqio.c → assembler/ext/src/easel/esl_sqio.c
- ext/src/easel/esl_sqio.h → assembler/ext/src/easel/esl_sqio.h
- ext/src/easel/esl_sqio_ascii.c → assembler/ext/src/easel/esl_sqio_ascii.c
- ext/src/easel/esl_sqio_ascii.h → assembler/ext/src/easel/esl_sqio_ascii.h
- ext/src/easel/esl_sqio_ncbi.c → assembler/ext/src/easel/esl_sqio_ncbi.c
- ext/src/easel/esl_sqio_ncbi.h → assembler/ext/src/easel/esl_sqio_ncbi.h
- ext/src/easel/esl_sse.c → assembler/ext/src/easel/esl_sse.c
- + assembler/ext/src/easel/esl_sse.h
- ext/src/easel/esl_ssi.c → assembler/ext/src/easel/esl_ssi.c
- ext/src/easel/esl_ssi.h → assembler/ext/src/easel/esl_ssi.h
- ext/src/easel/esl_stack.c → assembler/ext/src/easel/esl_stack.c
- ext/src/easel/esl_stack.h → assembler/ext/src/easel/esl_stack.h
- ext/src/easel/esl_stats.c → assembler/ext/src/easel/esl_stats.c
- ext/src/easel/esl_stats.h → assembler/ext/src/easel/esl_stats.h
- ext/src/easel/esl_stopwatch.c → assembler/ext/src/easel/esl_stopwatch.c
- ext/src/easel/esl_stopwatch.h → assembler/ext/src/easel/esl_stopwatch.h
- ext/src/easel/esl_stretchexp.c → assembler/ext/src/easel/esl_stretchexp.c
- ext/src/easel/esl_stretchexp.h → assembler/ext/src/easel/esl_stretchexp.h
- ext/src/easel/esl_swat.c → assembler/ext/src/easel/esl_swat.c
- ext/src/easel/esl_threads.c → assembler/ext/src/easel/esl_threads.c
- ext/src/easel/esl_threads.h → assembler/ext/src/easel/esl_threads.h
- ext/src/easel/esl_tree.c → assembler/ext/src/easel/esl_tree.c
- ext/src/easel/esl_tree.h → assembler/ext/src/easel/esl_tree.h
- + assembler/ext/src/easel/esl_vectorops.c
- + assembler/ext/src/easel/esl_vectorops.h
- ext/src/easel/esl_vmx.c → assembler/ext/src/easel/esl_vmx.c
- + assembler/ext/src/easel/esl_vmx.h
- ext/src/easel/esl_weibull.c → assembler/ext/src/easel/esl_weibull.c
- ext/src/easel/esl_weibull.h → assembler/ext/src/easel/esl_weibull.h
- ext/src/easel/esl_workqueue.c → assembler/ext/src/easel/esl_workqueue.c
- + assembler/ext/src/easel/esl_workqueue.h
- ext/src/easel/esl_wuss.c → assembler/ext/src/easel/esl_wuss.c
- ext/src/easel/esl_wuss.h → assembler/ext/src/easel/esl_wuss.h
- ext/src/easel/interface_gsl.c → assembler/ext/src/easel/interface_gsl.c
- ext/src/easel/interface_gsl.h → assembler/ext/src/easel/interface_gsl.h
- ext/src/easel/interface_lapack.c → assembler/ext/src/easel/interface_lapack.c
- ext/src/easel/interface_lapack.h → assembler/ext/src/easel/interface_lapack.h
- ext/src/edlib/CMakeLists.txt → assembler/ext/src/edlib/CMakeLists.txt
- ext/src/edlib/edlib.cpp → assembler/ext/src/edlib/edlib.cpp
- + assembler/ext/src/getopt_pp/CMakeLists.txt
- src/projects/mts/getopt_pp/getopt_pp.cpp → assembler/ext/src/getopt_pp/getopt_pp.cpp
- + assembler/ext/src/gfa1/CMakeLists.txt
- + assembler/ext/src/gfa1/gfa.c
- + assembler/ext/src/gfa1/kdq.h
- + assembler/ext/src/gfa1/khash.h
- + assembler/ext/src/gfa1/kseq.h
- + assembler/ext/src/gfa1/ksort.h
- + assembler/ext/src/gfa1/kstring.h
- ext/src/bwa/kvec.h → assembler/ext/src/gfa1/kvec.h
- + assembler/ext/src/googletest/.clang-format
- + assembler/ext/src/googletest/.gitignore
- + assembler/ext/src/googletest/.travis.yml
- + assembler/ext/src/googletest/BUILD.bazel
- + assembler/ext/src/googletest/CMakeLists.txt
- + assembler/ext/src/googletest/CONTRIBUTING.md
- + assembler/ext/src/googletest/LICENSE
- + assembler/ext/src/googletest/README.md
- + assembler/ext/src/googletest/WORKSPACE
- + assembler/ext/src/googletest/appveyor.yml
- + assembler/ext/src/googletest/ci/build-linux-bazel.sh
- + assembler/ext/src/googletest/ci/build-platformio.sh
- + assembler/ext/src/googletest/ci/env-linux.sh
- + assembler/ext/src/googletest/ci/env-osx.sh
- + assembler/ext/src/googletest/ci/get-nprocessors.sh
- + assembler/ext/src/googletest/ci/install-linux.sh
- + assembler/ext/src/googletest/ci/install-osx.sh
- + assembler/ext/src/googletest/ci/install-platformio.sh
- + assembler/ext/src/googletest/ci/log-config.sh
- + assembler/ext/src/googletest/ci/travis.sh
- + assembler/ext/src/googletest/googlemock/CMakeLists.txt
- + assembler/ext/src/googletest/googlemock/CONTRIBUTORS
- + assembler/ext/src/googletest/googlemock/LICENSE
- + assembler/ext/src/googletest/googlemock/README.md
- + assembler/ext/src/googletest/googlemock/cmake/gmock.pc.in
- + assembler/ext/src/googletest/googlemock/cmake/gmock_main.pc.in
- + assembler/ext/src/googletest/googlemock/docs/cheat_sheet.md
- + assembler/ext/src/googletest/googlemock/docs/community_created_documentation.md
- + assembler/ext/src/googletest/googlemock/docs/cook_book.md
- + assembler/ext/src/googletest/googlemock/docs/for_dummies.md
- + assembler/ext/src/googletest/googlemock/docs/gmock_faq.md
- + assembler/ext/src/googletest/googlemock/docs/pump_manual.md
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-actions.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-cardinalities.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-function-mocker.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-generated-actions.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-generated-actions.h.pump
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-matchers.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-more-matchers.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-nice-strict.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock-spec-builders.h
- + assembler/ext/src/googletest/googlemock/include/gmock/gmock.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/custom/README.md
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/custom/gmock-generated-actions.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/custom/gmock-generated-actions.h.pump
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/custom/gmock-matchers.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/custom/gmock-port.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/gmock-port.h
- + assembler/ext/src/googletest/googlemock/include/gmock/internal/gmock-pp.h
- + assembler/ext/src/googletest/googlemock/src/gmock-all.cc
- + assembler/ext/src/googletest/googlemock/src/gmock-cardinalities.cc
- + assembler/ext/src/googletest/googlemock/src/gmock-internal-utils.cc
- + assembler/ext/src/googletest/googlemock/src/gmock-matchers.cc
- + assembler/ext/src/googletest/googlemock/src/gmock-spec-builders.cc
- + assembler/ext/src/googletest/googlemock/src/gmock.cc
- + assembler/ext/src/googletest/googlemock/src/gmock_main.cc
- + assembler/ext/src/googletest/googlemock/test/BUILD.bazel
- + assembler/ext/src/googletest/googlemock/test/gmock-actions_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-cardinalities_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-function-mocker_nc.cc
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- + assembler/ext/src/googletest/googlemock/test/gmock-generated-actions_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-internal-utils_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-matchers_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-more-actions_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-nice-strict_test.cc
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- + assembler/ext/src/googletest/googlemock/test/gmock-pp-string_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-pp_test.cc
- + assembler/ext/src/googletest/googlemock/test/gmock-spec-builders_test.cc
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- + assembler/ext/src/googletest/googlemock/test/gmock_link2_test.cc
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- + assembler/ext/src/googletest/googletest/CONTRIBUTORS
- + assembler/ext/src/googletest/googletest/LICENSE
- + assembler/ext/src/googletest/googletest/README.md
- + assembler/ext/src/googletest/googletest/cmake/Config.cmake.in
- + assembler/ext/src/googletest/googletest/cmake/gtest.pc.in
- + assembler/ext/src/googletest/googletest/cmake/gtest_main.pc.in
- + assembler/ext/src/googletest/googletest/cmake/internal_utils.cmake
- + assembler/ext/src/googletest/googletest/cmake/libgtest.la.in
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- + assembler/ext/src/googletest/googletest/docs/Primer.md
- + assembler/ext/src/googletest/googletest/docs/Samples.md
- + assembler/ext/src/googletest/googletest/docs/advanced.md
- + assembler/ext/src/googletest/googletest/docs/pkgconfig.md
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-death-test.h
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- + assembler/ext/src/googletest/googletest/include/gtest/gtest-message.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-param-test.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-printers.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-spi.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-test-part.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest-typed-test.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest_pred_impl.h
- + assembler/ext/src/googletest/googletest/include/gtest/gtest_prod.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/custom/README.md
- + assembler/ext/src/googletest/googletest/include/gtest/internal/custom/gtest-port.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/custom/gtest-printers.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/custom/gtest.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-filepath.h
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- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-param-util.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-port-arch.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-port.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-string.h
- + assembler/ext/src/googletest/googletest/include/gtest/internal/gtest-type-util.h
- + assembler/ext/src/googletest/googletest/samples/prime_tables.h
- + assembler/ext/src/googletest/googletest/samples/sample1.cc
- + assembler/ext/src/googletest/googletest/samples/sample1.h
- + assembler/ext/src/googletest/googletest/samples/sample10_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample1_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample2.cc
- + assembler/ext/src/googletest/googletest/samples/sample2.h
- + assembler/ext/src/googletest/googletest/samples/sample2_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample3-inl.h
- + assembler/ext/src/googletest/googletest/samples/sample3_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample4.cc
- + assembler/ext/src/googletest/googletest/samples/sample4.h
- + assembler/ext/src/googletest/googletest/samples/sample4_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample5_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample6_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample7_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample8_unittest.cc
- + assembler/ext/src/googletest/googletest/samples/sample9_unittest.cc
- + assembler/ext/src/googletest/googletest/src/gtest-all.cc
- + assembler/ext/src/googletest/googletest/src/gtest-death-test.cc
- + assembler/ext/src/googletest/googletest/src/gtest-filepath.cc
- + assembler/ext/src/googletest/googletest/src/gtest-internal-inl.h
- + assembler/ext/src/googletest/googletest/src/gtest-matchers.cc
- + assembler/ext/src/googletest/googletest/src/gtest-port.cc
- + assembler/ext/src/googletest/googletest/src/gtest-printers.cc
- + assembler/ext/src/googletest/googletest/src/gtest-test-part.cc
- + assembler/ext/src/googletest/googletest/src/gtest-typed-test.cc
- + assembler/ext/src/googletest/googletest/src/gtest.cc
- + assembler/ext/src/googletest/googletest/src/gtest_main.cc
- + assembler/ext/src/googletest/googletest/test/BUILD.bazel
- + assembler/ext/src/googletest/googletest/test/googletest-break-on-failure-unittest.py
- + assembler/ext/src/googletest/googletest/test/googletest-break-on-failure-unittest_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-catch-exceptions-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-catch-exceptions-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-color-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-color-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-death-test-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-death-test_ex_test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-env-var-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-env-var-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-failfast-unittest.py
- + assembler/ext/src/googletest/googletest/test/googletest-failfast-unittest_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-filepath-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-filter-unittest.py
- + assembler/ext/src/googletest/googletest/test/googletest-filter-unittest_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-json-outfiles-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-json-output-unittest.py
- + assembler/ext/src/googletest/googletest/test/googletest-list-tests-unittest.py
- + assembler/ext/src/googletest/googletest/test/googletest-list-tests-unittest_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-listener-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-message-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-options-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-output-test-golden-lin.txt
- + assembler/ext/src/googletest/googletest/test/googletest-output-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-output-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-invalid-name1-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-invalid-name1-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-invalid-name2-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-invalid-name2-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-param-test-test.h
- + assembler/ext/src/googletest/googletest/test/googletest-param-test2-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-port-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-printers-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-setuptestsuite-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-setuptestsuite-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-shuffle-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-shuffle-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-test-part-test.cc
- + assembler/ext/src/googletest/googletest/test/googletest-throw-on-failure-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-throw-on-failure-test_.cc
- + assembler/ext/src/googletest/googletest/test/googletest-uninitialized-test.py
- + assembler/ext/src/googletest/googletest/test/googletest-uninitialized-test_.cc
- + assembler/ext/src/googletest/googletest/test/gtest-typed-test2_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest-typed-test_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest-typed-test_test.h
- + assembler/ext/src/googletest/googletest/test/gtest-unittest-api_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_all_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_assert_by_exception_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_environment_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_help_test.py
- + assembler/ext/src/googletest/googletest/test/gtest_help_test_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_json_test_utils.py
- + assembler/ext/src/googletest/googletest/test/gtest_list_output_unittest.py
- + assembler/ext/src/googletest/googletest/test/gtest_list_output_unittest_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_main_unittest.cc
- + assembler/ext/src/googletest/googletest/test/gtest_no_test_unittest.cc
- + assembler/ext/src/googletest/googletest/test/gtest_pred_impl_unittest.cc
- + assembler/ext/src/googletest/googletest/test/gtest_premature_exit_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_prod_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_repeat_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_skip_check_output_test.py
- + assembler/ext/src/googletest/googletest/test/gtest_skip_environment_check_output_test.py
- + assembler/ext/src/googletest/googletest/test/gtest_skip_in_environment_setup_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_skip_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_sole_header_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_stress_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_test_macro_stack_footprint_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_test_utils.py
- + assembler/ext/src/googletest/googletest/test/gtest_testbridge_test.py
- + assembler/ext/src/googletest/googletest/test/gtest_testbridge_test_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_throw_on_failure_ex_test.cc
- + assembler/ext/src/googletest/googletest/test/gtest_unittest.cc
- + assembler/ext/src/googletest/googletest/test/gtest_xml_outfile1_test_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_xml_outfile2_test_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_xml_outfiles_test.py
- + assembler/ext/src/googletest/googletest/test/gtest_xml_output_unittest.py
- + assembler/ext/src/googletest/googletest/test/gtest_xml_output_unittest_.cc
- + assembler/ext/src/googletest/googletest/test/gtest_xml_test_utils.py
- + assembler/ext/src/googletest/googletest/test/production.cc
- + assembler/ext/src/googletest/googletest/test/production.h
- + assembler/ext/src/googletest/library.json
- + assembler/ext/src/googletest/platformio.ini
- ext/src/gqf/CMakeLists.txt → assembler/ext/src/gqf/CMakeLists.txt
- ext/src/gqf/gqf.c → assembler/ext/src/gqf/gqf.c
- + assembler/ext/src/hmmer/CMakeLists.txt
- ext/src/hmmer/LICENSE → assembler/ext/src/hmmer/LICENSE
- ext/src/hmmer/libdivsufsort/AUTHORS → assembler/ext/src/hmmer/libdivsufsort/AUTHORS
- ext/src/hmmer/libdivsufsort/COPYING → assembler/ext/src/hmmer/libdivsufsort/COPYING
- ext/src/hmmer/libdivsufsort/Makefile.in → assembler/ext/src/hmmer/libdivsufsort/Makefile.in
- ext/src/hmmer/libdivsufsort/README → assembler/ext/src/hmmer/libdivsufsort/README
- ext/src/hmmer/libdivsufsort/VERSION → assembler/ext/src/hmmer/libdivsufsort/VERSION
- ext/src/hmmer/libdivsufsort/divsufsort.c → assembler/ext/src/hmmer/libdivsufsort/divsufsort.c
- ext/src/hmmer/libdivsufsort/divsufsort.h.in → assembler/ext/src/hmmer/libdivsufsort/divsufsort.h.in
- + assembler/ext/src/hmmer/src/Makefile.in
- ext/src/hmmer/src/alimask.c → assembler/ext/src/hmmer/src/alimask.c
- ext/src/hmmer/src/build.c → assembler/ext/src/hmmer/src/build.c
- ext/src/hmmer/src/cachedb.c → assembler/ext/src/hmmer/src/cachedb.c
- ext/src/hmmer/src/cachedb.h → assembler/ext/src/hmmer/src/cachedb.h
- ext/src/hmmer/src/emit.c → assembler/ext/src/hmmer/src/emit.c
- ext/src/hmmer/src/errors.c → assembler/ext/src/hmmer/src/errors.c
- ext/src/hmmer/src/evalues.c → assembler/ext/src/hmmer/src/evalues.c
- ext/src/hmmer/src/eweight.c → assembler/ext/src/hmmer/src/eweight.c
- ext/src/hmmer/src/fm_alphabet.c → assembler/ext/src/hmmer/src/fm_alphabet.c
- ext/src/hmmer/src/fm_general.c → assembler/ext/src/hmmer/src/fm_general.c
- ext/src/hmmer/src/fm_sse.c → assembler/ext/src/hmmer/src/fm_sse.c
- ext/src/hmmer/src/fm_ssv.c → assembler/ext/src/hmmer/src/fm_ssv.c
- ext/src/hmmer/src/generic_decoding.c → assembler/ext/src/hmmer/src/generic_decoding.c
- ext/src/hmmer/src/generic_fwdback.c → assembler/ext/src/hmmer/src/generic_fwdback.c
- ext/src/hmmer/src/generic_fwdback_banded.c → assembler/ext/src/hmmer/src/generic_fwdback_banded.c
- ext/src/hmmer/src/generic_fwdback_chk.c → assembler/ext/src/hmmer/src/generic_fwdback_chk.c
- ext/src/hmmer/src/generic_fwdback_rescaled.c → assembler/ext/src/hmmer/src/generic_fwdback_rescaled.c
- ext/src/hmmer/src/generic_msv.c → assembler/ext/src/hmmer/src/generic_msv.c
- ext/src/hmmer/src/generic_null2.c → assembler/ext/src/hmmer/src/generic_null2.c
- ext/src/hmmer/src/generic_optacc.c → assembler/ext/src/hmmer/src/generic_optacc.c
- ext/src/hmmer/src/generic_stotrace.c → assembler/ext/src/hmmer/src/generic_stotrace.c
- ext/src/hmmer/src/generic_viterbi.c → assembler/ext/src/hmmer/src/generic_viterbi.c
- ext/src/hmmer/src/generic_vtrace.c → assembler/ext/src/hmmer/src/generic_vtrace.c
- ext/src/hmmer/src/h2_io.c → assembler/ext/src/hmmer/src/h2_io.c
- ext/src/hmmer/src/heatmap.c → assembler/ext/src/hmmer/src/heatmap.c
- ext/src/hmmer/src/hmmalign.c → assembler/ext/src/hmmer/src/hmmalign.c
- ext/src/hmmer/src/hmmbuild.c → assembler/ext/src/hmmer/src/hmmbuild.c
- ext/src/hmmer/src/hmmc2.c → assembler/ext/src/hmmer/src/hmmc2.c
- ext/src/hmmer/src/hmmconvert.c → assembler/ext/src/hmmer/src/hmmconvert.c
- ext/src/hmmer/src/hmmdmstr.c → assembler/ext/src/hmmer/src/hmmdmstr.c
- ext/src/hmmer/src/hmmdutils.c → assembler/ext/src/hmmer/src/hmmdutils.c
- ext/src/hmmer/src/hmmdwrkr.c → assembler/ext/src/hmmer/src/hmmdwrkr.c
- ext/src/hmmer/src/hmmemit.c → assembler/ext/src/hmmer/src/hmmemit.c
- ext/src/hmmer/src/hmmer.c → assembler/ext/src/hmmer/src/hmmer.c
- ext/src/hmmer/src/hmmer.h → assembler/ext/src/hmmer/src/hmmer.h
- ext/src/hmmer/src/hmmerfm-exactmatch.c → assembler/ext/src/hmmer/src/hmmerfm-exactmatch.c
- ext/src/hmmer/src/hmmfetch.c → assembler/ext/src/hmmer/src/hmmfetch.c
- ext/src/hmmer/src/hmmlogo.c → assembler/ext/src/hmmer/src/hmmlogo.c
- ext/src/hmmer/src/hmmpgmd.c → assembler/ext/src/hmmer/src/hmmpgmd.c
- ext/src/hmmer/src/hmmpgmd.h → assembler/ext/src/hmmer/src/hmmpgmd.h
- + assembler/ext/src/hmmer/src/hmmpgmd2msa.c
- ext/src/hmmer/src/hmmpgmd_client_example.pl → assembler/ext/src/hmmer/src/hmmpgmd_client_example.pl
- + assembler/ext/src/hmmer/src/hmmpress.c
- ext/src/hmmer/src/hmmpress.itest.pl → assembler/ext/src/hmmer/src/hmmpress.itest.pl
- ext/src/hmmer/src/hmmscan.c → assembler/ext/src/hmmer/src/hmmscan.c
- ext/src/hmmer/src/hmmsearch.c → assembler/ext/src/hmmer/src/hmmsearch.c
- ext/src/hmmer/src/hmmsim.c → assembler/ext/src/hmmer/src/hmmsim.c
- + assembler/ext/src/hmmer/src/hmmstat.c
- + assembler/ext/src/hmmer/src/impl_dummy/Makefile.in
- + assembler/ext/src/hmmer/src/impl_dummy/decoding.c
- + assembler/ext/src/hmmer/src/impl_dummy/fwdback.c
- + assembler/ext/src/hmmer/src/impl_dummy/impl_dummy.h
- + assembler/ext/src/hmmer/src/impl_dummy/io.c
- + assembler/ext/src/hmmer/src/impl_dummy/mpi.c
- + assembler/ext/src/hmmer/src/impl_dummy/msvfilter.c
- + assembler/ext/src/hmmer/src/impl_dummy/null2.c
- + assembler/ext/src/hmmer/src/impl_dummy/optacc.c
- + assembler/ext/src/hmmer/src/impl_dummy/p7_omx.c
- + assembler/ext/src/hmmer/src/impl_dummy/p7_oprofile.c
- + assembler/ext/src/hmmer/src/impl_dummy/stotrace.c
- + assembler/ext/src/hmmer/src/impl_dummy/vitfilter.c
- + assembler/ext/src/hmmer/src/impl_dummy/vitscore.c
- ext/src/hmmer/src/impl_sse/00MANIFEST → assembler/ext/src/hmmer/src/impl_sse/00MANIFEST
- + assembler/ext/src/hmmer/src/impl_sse/Makefile.in
- + assembler/ext/src/hmmer/src/impl_sse/decoding.c
- ext/src/hmmer/src/impl_sse/fbparsers.tex → assembler/ext/src/hmmer/src/impl_sse/fbparsers.tex
- + assembler/ext/src/hmmer/src/impl_sse/fwdback.c
- ext/src/hmmer/src/impl_sse/impl_sse.h → assembler/ext/src/hmmer/src/impl_sse/impl_sse.h
- + assembler/ext/src/hmmer/src/impl_sse/io.c
- + assembler/ext/src/hmmer/src/impl_sse/mpi.c
- + assembler/ext/src/hmmer/src/impl_sse/msvfilter.c
- + assembler/ext/src/hmmer/src/impl_sse/null2.c
- + assembler/ext/src/hmmer/src/impl_sse/optacc.c
- ext/src/hmmer/src/impl_sse/p7_omx.ai → assembler/ext/src/hmmer/src/impl_sse/p7_omx.ai
- + assembler/ext/src/hmmer/src/impl_sse/p7_omx.c
- + assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c
- + assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c
- + assembler/ext/src/hmmer/src/impl_sse/stotrace.c
- + assembler/ext/src/hmmer/src/impl_sse/vitfilter.c
- + assembler/ext/src/hmmer/src/impl_sse/vitscore.c
- ext/src/hmmer/src/impl_vmx/00MANIFEST → assembler/ext/src/hmmer/src/impl_vmx/00MANIFEST
- + assembler/ext/src/hmmer/src/impl_vmx/Makefile.in
- + assembler/ext/src/hmmer/src/impl_vmx/decoding.c
- + assembler/ext/src/hmmer/src/impl_vmx/fwdback.c
- ext/src/hmmer/src/impl_vmx/impl_vmx.h → assembler/ext/src/hmmer/src/impl_vmx/impl_vmx.h
- + assembler/ext/src/hmmer/src/impl_vmx/io.c
- + assembler/ext/src/hmmer/src/impl_vmx/mpi.c
- + assembler/ext/src/hmmer/src/impl_vmx/msvfilter.c
- + assembler/ext/src/hmmer/src/impl_vmx/null2.c
- + assembler/ext/src/hmmer/src/impl_vmx/optacc.c
- + assembler/ext/src/hmmer/src/impl_vmx/p7_omx.c
- + assembler/ext/src/hmmer/src/impl_vmx/p7_oprofile.c
- + assembler/ext/src/hmmer/src/impl_vmx/stotrace.c
- + assembler/ext/src/hmmer/src/impl_vmx/vitfilter.c
- + assembler/ext/src/hmmer/src/impl_vmx/vitscore.c
- ext/src/hmmer/src/itest_brute.c → assembler/ext/src/hmmer/src/itest_brute.c
- ext/src/hmmer/src/jackhmmer.c → assembler/ext/src/hmmer/src/jackhmmer.c
- ext/src/hmmer/src/logsum.c → assembler/ext/src/hmmer/src/logsum.c
- ext/src/hmmer/src/makehmmerdb.c → assembler/ext/src/hmmer/src/makehmmerdb.c
- ext/src/hmmer/src/modelconfig.c → assembler/ext/src/hmmer/src/modelconfig.c
- ext/src/hmmer/src/modelstats.c → assembler/ext/src/hmmer/src/modelstats.c
- ext/src/hmmer/src/mpisupport.c → assembler/ext/src/hmmer/src/mpisupport.c
- ext/src/hmmer/src/nhmmer.c → assembler/ext/src/hmmer/src/nhmmer.c
- ext/src/hmmer/src/nhmmscan.c → assembler/ext/src/hmmer/src/nhmmscan.c
- + assembler/ext/src/hmmer/src/p7_alidisplay.c
- ext/src/hmmer/src/p7_bg.c → assembler/ext/src/hmmer/src/p7_bg.c
- ext/src/hmmer/src/p7_builder.c → assembler/ext/src/hmmer/src/p7_builder.c
- ext/src/hmmer/src/p7_config.h.cmake → assembler/ext/src/hmmer/src/p7_config.h.cmake
- ext/src/hmmer/src/p7_config.h.in → assembler/ext/src/hmmer/src/p7_config.h.in
- ext/src/hmmer/src/p7_domaindef.c → assembler/ext/src/hmmer/src/p7_domaindef.c
- ext/src/hmmer/src/p7_gbands.c → assembler/ext/src/hmmer/src/p7_gbands.c
- ext/src/hmmer/src/p7_gbands.h → assembler/ext/src/hmmer/src/p7_gbands.h
- ext/src/hmmer/src/p7_gmx.c → assembler/ext/src/hmmer/src/p7_gmx.c
- ext/src/hmmer/src/p7_gmxb.c → assembler/ext/src/hmmer/src/p7_gmxb.c
- ext/src/hmmer/src/p7_gmxb.h → assembler/ext/src/hmmer/src/p7_gmxb.h
- ext/src/hmmer/src/p7_gmxchk.c → assembler/ext/src/hmmer/src/p7_gmxchk.c
- ext/src/hmmer/src/p7_gmxchk.h → assembler/ext/src/hmmer/src/p7_gmxchk.h
- ext/src/hmmer/src/p7_hmm.c → assembler/ext/src/hmmer/src/p7_hmm.c
- ext/src/hmmer/src/p7_hmmcache.c → assembler/ext/src/hmmer/src/p7_hmmcache.c
- ext/src/hmmer/src/p7_hmmcache.h → assembler/ext/src/hmmer/src/p7_hmmcache.h
- ext/src/hmmer/src/p7_hmmfile.c → assembler/ext/src/hmmer/src/p7_hmmfile.c
- ext/src/hmmer/src/p7_hmmwindow.c → assembler/ext/src/hmmer/src/p7_hmmwindow.c
- ext/src/hmmer/src/p7_null3.c → assembler/ext/src/hmmer/src/p7_null3.c
- ext/src/hmmer/src/p7_pipeline.c → assembler/ext/src/hmmer/src/p7_pipeline.c
- ext/src/hmmer/src/p7_prior.c → assembler/ext/src/hmmer/src/p7_prior.c
- ext/src/hmmer/src/p7_profile.c → assembler/ext/src/hmmer/src/p7_profile.c
- ext/src/hmmer/src/p7_scoredata.c → assembler/ext/src/hmmer/src/p7_scoredata.c
- ext/src/hmmer/src/p7_spensemble.c → assembler/ext/src/hmmer/src/p7_spensemble.c
- ext/src/hmmer/src/p7_tophits.c → assembler/ext/src/hmmer/src/p7_tophits.c
- ext/src/hmmer/src/p7_trace.c → assembler/ext/src/hmmer/src/p7_trace.c
- ext/src/hmmer/src/phmmer.c → assembler/ext/src/hmmer/src/phmmer.c
- ext/src/hmmer/src/seqmodel.c → assembler/ext/src/hmmer/src/seqmodel.c
- ext/src/hmmer/src/tracealign.c → assembler/ext/src/hmmer/src/tracealign.c
- ext/src/llvm/APFloat.cpp → assembler/ext/src/llvm/APFloat.cpp
- ext/src/llvm/APInt.cpp → assembler/ext/src/llvm/APInt.cpp
- ext/src/llvm/ARMBuildAttributes.h → assembler/ext/src/llvm/ARMBuildAttributes.h
- ext/src/llvm/Atomic.cpp → assembler/ext/src/llvm/Atomic.cpp
- ext/src/llvm/CMakeLists.txt → assembler/ext/src/llvm/CMakeLists.txt
- ext/src/llvm/CrashRecoveryContext.cpp → assembler/ext/src/llvm/CrashRecoveryContext.cpp
- ext/src/llvm/Debug.cpp → assembler/ext/src/llvm/Debug.cpp
- ext/src/llvm/ELFAttributeParser.h → assembler/ext/src/llvm/ELFAttributeParser.h
- ext/src/llvm/ELFAttributes.h → assembler/ext/src/llvm/ELFAttributes.h
- ext/src/llvm/Errno.cpp → assembler/ext/src/llvm/Errno.cpp
- ext/src/llvm/Error.cpp → assembler/ext/src/llvm/Error.cpp
- ext/src/llvm/ErrorHandling.cpp → assembler/ext/src/llvm/ErrorHandling.cpp
- ext/src/llvm/FoldingSet.cpp → assembler/ext/src/llvm/FoldingSet.cpp
- ext/src/llvm/FormatVariadic.cpp → assembler/ext/src/llvm/FormatVariadic.cpp
- ext/src/llvm/Hashing.cpp → assembler/ext/src/llvm/Hashing.cpp
- ext/src/llvm/Host.cpp → assembler/ext/src/llvm/Host.cpp
- ext/src/llvm/Host.inc → assembler/ext/src/llvm/Host.inc
- ext/src/llvm/JSON.cpp → assembler/ext/src/llvm/JSON.cpp
- ext/src/llvm/LEB128.cpp → assembler/ext/src/llvm/LEB128.cpp
- ext/src/llvm/LineIterator.cpp → assembler/ext/src/llvm/LineIterator.cpp
- ext/src/llvm/Locale.cpp → assembler/ext/src/llvm/Locale.cpp
- ext/src/llvm/MD5.cpp → assembler/ext/src/llvm/MD5.cpp
- ext/src/llvm/ManagedStatic.cpp → assembler/ext/src/llvm/ManagedStatic.cpp
- ext/src/llvm/MemAlloc.cpp → assembler/ext/src/llvm/MemAlloc.cpp
- ext/src/llvm/MemoryBuffer.cpp → assembler/ext/src/llvm/MemoryBuffer.cpp
- ext/src/llvm/NativeFormatting.cpp → assembler/ext/src/llvm/NativeFormatting.cpp
- ext/src/llvm/Path.cpp → assembler/ext/src/llvm/Path.cpp
- ext/src/llvm/Path.inc → assembler/ext/src/llvm/Path.inc
- ext/src/llvm/Process.cpp → assembler/ext/src/llvm/Process.cpp
- ext/src/llvm/Process.inc → assembler/ext/src/llvm/Process.inc
- ext/src/llvm/Program.cpp → assembler/ext/src/llvm/Program.cpp
- ext/src/llvm/Program.inc → assembler/ext/src/llvm/Program.inc
- ext/src/llvm/Regex.cpp → assembler/ext/src/llvm/Regex.cpp
- ext/src/llvm/Signals.cpp → assembler/ext/src/llvm/Signals.cpp
- ext/src/llvm/Signals.inc → assembler/ext/src/llvm/Signals.inc
- ext/src/llvm/SmallVector.cpp → assembler/ext/src/llvm/SmallVector.cpp
- ext/src/llvm/SourceMgr.cpp → assembler/ext/src/llvm/SourceMgr.cpp
- ext/src/llvm/StringExtras.cpp → assembler/ext/src/llvm/StringExtras.cpp
- ext/src/llvm/StringMap.cpp → assembler/ext/src/llvm/StringMap.cpp
- ext/src/llvm/StringRef.cpp → assembler/ext/src/llvm/StringRef.cpp
- ext/src/llvm/StringSaver.cpp → assembler/ext/src/llvm/StringSaver.cpp
- ext/src/llvm/TargetParser.h → assembler/ext/src/llvm/TargetParser.h
- ext/src/llvm/ThreadLocal.cpp → assembler/ext/src/llvm/ThreadLocal.cpp
- ext/src/llvm/ThreadLocal.inc → assembler/ext/src/llvm/ThreadLocal.inc
- ext/src/llvm/Threading.cpp → assembler/ext/src/llvm/Threading.cpp
- ext/src/llvm/Threading.inc → assembler/ext/src/llvm/Threading.inc
- ext/src/llvm/TimeProfiler.cpp → assembler/ext/src/llvm/TimeProfiler.cpp
- ext/src/llvm/Twine.cpp → assembler/ext/src/llvm/Twine.cpp
- ext/src/llvm/Unicode.cpp → assembler/ext/src/llvm/Unicode.cpp
- ext/src/llvm/Unix.h → assembler/ext/src/llvm/Unix.h
- ext/src/llvm/WithColor.cpp → assembler/ext/src/llvm/WithColor.cpp
- ext/src/llvm/X86TargetParser.def → assembler/ext/src/llvm/X86TargetParser.def
- ext/src/llvm/YAMLParser.cpp → assembler/ext/src/llvm/YAMLParser.cpp
- ext/src/llvm/YAMLTraits.cpp → assembler/ext/src/llvm/YAMLTraits.cpp
- ext/src/llvm/raw_os_ostream.cpp → assembler/ext/src/llvm/raw_os_ostream.cpp
- ext/src/llvm/raw_ostream.cpp → assembler/ext/src/llvm/raw_ostream.cpp
- ext/src/llvm/regcomp.c → assembler/ext/src/llvm/regcomp.c
- ext/src/llvm/regengine.inc → assembler/ext/src/llvm/regengine.inc
- ext/src/llvm/regerror.c → assembler/ext/src/llvm/regerror.c
- ext/src/llvm/regex2.h → assembler/ext/src/llvm/regex2.h
- ext/src/llvm/regex_impl.h → assembler/ext/src/llvm/regex_impl.h
- ext/src/llvm/regexec.c → assembler/ext/src/llvm/regexec.c
- ext/src/llvm/regfree.c → assembler/ext/src/llvm/regfree.c
- ext/src/llvm/regstrlcpy.c → assembler/ext/src/llvm/regstrlcpy.c
- ext/src/llvm/regutils.h → assembler/ext/src/llvm/regutils.h
- + assembler/ext/src/mimalloc/.gitattributes
- ext/src/mimalloc/.gitignore → assembler/ext/src/mimalloc/.gitignore
- + assembler/ext/src/mimalloc/CMakeLists.txt
- + assembler/ext/src/mimalloc/LICENSE
- ext/src/mimalloc/cmake/mimalloc-config-version.cmake → assembler/ext/src/mimalloc/cmake/mimalloc-config-version.cmake
- + assembler/ext/src/mimalloc/cmake/mimalloc-config.cmake
- ext/src/mimalloc/include/mimalloc-atomic.h → assembler/ext/src/mimalloc/include/mimalloc-atomic.h
- + assembler/ext/src/mimalloc/include/mimalloc-internal.h
- ext/src/mimalloc/include/mimalloc-new-delete.h → assembler/ext/src/mimalloc/include/mimalloc-new-delete.h
- ext/src/mimalloc/include/mimalloc-override.h → assembler/ext/src/mimalloc/include/mimalloc-override.h
- ext/src/mimalloc/include/mimalloc-types.h → assembler/ext/src/mimalloc/include/mimalloc-types.h
- ext/src/mimalloc/include/mimalloc.h → assembler/ext/src/mimalloc/include/mimalloc.h
- ext/src/mimalloc/readme.md → assembler/ext/src/mimalloc/readme.md
- ext/src/mimalloc/src/alloc-aligned.c → assembler/ext/src/mimalloc/src/alloc-aligned.c
- + assembler/ext/src/mimalloc/src/alloc-override-osx.c
- + assembler/ext/src/mimalloc/src/alloc-override.c
- + assembler/ext/src/mimalloc/src/alloc-posix.c
- + assembler/ext/src/mimalloc/src/alloc-wrap.c
- ext/src/mimalloc/src/alloc.c → assembler/ext/src/mimalloc/src/alloc.c
- ext/src/mimalloc/src/arena.c → assembler/ext/src/mimalloc/src/arena.c
- ext/src/mimalloc/src/bitmap.c → assembler/ext/src/mimalloc/src/bitmap.c
- ext/src/mimalloc/src/bitmap.h → assembler/ext/src/mimalloc/src/bitmap.h
- ext/src/mimalloc/src/heap.c → assembler/ext/src/mimalloc/src/heap.c
- ext/src/mimalloc/src/init.c → assembler/ext/src/mimalloc/src/init.c
- ext/src/mimalloc/src/options.c → assembler/ext/src/mimalloc/src/options.c
- + assembler/ext/src/mimalloc/src/os.c
- ext/src/mimalloc/src/page-queue.c → assembler/ext/src/mimalloc/src/page-queue.c
- ext/src/mimalloc/src/page.c → assembler/ext/src/mimalloc/src/page.c
- ext/src/mimalloc/src/random.c → assembler/ext/src/mimalloc/src/random.c
- ext/src/mimalloc/src/region.c → assembler/ext/src/mimalloc/src/region.c
- + assembler/ext/src/mimalloc/src/segment.c
- ext/src/mimalloc/src/static.c → assembler/ext/src/mimalloc/src/static.c
- ext/src/mimalloc/src/stats.c → assembler/ext/src/mimalloc/src/stats.c
- ext/include/samtools/.gitignore → assembler/ext/src/samtools/.gitignore
- ext/include/samtools/AUTHORS → assembler/ext/src/samtools/AUTHORS
- + assembler/ext/src/samtools/CMakeLists.txt
- + assembler/ext/src/samtools/CMakeLists.txt.save
- ext/include/samtools/COPYING → assembler/ext/src/samtools/COPYING
- ext/include/samtools/ChangeLog.old → assembler/ext/src/samtools/ChangeLog.old
- ext/include/samtools/INSTALL → assembler/ext/src/samtools/INSTALL
- ext/src/samtools/Makefile → assembler/ext/src/samtools/Makefile
- ext/include/samtools/Makefile.mingw → assembler/ext/src/samtools/Makefile.mingw
- ext/include/samtools/NEWS → assembler/ext/src/samtools/NEWS
- ext/src/samtools/bam.c → assembler/ext/src/samtools/bam.c
- ext/include/samtools/bam.h → assembler/ext/src/samtools/bam.h
- ext/src/samtools/bam2bcf.c → assembler/ext/src/samtools/bam2bcf.c
- ext/include/samtools/bam2bcf.h → assembler/ext/src/samtools/bam2bcf.h
- ext/src/samtools/bam2bcf_indel.c → assembler/ext/src/samtools/bam2bcf_indel.c
- ext/src/samtools/bam2depth.c → assembler/ext/src/samtools/bam2depth.c
- ext/src/samtools/bam_aux.c → assembler/ext/src/samtools/bam_aux.c
- ext/src/samtools/bam_cat.c → assembler/ext/src/samtools/bam_cat.c
- ext/src/samtools/bam_color.c → assembler/ext/src/samtools/bam_color.c
- ext/include/samtools/bam_endian.h → assembler/ext/src/samtools/bam_endian.h
- ext/src/samtools/bam_import.c → assembler/ext/src/samtools/bam_import.c
- ext/src/samtools/bam_index.c → assembler/ext/src/samtools/bam_index.c
- ext/src/samtools/bam_lpileup.c → assembler/ext/src/samtools/bam_lpileup.c
- ext/src/samtools/bam_mate.c → assembler/ext/src/samtools/bam_mate.c
- ext/src/samtools/bam_md.c → assembler/ext/src/samtools/bam_md.c
- ext/src/samtools/bam_pileup.c → assembler/ext/src/samtools/bam_pileup.c
- ext/src/samtools/bam_plcmd.c → assembler/ext/src/samtools/bam_plcmd.c
- ext/src/samtools/bam_reheader.c → assembler/ext/src/samtools/bam_reheader.c
- ext/src/samtools/bam_rmdup.c → assembler/ext/src/samtools/bam_rmdup.c
- ext/src/samtools/bam_rmdupse.c → assembler/ext/src/samtools/bam_rmdupse.c
- ext/src/samtools/bam_sort.c → assembler/ext/src/samtools/bam_sort.c
- ext/src/samtools/bam_stat.c → assembler/ext/src/samtools/bam_stat.c
- ext/src/samtools/bam_tview.c → assembler/ext/src/samtools/bam_tview.c
- ext/include/samtools/bam_tview.h → assembler/ext/src/samtools/bam_tview.h
- ext/src/samtools/bam_tview_curses.c → assembler/ext/src/samtools/bam_tview_curses.c
- ext/src/samtools/bam_tview_html.c → assembler/ext/src/samtools/bam_tview_html.c
- ext/src/samtools/bamshuf.c → assembler/ext/src/samtools/bamshuf.c
- ext/src/samtools/bamtk.c → assembler/ext/src/samtools/bamtk.c
- ext/include/samtools/bcftools/Makefile → assembler/ext/src/samtools/bcftools/Makefile
- ext/include/samtools/bcftools/README → assembler/ext/src/samtools/bcftools/README
- ext/include/samtools/bcftools/bcf.c → assembler/ext/src/samtools/bcftools/bcf.c
- ext/include/samtools/bcftools/bcf.h → assembler/ext/src/samtools/bcftools/bcf.h
- ext/include/samtools/bcftools/bcf.tex → assembler/ext/src/samtools/bcftools/bcf.tex
- ext/include/samtools/bcftools/bcf2qcall.c → assembler/ext/src/samtools/bcftools/bcf2qcall.c
- ext/include/samtools/bcftools/bcfutils.c → assembler/ext/src/samtools/bcftools/bcfutils.c
- ext/include/samtools/bcftools/call1.c → assembler/ext/src/samtools/bcftools/call1.c
- ext/include/samtools/bcftools/em.c → assembler/ext/src/samtools/bcftools/em.c
- ext/include/samtools/bcftools/fet.c → assembler/ext/src/samtools/bcftools/fet.c
- ext/include/samtools/bcftools/index.c → assembler/ext/src/samtools/bcftools/index.c
- ext/include/samtools/bcftools/kfunc.c → assembler/ext/src/samtools/bcftools/kfunc.c
- ext/include/samtools/bcftools/kmin.c → assembler/ext/src/samtools/bcftools/kmin.c
- ext/include/samtools/bcftools/kmin.h → assembler/ext/src/samtools/bcftools/kmin.h
- ext/include/samtools/bcftools/main.c → assembler/ext/src/samtools/bcftools/main.c
- ext/include/samtools/bcftools/mut.c → assembler/ext/src/samtools/bcftools/mut.c
- ext/include/samtools/bcftools/prob1.c → assembler/ext/src/samtools/bcftools/prob1.c
- ext/include/samtools/bcftools/prob1.h → assembler/ext/src/samtools/bcftools/prob1.h
- ext/include/samtools/bcftools/vcf.c → assembler/ext/src/samtools/bcftools/vcf.c
- ext/include/samtools/bcftools/vcfutils.pl → assembler/ext/src/samtools/bcftools/vcfutils.pl
- ext/src/samtools/bedcov.c → assembler/ext/src/samtools/bedcov.c
- ext/src/samtools/bedidx.c → assembler/ext/src/samtools/bedidx.c
- ext/src/samtools/bgzf.c → assembler/ext/src/samtools/bgzf.c
- ext/include/samtools/bgzf.h → assembler/ext/src/samtools/bgzf.h
- ext/src/samtools/bgzip.c → assembler/ext/src/samtools/bgzip.c
- ext/src/samtools/cut_target.c → assembler/ext/src/samtools/cut_target.c
- ext/src/samtools/errmod.c → assembler/ext/src/samtools/errmod.c
- ext/include/samtools/errmod.h → assembler/ext/src/samtools/errmod.h
- ext/include/samtools/examples/00README.txt → assembler/ext/src/samtools/examples/00README.txt
- ext/include/samtools/examples/Makefile → assembler/ext/src/samtools/examples/Makefile
- ext/include/samtools/examples/bam2bed.c → assembler/ext/src/samtools/examples/bam2bed.c
- ext/include/samtools/examples/calDepth.c → assembler/ext/src/samtools/examples/calDepth.c
- ext/include/samtools/examples/chk_indel.c → assembler/ext/src/samtools/examples/chk_indel.c
- ext/include/samtools/examples/ex1.fa → assembler/ext/src/samtools/examples/ex1.fa
- ext/include/samtools/examples/ex1.fa.fai → assembler/ext/src/samtools/examples/ex1.fa.fai
- ext/include/samtools/examples/ex1.glf → assembler/ext/src/samtools/examples/ex1.glf
- ext/include/samtools/examples/toy.fa → assembler/ext/src/samtools/examples/toy.fa
- ext/include/samtools/examples/toy.sam → assembler/ext/src/samtools/examples/toy.sam
- ext/src/samtools/faidx.c → assembler/ext/src/samtools/faidx.c
- ext/include/samtools/faidx.h → assembler/ext/src/samtools/faidx.h
- ext/src/samtools/kaln.c → assembler/ext/src/samtools/kaln.c
- ext/include/samtools/kaln.h → assembler/ext/src/samtools/kaln.h
- ext/include/samtools/khash.h → assembler/ext/src/samtools/khash.h
- ext/include/samtools/klist.h → assembler/ext/src/samtools/klist.h
- + assembler/ext/src/samtools/knetfile.c
- ext/src/samtools/knetfile.h → assembler/ext/src/samtools/knetfile.h
- ext/src/samtools/kprobaln.c → assembler/ext/src/samtools/kprobaln.c
- ext/include/samtools/kprobaln.h → assembler/ext/src/samtools/kprobaln.h
- ext/include/samtools/kseq.h → assembler/ext/src/samtools/kseq.h
- ext/include/samtools/ksort.h → assembler/ext/src/samtools/ksort.h
- ext/src/samtools/kstring.c → assembler/ext/src/samtools/kstring.c
- ext/include/samtools/kstring.h → assembler/ext/src/samtools/kstring.h
- ext/src/samtools/misc/CMakeLists.txt → assembler/ext/src/samtools/misc/CMakeLists.txt
- ext/include/samtools/misc/HmmGlocal.java → assembler/ext/src/samtools/misc/HmmGlocal.java
- ext/include/samtools/misc/Makefile → assembler/ext/src/samtools/misc/Makefile
- ext/include/samtools/misc/ace2sam.c → assembler/ext/src/samtools/misc/ace2sam.c
- ext/include/samtools/misc/bamcheck.c → assembler/ext/src/samtools/misc/bamcheck.c
- ext/include/samtools/misc/blast2sam.pl → assembler/ext/src/samtools/misc/blast2sam.pl
- ext/include/samtools/misc/bowtie2sam.pl → assembler/ext/src/samtools/misc/bowtie2sam.pl
- ext/include/samtools/misc/export2sam.pl → assembler/ext/src/samtools/misc/export2sam.pl
- ext/include/samtools/misc/interpolate_sam.pl → assembler/ext/src/samtools/misc/interpolate_sam.pl
- ext/include/samtools/misc/maq2sam.c → assembler/ext/src/samtools/misc/maq2sam.c
- ext/include/samtools/misc/md5.c → assembler/ext/src/samtools/misc/md5.c
- ext/include/samtools/misc/md5.h → assembler/ext/src/samtools/misc/md5.h
- ext/include/samtools/misc/md5fa.c → assembler/ext/src/samtools/misc/md5fa.c
- ext/include/samtools/misc/novo2sam.pl → assembler/ext/src/samtools/misc/novo2sam.pl
- ext/include/samtools/misc/plot-bamcheck → assembler/ext/src/samtools/misc/plot-bamcheck
- ext/include/samtools/misc/psl2sam.pl → assembler/ext/src/samtools/misc/psl2sam.pl
- ext/include/samtools/misc/r2plot.lua → assembler/ext/src/samtools/misc/r2plot.lua
- ext/include/samtools/misc/sam2vcf.pl → assembler/ext/src/samtools/misc/sam2vcf.pl
- ext/include/samtools/misc/samtools.pl → assembler/ext/src/samtools/misc/samtools.pl
- ext/include/samtools/misc/soap2sam.pl → assembler/ext/src/samtools/misc/soap2sam.pl
- ext/include/samtools/misc/varfilter.py → assembler/ext/src/samtools/misc/varfilter.py
- ext/include/samtools/misc/vcfutils.lua → assembler/ext/src/samtools/misc/vcfutils.lua
- ext/include/samtools/misc/wgsim.c → assembler/ext/src/samtools/misc/wgsim.c
- ext/include/samtools/misc/wgsim_eval.pl → assembler/ext/src/samtools/misc/wgsim_eval.pl
- ext/include/samtools/misc/zoom2sam.pl → assembler/ext/src/samtools/misc/zoom2sam.pl
- ext/src/samtools/padding.c → assembler/ext/src/samtools/padding.c
- ext/src/samtools/phase.c → assembler/ext/src/samtools/phase.c
- ext/src/samtools/razf.c → assembler/ext/src/samtools/razf.c
- ext/include/samtools/razf.h → assembler/ext/src/samtools/razf.h
- ext/src/samtools/razip.c → assembler/ext/src/samtools/razip.c
- ext/src/samtools/sam.c → assembler/ext/src/samtools/sam.c
- ext/include/samtools/sam.h → assembler/ext/src/samtools/sam.h
- ext/src/samtools/sam_header.c → assembler/ext/src/samtools/sam_header.c
- ext/include/samtools/sam_header.h → assembler/ext/src/samtools/sam_header.h
- ext/src/samtools/sam_view.c → assembler/ext/src/samtools/sam_view.c
- ext/src/samtools/sample.c → assembler/ext/src/samtools/sample.c
- ext/include/samtools/sample.h → assembler/ext/src/samtools/sample.h
- ext/include/samtools/samtools.1 → assembler/ext/src/samtools/samtools.1
- ext/src/teamcity_gtest/CMakeLists.txt → assembler/ext/src/teamcity_gtest/CMakeLists.txt
- ext/src/teamcity_gtest/LICENSE → assembler/ext/src/teamcity_gtest/LICENSE
- ext/src/teamcity_gtest/teamcity_gtest.cpp → assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp
- ext/src/teamcity_gtest/teamcity_messages.cpp → assembler/ext/src/teamcity_gtest/teamcity_messages.cpp
- + assembler/makefile
- + assembler/manual.html
- src/projects/spades/pipeline/metaplasmidspades.py → assembler/metaplasmidspades.py
- src/projects/spades/pipeline/metaspades.py → assembler/metaspades.py
- src/projects/spades/pipeline/metaviralspades.py → assembler/metaviralspades.py
- src/projects/spades/pipeline/plasmidspades.py → assembler/plasmidspades.py
- + assembler/prepare_cfg
- src/projects/spades/pipeline/rnaspades.py → assembler/rnaspades.py
- + assembler/rnaspades_manual.html
- src/projects/spades/pipeline/rnaviralspades.py → assembler/rnaviralspades.py
- + assembler/run
- src/projects/spades/show_saves.py → assembler/show_saves.py
- src/projects/spades/pipeline/spades.py → assembler/spades.py
- spades_compile.sh → assembler/spades_compile.sh
- + assembler/spades_dev.sh
- src/projects/spades/pipeline/spades_init.py → assembler/spades_init.py
- src/.gitignore → assembler/src/.gitignore
- + assembler/src/CMakeLists.txt
- src/CMakeListsInternal.txt → assembler/src/CMakeListsInternal.txt
- src/cmake/Modules/FindCurses.cmake → assembler/src/cmake/Modules/FindCurses.cmake
- src/cmake/Modules/FindGooglePerfTools.cmake → assembler/src/cmake/Modules/FindGooglePerfTools.cmake
- src/cmake/Modules/FindReadline.cmake → assembler/src/cmake/Modules/FindReadline.cmake
- src/cmake/Modules/GetGitRevisionDescription.cmake → assembler/src/cmake/Modules/GetGitRevisionDescription.cmake
- src/cmake/Modules/GetGitRevisionDescription.cmake.in → assembler/src/cmake/Modules/GetGitRevisionDescription.cmake.in
- src/cmake/deps.cmake → assembler/src/cmake/deps.cmake
- src/cmake/flags.cmake → assembler/src/cmake/flags.cmake
- src/cmake/includes.cmake → assembler/src/cmake/includes.cmake
- src/cmake/libs.cmake → assembler/src/cmake/libs.cmake
- src/cmake/options.cmake → assembler/src/cmake/options.cmake
- + assembler/src/cmake/pack.cmake
- src/cmake/test.cmake → assembler/src/cmake/test.cmake
- + assembler/src/common/CMakeLists.txt
- src/common/adt/array_vector.hpp → assembler/src/common/adt/array_vector.hpp
- src/common/adt/bag.hpp → assembler/src/common/adt/bag.hpp
- + assembler/src/common/adt/bf.hpp
- src/common/adt/chained_iterator.hpp → assembler/src/common/adt/chained_iterator.hpp
- src/common/adt/concurrent_dsu.cpp → assembler/src/common/adt/concurrent_dsu.cpp
- src/common/adt/concurrent_dsu.hpp → assembler/src/common/adt/concurrent_dsu.hpp
- src/common/adt/cqf.hpp → assembler/src/common/adt/cqf.hpp
- src/common/adt/cyclichash.hpp → assembler/src/common/adt/cyclichash.hpp
- + assembler/src/common/adt/filter_iterator.hpp
- src/common/adt/flat_map.hpp → assembler/src/common/adt/flat_map.hpp
- src/common/adt/flat_set.hpp → assembler/src/common/adt/flat_set.hpp
- src/common/adt/hll.hpp → assembler/src/common/adt/hll.hpp
- + assembler/src/common/adt/iterator_range.hpp
- src/common/adt/kmer_vector.hpp → assembler/src/common/adt/kmer_vector.hpp
- src/common/adt/lemiere_mod_reduce.hpp → assembler/src/common/adt/lemiere_mod_reduce.hpp
- src/common/adt/loser_tree.hpp → assembler/src/common/adt/loser_tree.hpp
- + assembler/src/common/adt/pack.hpp
- src/common/adt/pointer_iterator.hpp → assembler/src/common/adt/pointer_iterator.hpp
- src/common/adt/queue_iterator.hpp → assembler/src/common/adt/queue_iterator.hpp
- src/common/adt/small_pod_vector.hpp → assembler/src/common/adt/small_pod_vector.hpp
- + assembler/src/common/assembly_graph/CMakeLists.txt
- src/common/assembly_graph/components/component_filters.hpp → assembler/src/common/assembly_graph/components/component_filters.hpp
- + assembler/src/common/assembly_graph/components/connected_component.cpp
- src/common/assembly_graph/components/connected_component.hpp → assembler/src/common/assembly_graph/components/connected_component.hpp
- src/common/assembly_graph/components/graph_component.hpp → assembler/src/common/assembly_graph/components/graph_component.hpp
- src/common/assembly_graph/components/splitters.hpp → assembler/src/common/assembly_graph/components/splitters.hpp
- src/common/assembly_graph/construction/debruijn_graph_constructor.hpp → assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp
- src/common/assembly_graph/construction/early_simplification.hpp → assembler/src/common/assembly_graph/construction/early_simplification.hpp
- src/common/assembly_graph/construction/early_simplification_extra.hpp → assembler/src/common/assembly_graph/construction/early_simplification_extra.hpp
- src/common/assembly_graph/core/action_handlers.hpp → assembler/src/common/assembly_graph/core/action_handlers.hpp
- src/common/assembly_graph/core/basic_graph_stats.hpp → assembler/src/common/assembly_graph/core/basic_graph_stats.hpp
- src/common/assembly_graph/core/construction_helper.hpp → assembler/src/common/assembly_graph/core/construction_helper.hpp
- + assembler/src/common/assembly_graph/core/coverage.hpp
- + assembler/src/common/assembly_graph/core/debruijn_data.hpp
- src/common/assembly_graph/core/directions.hpp → assembler/src/common/assembly_graph/core/directions.hpp
- + assembler/src/common/assembly_graph/core/graph.hpp
- src/common/assembly_graph/core/graph_core.hpp → assembler/src/common/assembly_graph/core/graph_core.hpp
- src/common/assembly_graph/core/graph_iterators.hpp → assembler/src/common/assembly_graph/core/graph_iterators.hpp
- src/common/assembly_graph/core/id_distributor.cpp → assembler/src/common/assembly_graph/core/id_distributor.cpp
- src/common/assembly_graph/core/id_distributor.hpp → assembler/src/common/assembly_graph/core/id_distributor.hpp
- + assembler/src/common/assembly_graph/core/kmer_iterator.hpp
- src/common/assembly_graph/core/observable_graph.hpp → assembler/src/common/assembly_graph/core/observable_graph.hpp
- src/common/assembly_graph/core/order_and_law.hpp → assembler/src/common/assembly_graph/core/order_and_law.hpp
- + assembler/src/common/assembly_graph/dijkstra/dijkstra_algorithm.hpp
- + assembler/src/common/assembly_graph/dijkstra/dijkstra_helper.hpp
- src/common/assembly_graph/dijkstra/dijkstra_settings.hpp → assembler/src/common/assembly_graph/dijkstra/dijkstra_settings.hpp
- src/common/assembly_graph/dijkstra/length_calculator.hpp → assembler/src/common/assembly_graph/dijkstra/length_calculator.hpp
- src/common/assembly_graph/dijkstra/neighbours_iterator.hpp → assembler/src/common/assembly_graph/dijkstra/neighbours_iterator.hpp
- src/common/assembly_graph/dijkstra/vertex_process_checker.hpp → assembler/src/common/assembly_graph/dijkstra/vertex_process_checker.hpp
- + assembler/src/common/assembly_graph/dijkstra/vertex_put_checker.hpp
- src/common/assembly_graph/graph_support/basic_edge_conditions.hpp → assembler/src/common/assembly_graph/graph_support/basic_edge_conditions.hpp
- src/common/assembly_graph/graph_support/basic_vertex_conditions.hpp → assembler/src/common/assembly_graph/graph_support/basic_vertex_conditions.hpp
- src/common/modules/simplification/chimera_stats.hpp → assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp
- src/common/assembly_graph/graph_support/comparators.hpp → assembler/src/common/assembly_graph/graph_support/comparators.hpp
- + assembler/src/common/assembly_graph/graph_support/contig_output.hpp
- src/common/assembly_graph/graph_support/coverage_filling.hpp → assembler/src/common/assembly_graph/graph_support/coverage_filling.hpp
- src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp → assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp
- src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp → assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp
- src/common/assembly_graph/graph_support/detail_coverage.hpp → assembler/src/common/assembly_graph/graph_support/detail_coverage.hpp
- src/common/assembly_graph/graph_support/edge_removal.hpp → assembler/src/common/assembly_graph/graph_support/edge_removal.hpp
- src/common/assembly_graph/graph_support/genomic_quality.hpp → assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp
- src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp → assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp
- src/common/assembly_graph/graph_support/marks_and_locks.hpp → assembler/src/common/assembly_graph/graph_support/marks_and_locks.hpp
- src/common/assembly_graph/graph_support/parallel_processing.hpp → assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp
- src/common/modules/path_extend/scaff_supplementary.cpp → assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp
- src/common/modules/path_extend/scaff_supplementary.hpp → assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp
- src/common/assembly_graph/handlers/edge_fate_position_handler.hpp → assembler/src/common/assembly_graph/handlers/edge_fate_position_handler.hpp
- src/common/assembly_graph/handlers/edges_position_handler.hpp → assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp
- src/common/assembly_graph/handlers/id_track_handler.hpp → assembler/src/common/assembly_graph/handlers/id_track_handler.hpp
- src/common/assembly_graph/handlers/used_edge_handler.hpp → assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp
- src/common/assembly_graph/index/edge_index_builders.hpp → assembler/src/common/assembly_graph/index/edge_index_builders.hpp
- src/common/assembly_graph/index/edge_info_updater.hpp → assembler/src/common/assembly_graph/index/edge_info_updater.hpp
- src/common/assembly_graph/index/edge_multi_index.hpp → assembler/src/common/assembly_graph/index/edge_multi_index.hpp
- src/common/assembly_graph/index/edge_position_index.hpp → assembler/src/common/assembly_graph/index/edge_position_index.hpp
- src/common/assembly_graph/paths/bidirectional_path.cpp → assembler/src/common/assembly_graph/paths/bidirectional_path.cpp
- src/common/assembly_graph/paths/bidirectional_path.hpp → assembler/src/common/assembly_graph/paths/bidirectional_path.hpp
- src/common/assembly_graph/paths/bidirectional_path_container.hpp → assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp
- + assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp
- + assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp
- src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp → assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp
- src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp → assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp
- src/common/assembly_graph/paths/mapping_path.hpp → assembler/src/common/assembly_graph/paths/mapping_path.hpp
- src/common/assembly_graph/paths/path_finders.hpp → assembler/src/common/assembly_graph/paths/path_finders.hpp
- src/common/assembly_graph/paths/path_processor.hpp → assembler/src/common/assembly_graph/paths/path_processor.hpp
- + assembler/src/common/assembly_graph/paths/path_utils.hpp
- src/common/assembly_graph/stats/picture_dump.hpp → assembler/src/common/assembly_graph/stats/picture_dump.hpp
- src/common/assembly_graph/stats/statistics.hpp → assembler/src/common/assembly_graph/stats/statistics.hpp
- + assembler/src/common/func/function_traits.hpp
- src/common/func/pred.hpp → assembler/src/common/func/pred.hpp
- + assembler/src/common/hmm/CMakeLists.txt
- src/common/hmm/hmmer_fwd.h → assembler/src/common/hmm/hmmer_fwd.h
- src/common/hmm/hmmfile.cpp → assembler/src/common/hmm/hmmfile.cpp
- src/common/hmm/hmmfile.hpp → assembler/src/common/hmm/hmmfile.hpp
- src/common/hmm/hmmmatcher.cpp → assembler/src/common/hmm/hmmmatcher.cpp
- src/common/hmm/hmmmatcher.hpp → assembler/src/common/hmm/hmmmatcher.hpp
- + assembler/src/common/io/CMakeLists.txt
- + assembler/src/common/io/binary/CMakeLists.txt
- + assembler/src/common/io/binary/access.hpp
- src/common/io/binary/basic.hpp → assembler/src/common/io/binary/basic.hpp
- + assembler/src/common/io/binary/binary.hpp
- + assembler/src/common/io/binary/coverage.hpp
- + assembler/src/common/io/binary/edge_index.hpp
- src/common/io/binary/genomic_info.cpp → assembler/src/common/io/binary/genomic_info.cpp
- + assembler/src/common/io/binary/genomic_info.hpp
- + assembler/src/common/io/binary/graph.hpp
- + assembler/src/common/io/binary/graph_pack.cpp
- + assembler/src/common/io/binary/graph_pack.hpp
- src/common/io/binary/io_base.hpp → assembler/src/common/io/binary/io_base.hpp
- + assembler/src/common/io/binary/kmer_mapper.hpp
- src/common/io/binary/long_reads.hpp → assembler/src/common/io/binary/long_reads.hpp
- src/common/io/binary/paired_index.hpp → assembler/src/common/io/binary/paired_index.hpp
- src/common/io/binary/positions.hpp → assembler/src/common/io/binary/positions.hpp
- + assembler/src/common/io/binary/ss_coverage.hpp
- src/common/io/binary/trusted_paths.hpp → assembler/src/common/io/binary/trusted_paths.hpp
- + assembler/src/common/io/binary/types/boost_optional.hpp
- src/common/io/binary/types/phmap.hpp → assembler/src/common/io/binary/types/phmap.hpp
- + assembler/src/common/io/dataset_support/dataset_readers.cpp
- + assembler/src/common/io/dataset_support/dataset_readers.hpp
- src/common/io/dataset_support/read_converter.cpp → assembler/src/common/io/dataset_support/read_converter.cpp
- src/common/io/dataset_support/read_converter.hpp → assembler/src/common/io/dataset_support/read_converter.hpp
- + assembler/src/common/io/graph/CMakeLists.txt
- src/common/io/graph/fastg_writer.cpp → assembler/src/common/io/graph/fastg_writer.cpp
- src/common/io/graph/fastg_writer.hpp → assembler/src/common/io/graph/fastg_writer.hpp
- + assembler/src/common/io/graph/gfa_reader.cpp
- + assembler/src/common/io/graph/gfa_reader.hpp
- + assembler/src/common/io/graph/gfa_writer.cpp
- + assembler/src/common/io/graph/gfa_writer.hpp
- + assembler/src/common/io/kmers/kmer_iterator.hpp
- src/common/io/kmers/mmapped_reader.hpp → assembler/src/common/io/kmers/mmapped_reader.hpp
- src/common/io/kmers/mmapped_writer.hpp → assembler/src/common/io/kmers/mmapped_writer.hpp
- src/common/io/reads/async_read_stream.hpp → assembler/src/common/io/reads/async_read_stream.hpp
- + assembler/src/common/io/reads/binary_converter.cpp
- + assembler/src/common/io/reads/binary_converter.hpp
- + assembler/src/common/io/reads/binary_streams.cpp
- src/common/io/reads/binary_streams.hpp → assembler/src/common/io/reads/binary_streams.hpp
- src/common/io/reads/converting_reader_wrapper.hpp → assembler/src/common/io/reads/converting_reader_wrapper.hpp
- src/common/io/reads/coverage_filtering_read_wrapper.hpp → assembler/src/common/io/reads/coverage_filtering_read_wrapper.hpp
- src/common/io/reads/delegating_reader_wrapper.hpp → assembler/src/common/io/reads/delegating_reader_wrapper.hpp
- src/common/io/reads/edge_sequences_reader.hpp → assembler/src/common/io/reads/edge_sequences_reader.hpp
- src/common/io/reads/fasta_fastq_gz_parser.hpp → assembler/src/common/io/reads/fasta_fastq_gz_parser.hpp
- + assembler/src/common/io/reads/file_read_flags.hpp
- src/common/io/reads/file_reader.hpp → assembler/src/common/io/reads/file_reader.hpp
- src/common/io/reads/filtering_reader_wrapper.hpp → assembler/src/common/io/reads/filtering_reader_wrapper.hpp
- src/common/io/reads/header_naming.hpp → assembler/src/common/io/reads/header_naming.hpp
- + assembler/src/common/io/reads/io_helper.cpp
- + assembler/src/common/io/reads/io_helper.hpp
- src/common/io/reads/ireadstream.hpp → assembler/src/common/io/reads/ireadstream.hpp
- src/common/io/reads/longest_valid_wrapper.hpp → assembler/src/common/io/reads/longest_valid_wrapper.hpp
- src/common/io/reads/modifying_reader_wrapper.hpp → assembler/src/common/io/reads/modifying_reader_wrapper.hpp
- src/common/io/reads/mpmc_bounded.hpp → assembler/src/common/io/reads/mpmc_bounded.hpp
- src/common/io/reads/multifile_reader.hpp → assembler/src/common/io/reads/multifile_reader.hpp
- src/common/io/reads/orientation.hpp → assembler/src/common/io/reads/orientation.hpp
- src/common/io/reads/osequencestream.hpp → assembler/src/common/io/reads/osequencestream.hpp
- src/common/io/reads/paired_read.hpp → assembler/src/common/io/reads/paired_read.hpp
- + assembler/src/common/io/reads/paired_readers.cpp
- + assembler/src/common/io/reads/paired_readers.hpp
- + assembler/src/common/io/reads/parser.cpp
- + assembler/src/common/io/reads/parser.hpp
- src/common/io/reads/rc_reader_wrapper.hpp → assembler/src/common/io/reads/rc_reader_wrapper.hpp
- + assembler/src/common/io/reads/read.hpp
- src/common/io/reads/read_processor.hpp → assembler/src/common/io/reads/read_processor.hpp
- src/common/io/reads/read_stream.hpp → assembler/src/common/io/reads/read_stream.hpp
- src/common/io/reads/read_stream_vector.hpp → assembler/src/common/io/reads/read_stream_vector.hpp
- src/common/io/reads/sequence_reader.hpp → assembler/src/common/io/reads/sequence_reader.hpp
- src/common/io/reads/single_read.hpp → assembler/src/common/io/reads/single_read.hpp
- src/common/io/reads/splitting_wrapper.hpp → assembler/src/common/io/reads/splitting_wrapper.hpp
- src/common/io/reads/vector_reader.hpp → assembler/src/common/io/reads/vector_reader.hpp
- src/common/io/reads/wrapper_collection.hpp → assembler/src/common/io/reads/wrapper_collection.hpp
- + assembler/src/common/io/sam/bam_parser.hpp
- src/common/io/sam/bam_reader.hpp → assembler/src/common/io/sam/bam_reader.hpp
- src/common/io/sam/read.cpp → assembler/src/common/io/sam/read.cpp
- + assembler/src/common/io/sam/read.hpp
- src/common/io/sam/sam_reader.cpp → assembler/src/common/io/sam/sam_reader.cpp
- src/common/io/sam/sam_reader.hpp → assembler/src/common/io/sam/sam_reader.hpp
- src/common/io/utils/edge_namer.hpp → assembler/src/common/io/utils/edge_namer.hpp
- + assembler/src/common/io/utils/id_mapper.hpp
- src/common/math/log.hpp → assembler/src/common/math/log.hpp
- src/common/math/smooth.hpp → assembler/src/common/math/smooth.hpp
- src/common/math/xmath.h → assembler/src/common/math/xmath.h
- + assembler/src/common/modules/CMakeLists.txt
- src/common/alignment/bwa_index.cpp → assembler/src/common/modules/alignment/bwa_index.cpp
- src/common/alignment/bwa_index.hpp → assembler/src/common/modules/alignment/bwa_index.hpp
- src/common/alignment/bwa_sequence_mapper.hpp → assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp
- + assembler/src/common/modules/alignment/edge_index.hpp
- + assembler/src/common/modules/alignment/edge_index_refiller.cpp
- src/common/alignment/edge_index_refiller.hpp → assembler/src/common/modules/alignment/edge_index_refiller.hpp
- src/common/alignment/gap_info.cpp → assembler/src/common/modules/alignment/gap_info.cpp
- src/common/alignment/gap_info.hpp → assembler/src/common/modules/alignment/gap_info.hpp
- src/common/alignment/kmer_map.hpp → assembler/src/common/modules/alignment/kmer_map.hpp
- + assembler/src/common/modules/alignment/kmer_mapper.hpp
- src/common/alignment/kmer_mapper_logger.hpp → assembler/src/common/modules/alignment/kmer_mapper_logger.hpp
- src/common/alignment/long_read_mapper.cpp → assembler/src/common/modules/alignment/long_read_mapper.cpp
- src/common/alignment/long_read_mapper.hpp → assembler/src/common/modules/alignment/long_read_mapper.hpp
- src/common/alignment/long_read_storage.hpp → assembler/src/common/modules/alignment/long_read_storage.hpp
- src/common/alignment/pacbio/g_aligner.cpp → assembler/src/common/modules/alignment/pacbio/g_aligner.cpp
- src/common/alignment/pacbio/g_aligner.hpp → assembler/src/common/modules/alignment/pacbio/g_aligner.hpp
- src/common/alignment/pacbio/gap_dijkstra.cpp → assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp
- src/common/alignment/pacbio/gap_dijkstra.hpp → assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp
- src/common/alignment/pacbio/gap_filler.cpp → assembler/src/common/modules/alignment/pacbio/gap_filler.cpp
- src/common/alignment/pacbio/gap_filler.hpp → assembler/src/common/modules/alignment/pacbio/gap_filler.hpp
- src/common/alignment/pacbio/pac_index.hpp → assembler/src/common/modules/alignment/pacbio/pac_index.hpp
- src/common/alignment/pacbio/pacbio_read_structures.hpp → assembler/src/common/modules/alignment/pacbio/pacbio_read_structures.hpp
- + assembler/src/common/modules/alignment/rna/ss_coverage.hpp
- src/common/alignment/rna/ss_coverage_filler.hpp → assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp
- + assembler/src/common/modules/alignment/sequence_mapper.cpp
- src/common/alignment/sequence_mapper.hpp → assembler/src/common/modules/alignment/sequence_mapper.hpp
- src/common/alignment/sequence_mapper_notifier.cpp → assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp
- src/common/alignment/sequence_mapper_notifier.hpp → assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp
- src/common/modules/chromosome_remover.cpp → assembler/src/common/modules/chromosome_remover.cpp
- src/common/modules/chromosome_remover.hpp → assembler/src/common/modules/chromosome_remover.hpp
- + assembler/src/common/modules/coverage_model/CMakeLists.txt
- src/common/modules/coverage_model/kmer_coverage_model.cpp → assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp
- src/common/modules/coverage_model/kmer_coverage_model.hpp → assembler/src/common/modules/coverage_model/kmer_coverage_model.hpp
- src/common/modules/genome_consistance_checker.cpp → assembler/src/common/modules/genome_consistance_checker.cpp
- src/common/modules/genome_consistance_checker.hpp → assembler/src/common/modules/genome_consistance_checker.hpp
- src/common/modules/graph_construction.hpp → assembler/src/common/modules/graph_construction.hpp
- src/common/modules/graph_read_correction.hpp → assembler/src/common/modules/graph_read_correction.hpp
- src/common/modules/path_extend/.gitignore → assembler/src/common/modules/path_extend/.gitignore
- + assembler/src/common/modules/path_extend/CMakeLists.txt
- src/common/modules/path_extend/extension_chooser.hpp → assembler/src/common/modules/path_extend/extension_chooser.hpp
- src/common/modules/path_extend/gap_analyzer.cpp → assembler/src/common/modules/path_extend/gap_analyzer.cpp
- src/common/modules/path_extend/gap_analyzer.hpp → assembler/src/common/modules/path_extend/gap_analyzer.hpp
- src/common/modules/path_extend/ideal_pair_info.hpp → assembler/src/common/modules/path_extend/ideal_pair_info.hpp
- src/common/modules/path_extend/loop_detector.cpp → assembler/src/common/modules/path_extend/loop_detector.cpp
- src/common/modules/path_extend/loop_traverser.cpp → assembler/src/common/modules/path_extend/loop_traverser.cpp
- src/common/modules/path_extend/loop_traverser.hpp → assembler/src/common/modules/path_extend/loop_traverser.hpp
- src/common/modules/path_extend/overlap_analysis.hpp → assembler/src/common/modules/path_extend/overlap_analysis.hpp
- src/common/modules/path_extend/overlap_remover.cpp → assembler/src/common/modules/path_extend/overlap_remover.cpp
- src/common/modules/path_extend/overlap_remover.hpp → assembler/src/common/modules/path_extend/overlap_remover.hpp
- src/common/modules/path_extend/paired_library.hpp → assembler/src/common/modules/path_extend/paired_library.hpp
- src/common/modules/path_extend/path_deduplicator.hpp → assembler/src/common/modules/path_extend/path_deduplicator.hpp
- src/common/modules/path_extend/path_extender.hpp → assembler/src/common/modules/path_extend/path_extender.hpp
- src/common/modules/path_extend/path_extenders.cpp → assembler/src/common/modules/path_extend/path_extenders.cpp
- src/common/modules/path_extend/path_filter.hpp → assembler/src/common/modules/path_extend/path_filter.hpp
- src/common/modules/path_extend/path_visualizer.hpp → assembler/src/common/modules/path_extend/path_visualizer.hpp
- src/common/configs/pe_config_struct.cpp → assembler/src/common/modules/path_extend/pe_config_struct.cpp
- src/common/configs/pe_config_struct.hpp → assembler/src/common/modules/path_extend/pe_config_struct.hpp
- src/common/modules/path_extend/pe_resolver.cpp → assembler/src/common/modules/path_extend/pe_resolver.cpp
- src/common/modules/path_extend/pe_resolver.hpp → assembler/src/common/modules/path_extend/pe_resolver.hpp
- src/common/modules/path_extend/pe_utils.hpp → assembler/src/common/modules/path_extend/pe_utils.hpp
- src/common/modules/path_extend/pipeline/extenders_logic.cpp → assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp
- src/common/modules/path_extend/pipeline/extenders_logic.hpp → assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp
- src/common/modules/path_extend/pipeline/launch_support.cpp → assembler/src/common/modules/path_extend/pipeline/launch_support.cpp
- src/common/modules/path_extend/pipeline/launch_support.hpp → assembler/src/common/modules/path_extend/pipeline/launch_support.hpp
- src/common/modules/path_extend/pipeline/launcher.cpp → assembler/src/common/modules/path_extend/pipeline/launcher.cpp
- src/common/modules/path_extend/pipeline/launcher.hpp → assembler/src/common/modules/path_extend/pipeline/launcher.hpp
- src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp → assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp
- src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp → assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp
- src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp → assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp
- src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp → assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp
- src/common/modules/path_extend/scaffolder2015/path_polisher.cpp → assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp
- src/common/modules/path_extend/scaffolder2015/path_polisher.hpp → assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp
- src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp → assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
- src/common/modules/path_extend/weight_counter.hpp → assembler/src/common/modules/path_extend/weight_counter.hpp
- src/common/modules/simplification/bulge_remover.hpp → assembler/src/common/modules/simplification/bulge_remover.hpp
- src/common/modules/simplification/cleaner.hpp → assembler/src/common/modules/simplification/cleaner.hpp
- src/common/modules/simplification/complex_bulge_remover.hpp → assembler/src/common/modules/simplification/complex_bulge_remover.hpp
- src/common/modules/simplification/complex_tip_clipper.hpp → assembler/src/common/modules/simplification/complex_tip_clipper.hpp
- src/common/modules/simplification/compressor.hpp → assembler/src/common/modules/simplification/compressor.hpp
- src/common/modules/simplification/dominated_set_finder.hpp → assembler/src/common/modules/simplification/dominated_set_finder.hpp
- src/common/modules/simplification/ec_threshold_finder.hpp → assembler/src/common/modules/simplification/ec_threshold_finder.hpp
- src/common/modules/simplification/erroneous_connection_remover.hpp → assembler/src/common/modules/simplification/erroneous_connection_remover.hpp
- src/common/modules/simplification/mf_ec_remover.hpp → assembler/src/common/modules/simplification/mf_ec_remover.hpp
- src/common/modules/simplification/parallel_simplification_algorithms.hpp → assembler/src/common/modules/simplification/parallel_simplification_algorithms.hpp
- src/common/modules/simplification/relative_coverage_remover.hpp → assembler/src/common/modules/simplification/relative_coverage_remover.hpp
- src/common/modules/simplification/superbubble_finder.hpp → assembler/src/common/modules/simplification/superbubble_finder.hpp
- src/common/modules/simplification/tip_clipper.hpp → assembler/src/common/modules/simplification/tip_clipper.hpp
- src/common/modules/simplification/topological_edge_conditions.hpp → assembler/src/common/modules/simplification/topological_edge_conditions.hpp
- + assembler/src/common/paired_info/CMakeLists.txt
- src/common/paired_info/concurrent_pair_info_buffer.hpp → assembler/src/common/paired_info/concurrent_pair_info_buffer.hpp
- src/common/paired_info/data_divider.hpp → assembler/src/common/paired_info/data_divider.hpp
- + assembler/src/common/paired_info/distance_estimation.cpp
- + assembler/src/common/paired_info/distance_estimation.hpp
- src/common/paired_info/histogram.hpp → assembler/src/common/paired_info/histogram.hpp
- src/common/paired_info/histptr.hpp → assembler/src/common/paired_info/histptr.hpp
- src/common/paired_info/index_point.hpp → assembler/src/common/paired_info/index_point.hpp
- src/common/paired_info/insert_size_refiner.hpp → assembler/src/common/paired_info/insert_size_refiner.hpp
- src/common/paired_info/is_counter.hpp → assembler/src/common/paired_info/is_counter.hpp
- src/common/paired_info/pair_info_bounds.hpp → assembler/src/common/paired_info/pair_info_bounds.hpp
- src/common/paired_info/pair_info_filler.hpp → assembler/src/common/paired_info/pair_info_filler.hpp
- src/common/paired_info/pair_info_filters.hpp → assembler/src/common/paired_info/pair_info_filters.hpp
- + assembler/src/common/paired_info/pair_info_improver.hpp
- src/common/paired_info/paired_info.hpp → assembler/src/common/paired_info/paired_info.hpp
- src/common/paired_info/paired_info_buffer.hpp → assembler/src/common/paired_info/paired_info_buffer.hpp
- src/common/paired_info/paired_info_helpers.hpp → assembler/src/common/paired_info/paired_info_helpers.hpp
- src/common/paired_info/peak_finder.hpp → assembler/src/common/paired_info/peak_finder.hpp
- src/common/paired_info/smoothing_distance_estimation.cpp → assembler/src/common/paired_info/smoothing_distance_estimation.cpp
- src/common/paired_info/smoothing_distance_estimation.hpp → assembler/src/common/paired_info/smoothing_distance_estimation.hpp
- src/common/paired_info/split_path_constructor.hpp → assembler/src/common/paired_info/split_path_constructor.hpp
- src/common/paired_info/weighted_distance_estimation.cpp → assembler/src/common/paired_info/weighted_distance_estimation.cpp
- src/common/paired_info/weighted_distance_estimation.hpp → assembler/src/common/paired_info/weighted_distance_estimation.hpp
- src/common/paired_info/weights.hpp → assembler/src/common/paired_info/weights.hpp
- + assembler/src/common/pipeline/CMakeLists.txt
- + assembler/src/common/pipeline/config_common.hpp
- src/common/configs/config_singl.hpp → assembler/src/common/pipeline/config_singl.hpp
- + assembler/src/common/pipeline/config_struct.cpp
- + assembler/src/common/pipeline/config_struct.hpp
- src/common/configs/aligner_config.hpp → assembler/src/common/pipeline/configs/aligner_config.hpp
- + assembler/src/common/pipeline/genomic_info.hpp
- + assembler/src/common/pipeline/graph_pack.cpp
- + assembler/src/common/pipeline/graph_pack.hpp
- src/common/library/library.cpp → assembler/src/common/pipeline/library.cpp
- + assembler/src/common/pipeline/library.hpp
- src/common/library/library.inl → assembler/src/common/pipeline/library.inl
- src/common/library/library_data.cpp → assembler/src/common/pipeline/library_data.cpp
- src/common/library/library_data.hpp → assembler/src/common/pipeline/library_data.hpp
- src/common/library/library_fwd.hpp → assembler/src/common/pipeline/library_fwd.hpp
- src/common/pipeline/stage.cpp → assembler/src/common/pipeline/stage.cpp
- src/common/pipeline/stage.hpp → assembler/src/common/pipeline/stage.hpp
- + assembler/src/common/sequence/CMakeLists.txt
- src/common/sequence/aa.hpp → assembler/src/common/sequence/aa.hpp
- src/common/sequence/genome_storage.hpp → assembler/src/common/sequence/genome_storage.hpp
- src/common/sequence/levenshtein.hpp → assembler/src/common/sequence/levenshtein.hpp
- src/common/sequence/nucl.hpp → assembler/src/common/sequence/nucl.hpp
- src/common/sequence/quality.hpp → assembler/src/common/sequence/quality.hpp
- + assembler/src/common/sequence/range.hpp
- src/common/sequence/rtseq.hpp → assembler/src/common/sequence/rtseq.hpp
- + assembler/src/common/sequence/seq.hpp
- src/common/sequence/seq_common.hpp → assembler/src/common/sequence/seq_common.hpp
- + assembler/src/common/sequence/sequence.hpp
- src/common/sequence/sequence_tools.cpp → assembler/src/common/sequence/sequence_tools.cpp
- src/common/sequence/sequence_tools.hpp → assembler/src/common/sequence/sequence_tools.hpp
- src/common/sequence/simple_seq.hpp → assembler/src/common/sequence/simple_seq.hpp
- + assembler/src/common/stages/CMakeLists.txt
- src/common/stages/construction.cpp → assembler/src/common/stages/construction.cpp
- src/common/stages/construction.hpp → assembler/src/common/stages/construction.hpp
- src/common/stages/genomic_info_filler.cpp → assembler/src/common/stages/genomic_info_filler.cpp
- src/common/stages/genomic_info_filler.hpp → assembler/src/common/stages/genomic_info_filler.hpp
- + assembler/src/common/stages/read_conversion.cpp
- + assembler/src/common/stages/read_conversion.hpp
- src/common/stages/simplification.cpp → assembler/src/common/stages/simplification.cpp
- + assembler/src/common/stages/simplification.hpp
- src/common/stages/simplification_pipeline/graph_simplification.hpp → assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp
- src/common/stages/simplification_pipeline/rna_simplification.hpp → assembler/src/common/stages/simplification_pipeline/rna_simplification.hpp
- src/common/stages/simplification_pipeline/simplification_settings.hpp → assembler/src/common/stages/simplification_pipeline/simplification_settings.hpp
- src/common/stages/simplification_pipeline/single_cell_simplification.hpp → assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp
- src/common/stages/ss_edge_split.cpp → assembler/src/common/stages/ss_edge_split.cpp
- src/common/stages/ss_edge_split.hpp → assembler/src/common/stages/ss_edge_split.hpp
- src/common/toolchain/edge_label_helper.hpp → assembler/src/common/toolchain/edge_label_helper.hpp
- src/common/toolchain/subgraph_utils.hpp → assembler/src/common/toolchain/subgraph_utils.hpp
- + assembler/src/common/toolchain/utils.hpp
- + assembler/src/common/utils/CMakeLists.txt
- src/common/utils/autocompletion.cpp → assembler/src/common/utils/autocompletion.cpp
- src/common/utils/autocompletion.hpp → assembler/src/common/utils/autocompletion.hpp
- src/common/modules/simplification/bulge_utils.hpp → assembler/src/common/utils/bulge_utils.hpp
- src/common/utils/cpp_utils.hpp → assembler/src/common/utils/cpp_utils.hpp
- + assembler/src/common/utils/extension_index/kmer_extension_index.hpp
- src/common/kmer_index/extension_index/kmer_extension_index_builder.hpp → assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp
- + assembler/src/common/utils/filesystem/copy_file.cpp
- + assembler/src/common/utils/filesystem/copy_file.hpp
- src/common/utils/filesystem/file_limit.hpp → assembler/src/common/utils/filesystem/file_limit.hpp
- src/common/utils/filesystem/file_opener.hpp → assembler/src/common/utils/filesystem/file_opener.hpp
- src/common/utils/filesystem/glob.cpp → assembler/src/common/utils/filesystem/glob.cpp
- + assembler/src/common/utils/filesystem/glob.hpp
- + assembler/src/common/utils/filesystem/path_helper.cpp
- + assembler/src/common/utils/filesystem/path_helper.hpp
- + assembler/src/common/utils/filesystem/temporary.cpp
- + assembler/src/common/utils/filesystem/temporary.hpp
- src/common/kmer_index/kmer_counting.hpp → assembler/src/common/utils/kmer_counting.hpp
- + assembler/src/common/utils/kmer_mph/CMakeLists.txt
- + assembler/src/common/utils/kmer_mph/kmer_buckets.hpp
- src/common/kmer_index/kmer_mph/kmer_index.hpp → assembler/src/common/utils/kmer_mph/kmer_index.hpp
- src/common/kmer_index/kmer_mph/kmer_index_builder.hpp → assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp
- src/common/kmer_index/kmer_mph/kmer_index_traits.hpp → assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp
- src/common/kmer_index/kmer_mph/kmer_splitter.hpp → assembler/src/common/utils/kmer_mph/kmer_splitter.hpp
- src/common/kmer_index/kmer_mph/kmer_splitters.hpp → assembler/src/common/utils/kmer_mph/kmer_splitters.hpp
- src/common/utils/logger/decl_logger.hpp → assembler/src/common/utils/logger/decl_logger.hpp
- + assembler/src/common/utils/logger/log_writers.hpp
- + assembler/src/common/utils/logger/logger.hpp
- src/common/utils/logger/logger_impl.cpp → assembler/src/common/utils/logger/logger_impl.cpp
- + assembler/src/common/utils/md5.h
- src/common/utils/memory_limit.cpp → assembler/src/common/utils/memory_limit.cpp
- src/common/utils/memory_limit.hpp → assembler/src/common/utils/memory_limit.hpp
- src/common/utils/parallel/openmp_wrapper.h → assembler/src/common/utils/parallel/openmp_wrapper.h
- src/common/utils/parallel/parallel_wrapper.hpp → assembler/src/common/utils/parallel/parallel_wrapper.hpp
- + assembler/src/common/utils/perf/memory.hpp
- src/common/utils/perf/perfcounter.hpp → assembler/src/common/utils/perf/perfcounter.hpp
- src/common/utils/perf/timetracer.hpp → assembler/src/common/utils/perf/timetracer.hpp
- src/common/kmer_index/ph_map/coverage_hash_map_builder.hpp → assembler/src/common/utils/ph_map/coverage_hash_map_builder.hpp
- src/common/kmer_index/ph_map/cqf_hash_map.hpp → assembler/src/common/utils/ph_map/cqf_hash_map.hpp
- src/common/kmer_index/ph_map/key_with_hash.hpp → assembler/src/common/utils/ph_map/key_with_hash.hpp
- src/common/kmer_index/ph_map/kmer_maps.hpp → assembler/src/common/utils/ph_map/kmer_maps.hpp
- src/common/kmer_index/ph_map/perfect_hash_map.hpp → assembler/src/common/utils/ph_map/perfect_hash_map.hpp
- src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp → assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp
- src/common/kmer_index/ph_map/storing_traits.hpp → assembler/src/common/utils/ph_map/storing_traits.hpp
- src/common/utils/segfault_handler.hpp → assembler/src/common/utils/segfault_handler.hpp
- src/common/utils/stacktrace.hpp → assembler/src/common/utils/stacktrace.hpp
- + assembler/src/common/utils/stl_utils.hpp
- src/common/utils/verify.hpp → assembler/src/common/utils/verify.hpp
- + assembler/src/common/utils/version.cpp
- src/common/visualization/graph_colorer.hpp → assembler/src/common/visualization/graph_colorer.hpp
- src/common/visualization/graph_labeler.hpp → assembler/src/common/visualization/graph_labeler.hpp
- src/common/visualization/graph_print_utils.hpp → assembler/src/common/visualization/graph_print_utils.hpp
- src/common/visualization/graph_printer.hpp → assembler/src/common/visualization/graph_printer.hpp
- src/common/visualization/position_filler.hpp → assembler/src/common/visualization/position_filler.hpp
- src/common/visualization/printing_parameter_storage.hpp → assembler/src/common/visualization/printing_parameter_storage.hpp
- src/common/visualization/vertex_linker.hpp → assembler/src/common/visualization/vertex_linker.hpp
- + assembler/src/common/visualization/visualization.hpp
- src/common/visualization/visualization_utils.hpp → assembler/src/common/visualization/visualization_utils.hpp
- src/common/visualization/visualizers.hpp → assembler/src/common/visualization/visualizers.hpp
- src/include/config.hpp.in → assembler/src/include/config.hpp.in
- src/include/k_range.hpp.in → assembler/src/include/k_range.hpp.in
- + assembler/src/include/version-gen.hpp.in
- + assembler/src/include/version.hpp
- + assembler/src/projects/CMakeLists.txt
- + assembler/src/projects/bin_analysis/CMakeLists.txt
- src/projects/cds_subgraphs/bin_refinement.hpp → assembler/src/projects/bin_analysis/bin_refinement.hpp
- + assembler/src/projects/bin_analysis/main.cpp
- + assembler/src/projects/bin_converter/CMakeLists.txt
- src/projects/spades_tools/convert_bin_to_fasta.cpp → assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp
- + assembler/src/projects/cds_subgraphs/CMakeLists.txt
- + assembler/src/projects/cds_subgraphs/main.cpp
- + assembler/src/projects/cds_subgraphs/stats.cpp
- src/projects/cds_subgraphs/stop_condon_finder.cpp → assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp
- src/projects/cds_subgraphs/stop_condon_finder.hpp → assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp
- src/projects/cds_subgraphs/subgraph_extraction.cpp → assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp
- src/projects/cds_subgraphs/subgraph_extraction.hpp → assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp
- + assembler/src/projects/corrector/CMakeLists.txt
- + assembler/src/projects/corrector/config_struct.cpp
- + assembler/src/projects/corrector/config_struct.hpp
- src/projects/corrector/contig_processor.cpp → assembler/src/projects/corrector/contig_processor.cpp
- src/projects/corrector/contig_processor.hpp → assembler/src/projects/corrector/contig_processor.hpp
- src/projects/corrector/dataset_processor.cpp → assembler/src/projects/corrector/dataset_processor.cpp
- + assembler/src/projects/corrector/dataset_processor.hpp
- src/projects/corrector/interesting_pos_processor.cpp → assembler/src/projects/corrector/interesting_pos_processor.cpp
- src/projects/corrector/interesting_pos_processor.hpp → assembler/src/projects/corrector/interesting_pos_processor.hpp
- + assembler/src/projects/corrector/main.cpp
- src/projects/corrector/positional_read.cpp → assembler/src/projects/corrector/positional_read.cpp
- src/projects/corrector/positional_read.hpp → assembler/src/projects/corrector/positional_read.hpp
- src/projects/corrector/variants_table.hpp → assembler/src/projects/corrector/variants_table.hpp
- + assembler/src/projects/gbuilder/CMakeLists.txt
- + assembler/src/projects/gbuilder/main.cpp
- + assembler/src/projects/gmapper/CMakeLists.txt
- + assembler/src/projects/gmapper/main.cpp
- + assembler/src/projects/gsimplifier/CMakeLists.txt
- + assembler/src/projects/gsimplifier/main.cpp
- src/projects/spades_tools/position_storage.hpp → assembler/src/projects/gsimplifier/position_storage.hpp
- + assembler/src/projects/gsimplifier/simplification.hpp
- + assembler/src/projects/hammer/CMakeLists.txt
- src/projects/hammer/config_struct_hammer.cpp → assembler/src/projects/hammer/config_struct_hammer.cpp
- src/projects/hammer/config_struct_hammer.hpp → assembler/src/projects/hammer/config_struct_hammer.hpp
- src/projects/hammer/expander.cpp → assembler/src/projects/hammer/expander.cpp
- src/projects/hammer/expander.hpp → assembler/src/projects/hammer/expander.hpp
- src/projects/hammer/globals.hpp → assembler/src/projects/hammer/globals.hpp
- src/projects/hammer/hamcluster.cpp → assembler/src/projects/hammer/hamcluster.cpp
- src/projects/hammer/hamcluster.hpp → assembler/src/projects/hammer/hamcluster.hpp
- src/projects/hammer/hammer_tools.cpp → assembler/src/projects/hammer/hammer_tools.cpp
- src/projects/hammer/hammer_tools.hpp → assembler/src/projects/hammer/hammer_tools.hpp
- src/projects/hammer/kmer_cluster.cpp → assembler/src/projects/hammer/kmer_cluster.cpp
- src/projects/hammer/kmer_cluster.hpp → assembler/src/projects/hammer/kmer_cluster.hpp
- + assembler/src/projects/hammer/kmer_data.cpp
- + assembler/src/projects/hammer/kmer_data.hpp
- src/projects/hammer/kmer_stat.hpp → assembler/src/projects/hammer/kmer_stat.hpp
- + assembler/src/projects/hammer/main.cpp
- src/projects/hammer/parallel_radix_sort.hpp → assembler/src/projects/hammer/parallel_radix_sort.hpp
- src/projects/hammer/read_corrector.cpp → assembler/src/projects/hammer/read_corrector.cpp
- + assembler/src/projects/hammer/read_corrector.hpp
- src/projects/hammer/valid_kmer_generator.hpp → assembler/src/projects/hammer/valid_kmer_generator.hpp
- + assembler/src/projects/ionhammer/CMakeLists.txt
- src/projects/ionhammer/HSeq.hpp → assembler/src/projects/ionhammer/HSeq.hpp
- + assembler/src/projects/ionhammer/comparator.py
- + assembler/src/projects/ionhammer/config_struct.cpp
- + assembler/src/projects/ionhammer/config_struct.hpp
- src/projects/ionhammer/consensus.hpp → assembler/src/projects/ionhammer/consensus.hpp
- src/projects/ionhammer/err_helper_table.cpp → assembler/src/projects/ionhammer/err_helper_table.cpp
- src/projects/ionhammer/err_helper_table.hpp → assembler/src/projects/ionhammer/err_helper_table.hpp
- src/projects/ionhammer/err_helper_table.inc → assembler/src/projects/ionhammer/err_helper_table.inc
- src/projects/ionhammer/flow_space_read.hpp → assembler/src/projects/ionhammer/flow_space_read.hpp
- + assembler/src/projects/ionhammer/gamma_poisson_model.cpp
- src/projects/ionhammer/gamma_poisson_model.hpp → assembler/src/projects/ionhammer/gamma_poisson_model.hpp
- + assembler/src/projects/ionhammer/hamcluster_1.cpp
- src/projects/ionhammer/hamcluster_1.h → assembler/src/projects/ionhammer/hamcluster_1.h
- src/projects/ionhammer/hkmer.hpp → assembler/src/projects/ionhammer/hkmer.hpp
- src/projects/ionhammer/hkmer_distance.hpp → assembler/src/projects/ionhammer/hkmer_distance.hpp
- src/projects/ionhammer/io_read_corrector.hpp → assembler/src/projects/ionhammer/io_read_corrector.hpp
- + assembler/src/projects/ionhammer/kmer_data.cpp
- + assembler/src/projects/ionhammer/kmer_data.hpp
- + assembler/src/projects/ionhammer/kmer_evaluator.cpp
- + assembler/src/projects/ionhammer/kmer_helpers.cpp
- src/projects/ionhammer/kmer_helpers.h → assembler/src/projects/ionhammer/kmer_helpers.h
- + assembler/src/projects/ionhammer/main.cpp
- + assembler/src/projects/ionhammer/normal_quality_model.cpp
- src/projects/ionhammer/normal_quality_model.hpp → assembler/src/projects/ionhammer/normal_quality_model.hpp
- src/projects/ionhammer/penalty_estimator.hpp → assembler/src/projects/ionhammer/penalty_estimator.hpp
- + assembler/src/projects/ionhammer/quality_metrics.cpp
- src/projects/ionhammer/quality_metrics.h → assembler/src/projects/ionhammer/quality_metrics.h
- + assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp
- src/projects/ionhammer/quality_thresholds_estimator.h → assembler/src/projects/ionhammer/quality_thresholds_estimator.h
- + assembler/src/projects/ionhammer/read_corrector.hpp
- src/projects/ionhammer/read_corrector_new.hpp → assembler/src/projects/ionhammer/read_corrector_new.hpp
- src/projects/ionhammer/read_corrector_structs_new.h → assembler/src/projects/ionhammer/read_corrector_structs_new.h
- + assembler/src/projects/ionhammer/reference.cpp
- src/projects/ionhammer/reference.h → assembler/src/projects/ionhammer/reference.h
- src/projects/ionhammer/seqeval/BaseCallerUtils.h → assembler/src/projects/ionhammer/seqeval/BaseCallerUtils.h
- src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp → assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp
- src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.h → assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.h
- src/projects/ionhammer/seqeval/TreephaserLite.cpp → assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp
- src/projects/ionhammer/seqeval/TreephaserLite.h → assembler/src/projects/ionhammer/seqeval/TreephaserLite.h
- src/projects/ionhammer/subcluster.cpp → assembler/src/projects/ionhammer/subcluster.cpp
- src/projects/ionhammer/subcluster.hpp → assembler/src/projects/ionhammer/subcluster.hpp
- src/projects/ionhammer/thread_utils.h → assembler/src/projects/ionhammer/thread_utils.h
- src/projects/ionhammer/valid_hkmer_generator.hpp → assembler/src/projects/ionhammer/valid_hkmer_generator.hpp
- + assembler/src/projects/kmercount/CMakeLists.txt
- src/projects/spades_tools/kmer_estimating.cpp → assembler/src/projects/kmercount/kmer_estimating.cpp
- src/projects/spades_tools/kmerbin_converter.py → assembler/src/projects/kmercount/kmerbin_converter.py
- + assembler/src/projects/kmercount/main.cpp
- src/projects/spades_tools/read_filter.cpp → assembler/src/projects/kmercount/read_filter.cpp
- + assembler/src/projects/mts/CMakeLists.txt
- src/projects/mts/Common.snake → assembler/src/projects/mts/Common.snake
- src/projects/mts/README → assembler/src/projects/mts/README
- src/projects/mts/Reassembly.snake → assembler/src/projects/mts/Reassembly.snake
- src/projects/mts/Snakefile → assembler/src/projects/mts/Snakefile
- src/projects/mts/Stats.snake → assembler/src/projects/mts/Stats.snake
- src/projects/mts/annotation.cpp → assembler/src/projects/mts/annotation.cpp
- src/projects/mts/annotation.hpp → assembler/src/projects/mts/annotation.hpp
- src/projects/mts/binners/binsanity.snake → assembler/src/projects/mts/binners/binsanity.snake
- src/projects/mts/binners/canopy.snake → assembler/src/projects/mts/binners/canopy.snake
- src/projects/mts/binners/concoct.snake → assembler/src/projects/mts/binners/concoct.snake
- src/projects/mts/binners/gattaca.snake → assembler/src/projects/mts/binners/gattaca.snake
- src/projects/mts/binners/maxbin.snake → assembler/src/projects/mts/binners/maxbin.snake
- src/projects/mts/binners/metabat.snake → assembler/src/projects/mts/binners/metabat.snake
- src/projects/mts/config.yaml → assembler/src/projects/mts/config.yaml
- src/projects/mts/contig_abundance.cpp → assembler/src/projects/mts/contig_abundance.cpp
- src/projects/mts/contig_abundance.hpp → assembler/src/projects/mts/contig_abundance.hpp
- src/projects/mts/contig_abundance_counter.cpp → assembler/src/projects/mts/contig_abundance_counter.cpp
- src/projects/mts/formats.hpp → assembler/src/projects/mts/formats.hpp
- src/projects/mts/gzstream/gzstream.C → assembler/src/projects/mts/gzstream/gzstream.C
- + assembler/src/projects/mts/gzstream/gzstream.h
- src/projects/mts/kmc_api/kmc_file.cpp → assembler/src/projects/mts/kmc_api/kmc_file.cpp
- src/projects/mts/kmc_api/kmc_file.h → assembler/src/projects/mts/kmc_api/kmc_file.h
- src/projects/mts/kmc_api/kmer_api.cpp → assembler/src/projects/mts/kmc_api/kmer_api.cpp
- src/projects/mts/kmc_api/kmer_api.h → assembler/src/projects/mts/kmc_api/kmer_api.h
- src/projects/mts/kmc_api/kmer_defs.h → assembler/src/projects/mts/kmc_api/kmer_defs.h
- src/projects/mts/kmc_api/mmer.cpp → assembler/src/projects/mts/kmc_api/mmer.cpp
- src/projects/mts/kmc_api/mmer.h → assembler/src/projects/mts/kmc_api/mmer.h
- + assembler/src/projects/mts/kmc_api/stdafx.h
- src/projects/mts/kmer_multiplicity_counter.cpp → assembler/src/projects/mts/kmer_multiplicity_counter.cpp
- src/projects/mts/log.properties → assembler/src/projects/mts/log.properties
- + assembler/src/projects/mts/logger.hpp
- src/projects/mts/mts.py → assembler/src/projects/mts/mts.py
- src/projects/mts/multirun.py → assembler/src/projects/mts/multirun.py
- src/projects/mts/profilers/jgi.snake → assembler/src/projects/mts/profilers/jgi.snake
- src/projects/mts/profilers/mts.snake → assembler/src/projects/mts/profilers/mts.snake
- src/projects/mts/prop_binning.cpp → assembler/src/projects/mts/prop_binning.cpp
- src/projects/mts/propagate.cpp → assembler/src/projects/mts/propagate.cpp
- src/projects/mts/propagate.hpp → assembler/src/projects/mts/propagate.hpp
- src/projects/mts/read_binning.cpp → assembler/src/projects/mts/read_binning.cpp
- src/projects/mts/read_binning.hpp → assembler/src/projects/mts/read_binning.hpp
- src/projects/mts/scripts/Dataset_analysis.ipynb → assembler/src/projects/mts/scripts/Dataset_analysis.ipynb
- ext/include/folly/folly-config.h → assembler/src/projects/mts/scripts/__init__.py
- src/projects/mts/scripts/bhtsne.py → assembler/src/projects/mts/scripts/bhtsne.py
- src/projects/mts/scripts/bin_profiles.py → assembler/src/projects/mts/scripts/bin_profiles.py
- src/projects/mts/scripts/choose_bins.py → assembler/src/projects/mts/scripts/choose_bins.py
- src/projects/mts/scripts/choose_samples.py → assembler/src/projects/mts/scripts/choose_samples.py
- src/projects/mts/scripts/clusters2csv.py → assembler/src/projects/mts/scripts/clusters2csv.py
- + assembler/src/projects/mts/scripts/combine_contigs.py
- + assembler/src/projects/mts/scripts/common.py
- src/projects/mts/scripts/contig_name_filter.py → assembler/src/projects/mts/scripts/contig_name_filter.py
- src/projects/mts/scripts/converters.py → assembler/src/projects/mts/scripts/converters.py
- src/projects/mts/scripts/cut_fasta.py → assembler/src/projects/mts/scripts/cut_fasta.py
- src/projects/mts/scripts/filter_nucmer.py → assembler/src/projects/mts/scripts/filter_nucmer.py
- src/projects/mts/scripts/gather_stats.py → assembler/src/projects/mts/scripts/gather_stats.py
- src/projects/mts/scripts/gen_samples.py → assembler/src/projects/mts/scripts/gen_samples.py
- src/projects/mts/scripts/multi_stats.py → assembler/src/projects/mts/scripts/multi_stats.py
- src/projects/mts/scripts/pca.R → assembler/src/projects/mts/scripts/pca.R
- src/projects/mts/scripts/run_tsne.py → assembler/src/projects/mts/scripts/run_tsne.py
- src/projects/mts/scripts/split_bins.py → assembler/src/projects/mts/scripts/split_bins.py
- src/projects/mts/scripts/subsample.py → assembler/src/projects/mts/scripts/subsample.py
- src/projects/mts/scripts/validate.pl → assembler/src/projects/mts/scripts/validate.pl
- + assembler/src/projects/mts/stats.cpp
- src/projects/mts/test.py → assembler/src/projects/mts/test.py
- + assembler/src/projects/mts/visualization.hpp
- + assembler/src/projects/online_vis/CMakeLists.txt
- src/projects/online_vis/argument_list.hpp → assembler/src/projects/online_vis/argument_list.hpp
- src/projects/online_vis/base_commands.hpp → assembler/src/projects/online_vis/base_commands.hpp
- src/projects/online_vis/command.hpp → assembler/src/projects/online_vis/command.hpp
- src/projects/online_vis/command_mapping.hpp → assembler/src/projects/online_vis/command_mapping.hpp
- src/projects/online_vis/debruijn_commands.hpp → assembler/src/projects/online_vis/debruijn_commands.hpp
- src/projects/online_vis/debruijn_environment.hpp → assembler/src/projects/online_vis/debruijn_environment.hpp
- src/projects/online_vis/debruijn_online_visualizer.hpp → assembler/src/projects/online_vis/debruijn_online_visualizer.hpp
- src/projects/online_vis/drawing_commands.hpp → assembler/src/projects/online_vis/drawing_commands.hpp
- src/projects/online_vis/drawing_commands/draw_connected_command.hpp → assembler/src/projects/online_vis/drawing_commands/draw_connected_command.hpp
- src/projects/online_vis/drawing_commands/draw_contig_command.hpp → assembler/src/projects/online_vis/drawing_commands/draw_contig_command.hpp
- src/projects/online_vis/drawing_commands/draw_missasemblies.hpp → assembler/src/projects/online_vis/drawing_commands/draw_missasemblies.hpp
- src/projects/online_vis/drawing_commands/draw_part_of_genome_command.hpp → assembler/src/projects/online_vis/drawing_commands/draw_part_of_genome_command.hpp
- src/projects/online_vis/drawing_commands/draw_polymorphic_regions.hpp → assembler/src/projects/online_vis/drawing_commands/draw_polymorphic_regions.hpp
- src/projects/online_vis/drawing_commands/draw_poorly_assembled.hpp → assembler/src/projects/online_vis/drawing_commands/draw_poorly_assembled.hpp
- src/projects/online_vis/drawing_commands/draw_position_command.hpp → assembler/src/projects/online_vis/drawing_commands/draw_position_command.hpp
- + assembler/src/projects/online_vis/drawing_commands/drawing_command.hpp
- src/projects/online_vis/drawing_commands/show_position_command.hpp → assembler/src/projects/online_vis/drawing_commands/show_position_command.hpp
- + assembler/src/projects/online_vis/environment.hpp
- + assembler/src/projects/online_vis/errors.hpp
- src/projects/online_vis/history.hpp → assembler/src/projects/online_vis/history.hpp
- src/projects/online_vis/loaded_environments.hpp → assembler/src/projects/online_vis/loaded_environments.hpp
- + assembler/src/projects/online_vis/main.cpp
- src/projects/online_vis/online_visualizer.hpp → assembler/src/projects/online_vis/online_visualizer.hpp
- src/projects/online_vis/position_commands.hpp → assembler/src/projects/online_vis/position_commands.hpp
- src/projects/online_vis/position_commands/clear_position_command.hpp → assembler/src/projects/online_vis/position_commands/clear_position_command.hpp
- src/projects/online_vis/position_commands/fill_position_command.hpp → assembler/src/projects/online_vis/position_commands/fill_position_command.hpp
- src/projects/online_vis/processing_commands.hpp → assembler/src/projects/online_vis/processing_commands.hpp
- src/projects/online_vis/setting_commands.hpp → assembler/src/projects/online_vis/setting_commands.hpp
- src/projects/online_vis/standard_vis.hpp → assembler/src/projects/online_vis/standard_vis.hpp
- src/projects/online_vis/statistics_commands.hpp → assembler/src/projects/online_vis/statistics_commands.hpp
- src/projects/online_vis/statistics_commands/junction_sequence_command.hpp → assembler/src/projects/online_vis/statistics_commands/junction_sequence_command.hpp
- src/projects/online_vis/statistics_commands/print_contigs_stats.hpp → assembler/src/projects/online_vis/statistics_commands/print_contigs_stats.hpp
- src/projects/online_vis/statistics_commands/print_edge_command.hpp → assembler/src/projects/online_vis/statistics_commands/print_edge_command.hpp
- src/projects/online_vis/statistics_commands/print_paths_command.hpp → assembler/src/projects/online_vis/statistics_commands/print_paths_command.hpp
- src/projects/online_vis/vis_logger.hpp → assembler/src/projects/online_vis/vis_logger.hpp
- src/projects/online_vis/vis_utils.hpp → assembler/src/projects/online_vis/vis_utils.hpp
- + assembler/src/projects/scaffold_correction/CMakeLists.txt
- + assembler/src/projects/scaffold_correction/main.cpp
- + assembler/src/projects/scaffold_correction/scaffold_correction.hpp
- + assembler/src/projects/spades/CMakeLists.txt
- src/projects/spades/chromosome_removal.cpp → assembler/src/projects/spades/chromosome_removal.cpp
- src/projects/spades/chromosome_removal.hpp → assembler/src/projects/spades/chromosome_removal.hpp
- src/projects/spades/contig_output_stage.cpp → assembler/src/projects/spades/contig_output_stage.cpp
- src/projects/spades/contig_output_stage.hpp → assembler/src/projects/spades/contig_output_stage.hpp
- + assembler/src/projects/spades/distance_estimation.cpp
- + assembler/src/projects/spades/distance_estimation.hpp
- src/projects/spades/domain_graph.cpp → assembler/src/projects/spades/domain_graph.cpp
- src/projects/spades/domain_graph.hpp → assembler/src/projects/spades/domain_graph.hpp
- src/projects/spades/domain_graph_construction.cpp → assembler/src/projects/spades/domain_graph_construction.cpp
- src/projects/spades/domain_graph_construction.hpp → assembler/src/projects/spades/domain_graph_construction.hpp
- src/projects/spades/domain_matcher.cpp → assembler/src/projects/spades/domain_matcher.cpp
- src/projects/spades/domain_matcher.hpp → assembler/src/projects/spades/domain_matcher.hpp
- src/projects/spades/extract_domains.cpp → assembler/src/projects/spades/extract_domains.cpp
- src/projects/spades/extract_domains.hpp → assembler/src/projects/spades/extract_domains.hpp
- src/projects/spades/gap_closer.cpp → assembler/src/projects/spades/gap_closer.cpp
- src/projects/spades/gap_closer.hpp → assembler/src/projects/spades/gap_closer.hpp
- src/projects/spades/gap_closing.hpp → assembler/src/projects/spades/gap_closing.hpp
- src/projects/spades/hybrid_aligning.cpp → assembler/src/projects/spades/hybrid_aligning.cpp
- src/projects/spades/hybrid_aligning.hpp → assembler/src/projects/spades/hybrid_aligning.hpp
- src/projects/spades/hybrid_gap_closer.hpp → assembler/src/projects/spades/hybrid_gap_closer.hpp
- + assembler/src/projects/spades/load_graph.cpp
- src/projects/spades/load_graph.hpp → assembler/src/projects/spades/load_graph.hpp
- + assembler/src/projects/spades/main.cpp
- src/projects/spades/mismatch_correction.cpp → assembler/src/projects/spades/mismatch_correction.cpp
- src/projects/spades/mismatch_correction.hpp → assembler/src/projects/spades/mismatch_correction.hpp
- + assembler/src/projects/spades/pair_info_count.cpp
- src/projects/spades/pair_info_count.hpp → assembler/src/projects/spades/pair_info_count.hpp
- src/projects/spades/pipeline.cpp → assembler/src/projects/spades/pipeline.cpp
- src/projects/spades/repeat_resolving.cpp → assembler/src/projects/spades/repeat_resolving.cpp
- src/projects/spades/repeat_resolving.hpp → assembler/src/projects/spades/repeat_resolving.hpp
- + assembler/src/projects/spades/restricted_edges_filling.cpp
- src/projects/spades/restricted_edges_filling.hpp → assembler/src/projects/spades/restricted_edges_filling.hpp
- src/projects/spades/second_phase_setup.cpp → assembler/src/projects/spades/second_phase_setup.cpp
- src/projects/spades/second_phase_setup.hpp → assembler/src/projects/spades/second_phase_setup.hpp
- src/projects/spades/series_analysis.cpp → assembler/src/projects/spades/series_analysis.cpp
- + assembler/src/projects/spades/series_analysis.hpp
- + assembler/src/projects/spaligner/CMakeLists.txt
- + assembler/src/projects/spaligner/README.md
- src/projects/spaligner/align_longreads.cpp → assembler/src/projects/spaligner/align_longreads.cpp
- src/projects/spaligner/benchmarking/GraphAligner.snake → assembler/src/projects/spaligner/benchmarking/GraphAligner.snake
- src/projects/spaligner/benchmarking/SPAligner.snake → assembler/src/projects/spaligner/benchmarking/SPAligner.snake
- src/projects/spaligner/benchmarking/benchmarking_stats.py → assembler/src/projects/spaligner/benchmarking/benchmarking_stats.py
- src/projects/spaligner/benchmarking/config.yaml → assembler/src/projects/spaligner/benchmarking/config.yaml
- src/projects/spaligner/benchmarking/data_gen/build_idealpaths.py → assembler/src/projects/spaligner/benchmarking/data_gen/build_idealpaths.py
- + assembler/src/projects/spaligner/benchmarking/data_gen/filter_unaligned.py
- + assembler/src/projects/spaligner/benchmarking/data_gen/filterbylength.py
- src/projects/spaligner/benchmarking/data_gen/gen_benchmark_data.sh → assembler/src/projects/spaligner/benchmarking/data_gen/gen_benchmark_data.sh
- src/projects/spaligner/benchmarking/data_gen/gen_benchmark_data_simnp.sh → assembler/src/projects/spaligner/benchmarking/data_gen/gen_benchmark_data_simnp.sh
- src/projects/spaligner/benchmarking/data_gen/gen_mapped_reads.sh → assembler/src/projects/spaligner/benchmarking/data_gen/gen_mapped_reads.sh
- src/projects/spaligner/benchmarking/data_gen/readme_celegans.txt → assembler/src/projects/spaligner/benchmarking/data_gen/readme_celegans.txt
- src/projects/spaligner/benchmarking/data_gen/readme_ecoli.txt → assembler/src/projects/spaligner/benchmarking/data_gen/readme_ecoli.txt
- src/projects/spaligner/benchmarking/data_gen/readme_scerevisiae.txt → assembler/src/projects/spaligner/benchmarking/data_gen/readme_scerevisiae.txt
- + assembler/src/projects/spaligner/benchmarking/data_gen/sim_illumina.sh
- + assembler/src/projects/spaligner/benchmarking/data_gen/sim_nanopore_circular.sh
- src/projects/spaligner/benchmarking/data_gen/sim_nanopore_linear.sh → assembler/src/projects/spaligner/benchmarking/data_gen/sim_nanopore_linear.sh
- + assembler/src/projects/spaligner/benchmarking/data_gen/sim_pacbio.sh
- src/projects/spaligner/benchmarking/spaligner_config_template.yaml → assembler/src/projects/spaligner/benchmarking/spaligner_config_template.yaml
- src/projects/spaligner/benchmarking/test_spaligner.py → assembler/src/projects/spaligner/benchmarking/test_spaligner.py
- src/projects/spaligner/benchmarking/vg.snake → assembler/src/projects/spaligner/benchmarking/vg.snake
- src/projects/spaligner/form_truealignments.cpp → assembler/src/projects/spaligner/form_truealignments.cpp
- src/projects/spaligner/mapping_printer.cpp → assembler/src/projects/spaligner/mapping_printer.cpp
- src/projects/spaligner/mapping_printer.hpp → assembler/src/projects/spaligner/mapping_printer.hpp
- docs/spaligner.jpg → assembler/src/projects/spaligner/pipeline.jpg
- src/projects/spaligner/spaligner_config.yaml → assembler/src/projects/spaligner/spaligner_config.yaml
- + assembler/src/projects/truseq_analysis/AlignmentAnalyserNew.cpp
- + assembler/src/projects/truseq_analysis/AlignmentAnalyserNew.hpp
- + assembler/src/projects/truseq_analysis/CMakeLists.txt
- + assembler/src/projects/truseq_analysis/alignment_analyser.cpp
- + assembler/src/projects/truseq_analysis/alignment_analyser.hpp
- + assembler/src/projects/truseq_analysis/analysis_pipeline.cpp
- + assembler/src/projects/truseq_analysis/analysis_pipeline.hpp
- + assembler/src/projects/truseq_analysis/consistent_mapping.cpp
- + assembler/src/projects/truseq_analysis/consistent_mapping.h
- + assembler/src/projects/truseq_analysis/main.cpp
- + assembler/src/projects/unitig_coverage/CMakeLists.txt
- + assembler/src/projects/unitig_coverage/main.cpp
- src/projects/cds_subgraphs/profile_storage.cpp → assembler/src/projects/unitig_coverage/profile_storage.cpp
- src/projects/cds_subgraphs/profile_storage.hpp → assembler/src/projects/unitig_coverage/profile_storage.hpp
- + assembler/src/spades_pipeline/CMakeLists.txt
- src/projects/spades/pipeline/spades_pipeline/commands_parser.py → assembler/src/spades_pipeline/commands_parser.py
- src/projects/spades/pipeline/spades_pipeline/common/SeqIO.py → assembler/src/spades_pipeline/common/SeqIO.py
- ext/src/samtools/examples/ex1.glf → assembler/src/spades_pipeline/common/__init__.py
- src/projects/spades/pipeline/spades_pipeline/common/alignment.py → assembler/src/spades_pipeline/common/alignment.py
- src/projects/spades/pipeline/spades_pipeline/common/parallel_launcher.py → assembler/src/spades_pipeline/common/parallel_launcher.py
- src/projects/spades/pipeline/spades_pipeline/common/sam_parser.py → assembler/src/spades_pipeline/common/sam_parser.py
- src/projects/spades/pipeline/spades_pipeline/executors/executor_local.py → assembler/src/spades_pipeline/executors/executor_local.py
- src/projects/spades/pipeline/spades_pipeline/executors/executor_save_yaml.py → assembler/src/spades_pipeline/executors/executor_save_yaml.py
- src/projects/spades/pipeline/spades_pipeline/executors/executors.py → assembler/src/spades_pipeline/executors/executors.py
- src/projects/spades/pipeline/spades_pipeline/options_parser.py → assembler/src/spades_pipeline/options_parser.py
- src/projects/spades/pipeline/spades_pipeline/options_storage.py → assembler/src/spades_pipeline/options_storage.py
- + assembler/src/spades_pipeline/process_cfg.py
- + assembler/src/spades_pipeline/run_contig_breaker.py
- src/projects/spades/pipeline/spades_pipeline/scripts/breaking_scaffolds_script.py → assembler/src/spades_pipeline/scripts/breaking_scaffolds_script.py
- src/projects/spades/pipeline/spades_pipeline/scripts/check_test_script.py → assembler/src/spades_pipeline/scripts/check_test_script.py
- src/projects/spades/pipeline/spades_pipeline/scripts/compress_all.py → assembler/src/spades_pipeline/scripts/compress_all.py
- src/projects/spades/pipeline/spades_pipeline/scripts/copy_files.py → assembler/src/spades_pipeline/scripts/copy_files.py
- src/projects/spades/pipeline/spades_pipeline/scripts/correction_iteration_script.py → assembler/src/spades_pipeline/scripts/correction_iteration_script.py
- src/projects/spades/pipeline/spades_pipeline/scripts/plasmid_glue.py → assembler/src/spades_pipeline/scripts/plasmid_glue.py
- + assembler/src/spades_pipeline/scripts/postprocessing_script.py
- src/projects/spades/pipeline/spades_pipeline/scripts/preprocess_contigs.py → assembler/src/spades_pipeline/scripts/preprocess_contigs.py
- src/projects/spades/pipeline/spades_pipeline/scripts/preprocess_interlaced_reads.py → assembler/src/spades_pipeline/scripts/preprocess_interlaced_reads.py
- + assembler/src/spades_pipeline/stages/__init__.py
- src/projects/spades/pipeline/spades_pipeline/stages/before_start_stage.py → assembler/src/spades_pipeline/stages/before_start_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/breaking_scaffolds_stage.py → assembler/src/spades_pipeline/stages/breaking_scaffolds_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/check_test_stage.py → assembler/src/spades_pipeline/stages/check_test_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/correction_stage.py → assembler/src/spades_pipeline/stages/correction_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/error_correction_stage.py → assembler/src/spades_pipeline/stages/error_correction_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/pipeline.py → assembler/src/spades_pipeline/stages/pipeline.py
- + assembler/src/spades_pipeline/stages/postprocessing_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/preprocess_reads_stage.py → assembler/src/spades_pipeline/stages/preprocess_reads_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/spades_iteration_stage.py → assembler/src/spades_pipeline/stages/spades_iteration_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/spades_stage.py → assembler/src/spades_pipeline/stages/spades_stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/stage.py → assembler/src/spades_pipeline/stages/stage.py
- src/projects/spades/pipeline/spades_pipeline/stages/terminating_stage.py → assembler/src/spades_pipeline/stages/terminating_stage.py
- src/projects/spades/pipeline/spades_pipeline/support.py → assembler/src/spades_pipeline/support.py
- + assembler/src/spades_pipeline/truspades/__init__.py
- + assembler/src/spades_pipeline/truspades/barcode_extraction.py
- + assembler/src/spades_pipeline/truspades/break_by_coverage.py
- + assembler/src/spades_pipeline/truspades/generate_quality.py
- + assembler/src/spades_pipeline/truspades/id_generation.py
- + assembler/src/spades_pipeline/truspades/launch_options.py
- + assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
- + assembler/src/spades_pipeline/truspades/moleculo_postprocessing.py
- + assembler/src/spades_pipeline/truspades/reference_construction.py
- + assembler/src/spades_pipeline/truspades/string_dist_utils.py
- + assembler/src/test/adt/CMakeLists.txt
- src/test/adt/loser_tree_test.cpp → assembler/src/test/adt/loser_tree_test.cpp
- src/test/adt/pack_demo.cpp → assembler/src/test/adt/pack_demo.cpp
- src/test/adt/phm_test.cpp → assembler/src/test/adt/phm_test.cpp
- src/test/data/s_6_1.fastq.gz → assembler/src/test/data/s_6_1.fastq.gz
- src/test/data/s_6_2.fastq.gz → assembler/src/test/data/s_6_2.fastq.gz
- src/test/data/s_test.fastq.gz → assembler/src/test/data/s_test.fastq.gz
- src/test/data/s_test_2.fastq.gz → assembler/src/test/data/s_test_2.fastq.gz
- + assembler/src/test/debruijn/CMakeLists.txt
- src/test/debruijn/construction_test.cpp → assembler/src/test/debruijn/construction_test.cpp
- src/test/debruijn/graph_alignment_test.cpp → assembler/src/test/debruijn/graph_alignment_test.cpp
- src/test/debruijn/graph_core_test.cpp → assembler/src/test/debruijn/graph_core_test.cpp
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.cvr → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.cvr
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.dot → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.dot
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.flcvr → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.flcvr
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.pos → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.pos
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.sqn → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.sqn
- src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge_res.dot → assembler/src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge_res.dot
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.cvr → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.cvr
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.dot → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.dot
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.flcvr → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.flcvr
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.pos → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.pos
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.sqn → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.sqn
- src/test/debruijn/graph_fragments/complex_bulge/complex_bulge_res.dot → assembler/src/test/debruijn/graph_fragments/complex_bulge/complex_bulge_res.dot
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.cvr → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.cvr
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.dot → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.dot
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.flcvr → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.flcvr
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.gid → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.gid
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp
- src/test/debruijn/graph_fragments/complex_bulge_2/graph.sqn → assembler/src/test/debruijn/graph_fragments/complex_bulge_2/graph.sqn
- src/test/debruijn/graph_fragments/compression/graph.cvr → assembler/src/test/debruijn/graph_fragments/compression/graph.cvr
- src/test/debruijn/graph_fragments/compression/graph.dot → assembler/src/test/debruijn/graph_fragments/compression/graph.dot
- src/test/debruijn/graph_fragments/compression/graph.flcvr → assembler/src/test/debruijn/graph_fragments/compression/graph.flcvr
- src/test/debruijn/graph_fragments/compression/graph.gid → assembler/src/test/debruijn/graph_fragments/compression/graph.gid
- src/test/debruijn/graph_fragments/compression/graph.grp → assembler/src/test/debruijn/graph_fragments/compression/graph.grp
- src/test/debruijn/graph_fragments/compression/graph.sqn → assembler/src/test/debruijn/graph_fragments/compression/graph.sqn
- src/test/debruijn/graph_fragments/compression/graph.svg → assembler/src/test/debruijn/graph_fragments/compression/graph.svg
- src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.dot → assembler/src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.dot
- src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.pdf → assembler/src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.pdf
- src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.svg → assembler/src/test/debruijn/graph_fragments/ecoli_400k/basic_repeat.svg
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.cvr → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.cvr
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.flcvr → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.flcvr
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.gid → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.gid
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.ginfo → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.ginfo
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp
- src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.sqn → assembler/src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.sqn
- src/test/debruijn/graph_fragments/ecoli_400k/loop.dot → assembler/src/test/debruijn/graph_fragments/ecoli_400k/loop.dot
- src/test/debruijn/graph_fragments/ecoli_400k/loop.pdf → assembler/src/test/debruijn/graph_fragments/ecoli_400k/loop.pdf
- src/test/debruijn/graph_fragments/ecoli_400k/loop.svg → assembler/src/test/debruijn/graph_fragments/ecoli_400k/loop.svg
- src/test/debruijn/graph_fragments/path_extend/distance_estimation.cvr → assembler/src/test/debruijn/graph_fragments/path_extend/distance_estimation.cvr
- src/test/debruijn/graph_fragments/path_extend/distance_estimation.dot → assembler/src/test/debruijn/graph_fragments/path_extend/distance_estimation.dot
- src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp → assembler/src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp
- src/test/debruijn/graph_fragments/path_extend/distance_estimation.sqn → assembler/src/test/debruijn/graph_fragments/path_extend/distance_estimation.sqn
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.cvr → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.cvr
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.flcvr → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.flcvr
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.pos → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.pos
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.sqn → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.sqn
- src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph_est_params.info → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph_est_params.info
- src/test/debruijn/graph_fragments/rel_cov_ec/rel_ec.svg → assembler/src/test/debruijn/graph_fragments/rel_cov_ec/rel_ec.svg
- src/test/debruijn/graph_fragments/saves/.gitignore → assembler/src/test/debruijn/graph_fragments/saves/.gitignore
- src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.cvr → assembler/src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.cvr
- src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp → assembler/src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp
- src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.sqn → assembler/src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.sqn
- src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.cvr → assembler/src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.cvr
- src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.dot → assembler/src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.dot
- src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp → assembler/src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp
- src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.sqn → assembler/src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.sqn
- src/test/debruijn/graph_fragments/tipobulge/tipobulge.cvr → assembler/src/test/debruijn/graph_fragments/tipobulge/tipobulge.cvr
- src/test/debruijn/graph_fragments/tipobulge/tipobulge.dot → assembler/src/test/debruijn/graph_fragments/tipobulge/tipobulge.dot
- src/test/debruijn/graph_fragments/tipobulge/tipobulge.flcvr → assembler/src/test/debruijn/graph_fragments/tipobulge/tipobulge.flcvr
- src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp → assembler/src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp
- src/test/debruijn/graph_fragments/tipobulge/tipobulge.sqn → assembler/src/test/debruijn/graph_fragments/tipobulge/tipobulge.sqn
- src/test/debruijn/graph_fragments/tipobulge_2/graph.cvr → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.cvr
- src/test/debruijn/graph_fragments/tipobulge_2/graph.dot → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.dot
- src/test/debruijn/graph_fragments/tipobulge_2/graph.flcvr → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.flcvr
- src/test/debruijn/graph_fragments/tipobulge_2/graph.gid → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.gid
- src/test/debruijn/graph_fragments/tipobulge_2/graph.grp → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.grp
- src/test/debruijn/graph_fragments/tipobulge_2/graph.sqn → assembler/src/test/debruijn/graph_fragments/tipobulge_2/graph.sqn
- src/test/debruijn/graph_fragments/tips/graph.cvr → assembler/src/test/debruijn/graph_fragments/tips/graph.cvr
- src/test/debruijn/graph_fragments/tips/graph.dot → assembler/src/test/debruijn/graph_fragments/tips/graph.dot
- src/test/debruijn/graph_fragments/tips/graph.flcvr → assembler/src/test/debruijn/graph_fragments/tips/graph.flcvr
- src/test/debruijn/graph_fragments/tips/graph.gid → assembler/src/test/debruijn/graph_fragments/tips/graph.gid
- src/test/debruijn/graph_fragments/tips/graph.grp → assembler/src/test/debruijn/graph_fragments/tips/graph.grp
- src/test/debruijn/graph_fragments/tips/graph.sqn → assembler/src/test/debruijn/graph_fragments/tips/graph.sqn
- src/test/debruijn/graph_fragments/tips/graph.svg → assembler/src/test/debruijn/graph_fragments/tips/graph.svg
- src/test/debruijn/graph_fragments/topology_ec/big_bad.cvr → assembler/src/test/debruijn/graph_fragments/topology_ec/big_bad.cvr
- src/test/debruijn/graph_fragments/topology_ec/big_bad.dot → assembler/src/test/debruijn/graph_fragments/topology_ec/big_bad.dot
- src/test/debruijn/graph_fragments/topology_ec/big_bad.grp → assembler/src/test/debruijn/graph_fragments/topology_ec/big_bad.grp
- src/test/debruijn/graph_fragments/topology_ec/big_bad.sqn → assembler/src/test/debruijn/graph_fragments/topology_ec/big_bad.sqn
- src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.cvr → assembler/src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.cvr
- src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.dot → assembler/src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.dot
- src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp → assembler/src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp
- src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.sqn → assembler/src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.sqn
- src/test/debruijn/graph_fragments/topology_ec/self_comp.cvr → assembler/src/test/debruijn/graph_fragments/topology_ec/self_comp.cvr
- src/test/debruijn/graph_fragments/topology_ec/self_comp.dot → assembler/src/test/debruijn/graph_fragments/topology_ec/self_comp.dot
- src/test/debruijn/graph_fragments/topology_ec/self_comp.grp → assembler/src/test/debruijn/graph_fragments/topology_ec/self_comp.grp
- src/test/debruijn/graph_fragments/topology_ec/self_comp.sqn → assembler/src/test/debruijn/graph_fragments/topology_ec/self_comp.sqn
- src/test/debruijn/graph_fragments/topology_ec/unique_path.cvr → assembler/src/test/debruijn/graph_fragments/topology_ec/unique_path.cvr
- src/test/debruijn/graph_fragments/topology_ec/unique_path.dot → assembler/src/test/debruijn/graph_fragments/topology_ec/unique_path.dot
- src/test/debruijn/graph_fragments/topology_ec/unique_path.grp → assembler/src/test/debruijn/graph_fragments/topology_ec/unique_path.grp
- src/test/debruijn/graph_fragments/topology_ec/unique_path.sqn → assembler/src/test/debruijn/graph_fragments/topology_ec/unique_path.sqn
- src/test/debruijn/graphio.cpp → assembler/src/test/debruijn/graphio.cpp
- src/test/debruijn/graphio.hpp → assembler/src/test/debruijn/graphio.hpp
- src/test/debruijn/histogram_test.cpp → assembler/src/test/debruijn/histogram_test.cpp
- + assembler/src/test/debruijn/io_test.cpp
- src/test/debruijn/overlap_analysis_test.cpp → assembler/src/test/debruijn/overlap_analysis_test.cpp
- src/test/debruijn/overlap_removal_test.cpp → assembler/src/test/debruijn/overlap_removal_test.cpp
- src/test/debruijn/paired_info_test.cpp → assembler/src/test/debruijn/paired_info_test.cpp
- src/test/debruijn/path_extend_test.cpp → assembler/src/test/debruijn/path_extend_test.cpp
- src/test/debruijn/random_graph.hpp → assembler/src/test/debruijn/random_graph.hpp
- src/test/debruijn/simplification_test.cpp → assembler/src/test/debruijn/simplification_test.cpp
- + assembler/src/test/debruijn/test.cpp
- src/test/debruijn/test_utils.cpp → assembler/src/test/debruijn/test_utils.cpp
- src/test/debruijn/test_utils.hpp → assembler/src/test/debruijn/test_utils.hpp
- + assembler/src/test/debruijn/tmp_folder_fixture.hpp
- + assembler/src/test/examples/CMakeLists.txt
- src/test/examples/generate_component.cpp → assembler/src/test/examples/generate_component.cpp
- src/test/examples/reference_fixer.cpp → assembler/src/test/examples/reference_fixer.cpp
- src/test/examples/short_edge_contractor.cpp → assembler/src/test/examples/short_edge_contractor.cpp
- + assembler/src/test/examples/thread_sequences.cpp
- + assembler/src/test/include_test/CMakeLists.txt
- src/test/include_test/binary_test.cpp → assembler/src/test/include_test/binary_test.cpp
- src/test/include_test/cyclic_hash_test.cpp → assembler/src/test/include_test/cyclic_hash_test.cpp
- src/test/include_test/nucl_test.cpp → assembler/src/test/include_test/nucl_test.cpp
- src/test/include_test/quality_test.cpp → assembler/src/test/include_test/quality_test.cpp
- src/test/include_test/rtseq_test.cpp → assembler/src/test/include_test/rtseq_test.cpp
- src/test/include_test/seq_test.cpp → assembler/src/test/include_test/seq_test.cpp
- src/test/include_test/sequence_test.cpp → assembler/src/test/include_test/sequence_test.cpp
- + assembler/src/test/include_test/test.cpp
- src/test/teamcity/assess.py → assembler/src/test/teamcity/assess.py
- src/test/teamcity/assess_reads.py → assembler/src/test/teamcity/assess_reads.py
- src/test/teamcity/clean_old_contigs.py → assembler/src/test/teamcity/clean_old_contigs.py
- src/test/teamcity/compare_w_master.py → assembler/src/test/teamcity/compare_w_master.py
- src/test/teamcity/dataset_example.info → assembler/src/test/teamcity/dataset_example.info
- src/test/teamcity/deprecated/bh_config_ecoli_1k.info → assembler/src/test/teamcity/deprecated/bh_config_ecoli_1k.info
- src/test/teamcity/deprecated/bh_config_ecoli_mda_lane1.info → assembler/src/test/teamcity/deprecated/bh_config_ecoli_mda_lane1.info
- src/test/teamcity/deprecated/bh_ecoli_1k.sh → assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh
- src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh → assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh
- src/test/teamcity/deprecated/full_dataset_teamcity.sh → assembler/src/test/teamcity/deprecated/full_dataset_teamcity.sh
- src/test/teamcity/deprecated/full_run.sh → assembler/src/test/teamcity/deprecated/full_run.sh
- src/test/teamcity/deprecated/regenerate_etalons.sh → assembler/src/test/teamcity/deprecated/regenerate_etalons.sh
- src/test/teamcity/deprecated/spades_config_mc_is220.info → assembler/src/test/teamcity/deprecated/spades_config_mc_is220.info
- src/test/teamcity/deprecated/spades_config_mc_is220_100k_saves.info → assembler/src/test/teamcity/deprecated/spades_config_mc_is220_100k_saves.info
- src/test/teamcity/deprecated/spades_config_mc_is220_1k.info → assembler/src/test/teamcity/deprecated/spades_config_mc_is220_1k.info
- src/test/teamcity/deprecated/spades_config_mc_is480.info → assembler/src/test/teamcity/deprecated/spades_config_mc_is480.info
- src/test/teamcity/deprecated/spades_config_sc_lane1.info → assembler/src/test/teamcity/deprecated/spades_config_sc_lane1.info
- src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh → assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh
- src/test/teamcity/deprecated/spades_mc_is220.sh → assembler/src/test/teamcity/deprecated/spades_mc_is220.sh
- src/test/teamcity/deprecated/spades_mc_is220_100k_saves.sh → assembler/src/test/teamcity/deprecated/spades_mc_is220_100k_saves.sh
- src/test/teamcity/deprecated/spades_mc_is220_1k.sh → assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh
- src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh → assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh
- src/test/teamcity/deprecated/spades_mc_is480.sh → assembler/src/test/teamcity/deprecated/spades_mc_is480.sh
- src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh → assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh
- src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh → assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh
- src/test/teamcity/deprecated/spades_sc_lane1.sh → assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh
- src/test/teamcity/deprecated/spades_sc_lane1_full.sh → assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh
- src/test/teamcity/deprecated/spades_sc_mruber.sh → assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh
- src/test/teamcity/deprecated/spades_sc_mruber_pre.sh → assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh
- src/test/teamcity/deprecated/spades_sc_phepa.sh → assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh
- src/test/teamcity/deprecated/spades_sc_phepa_pre.sh → assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh
- src/test/teamcity/deprecated/spades_sc_pmarinus.sh → assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh
- src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh → assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh
- src/test/teamcity/deprecated/teamcity.sh → assembler/src/test/teamcity/deprecated/teamcity.sh
- src/test/teamcity/deprecated/teamcity_ant.sh → assembler/src/test/teamcity/deprecated/teamcity_ant.sh
- src/test/teamcity/detect_diffs.sh → assembler/src/test/teamcity/detect_diffs.sh
- src/test/teamcity/force_update_symlinks.py → assembler/src/test/teamcity/force_update_symlinks.py
- src/test/teamcity/misc/copy_data.sh → assembler/src/test/teamcity/misc/copy_data.sh
- src/test/teamcity/misc/copy_to_ant.sh → assembler/src/test/teamcity/misc/copy_to_ant.sh
- src/test/teamcity/misc/restart_all_agents.sh → assembler/src/test/teamcity/misc/restart_all_agents.sh
- src/test/teamcity/misc/run_all_agents.sh → assembler/src/test/teamcity/misc/run_all_agents.sh
- src/test/teamcity/spades_ace_benchmark.sh → assembler/src/test/teamcity/spades_ace_benchmark.sh
- src/test/teamcity/spades_ace_multicell_benchmark.sh → assembler/src/test/teamcity/spades_ace_multicell_benchmark.sh
- src/test/teamcity/spades_ant_benchmark.sh → assembler/src/test/teamcity/spades_ant_benchmark.sh
- src/test/teamcity/spades_ant_multicell_benchmark.sh → assembler/src/test/teamcity/spades_ant_multicell_benchmark.sh
- src/test/teamcity/spades_unit_test.sh → assembler/src/test/teamcity/spades_unit_test.sh
- src/test/teamcity/teamcity.py → assembler/src/test/teamcity/teamcity.py
- src/test/teamcity/teamcity_empty_plasmid_test.sh → assembler/src/test/teamcity/teamcity_empty_plasmid_test.sh
- src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py → assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py
- src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py → assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py
- src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py → assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py
- src/test/teamcity/teamcity_kmertools/teamcity_readfilter.py → assembler/src/test/teamcity/teamcity_kmertools/teamcity_readfilter.py
- src/test/teamcity/teamcity_support.py → assembler/src/test/teamcity/teamcity_support.py
- + assembler/src/test/teamcity/teamcity_truspades_test.py
- src/test/teamcity/teamcity_workflow/check_configs.py → assembler/src/test/teamcity/teamcity_workflow/check_configs.py
- src/test/teamcity/teamcity_workflow/teamcity_workflow.py → assembler/src/test/teamcity/teamcity_workflow/teamcity_workflow.py
- src/test/teamcity/teamcity_workflow/workflow_base.py → assembler/src/test/teamcity/teamcity_workflow/workflow_base.py
- src/test/teamcity/teamcity_workflow/workflow_kmer.py → assembler/src/test/teamcity/teamcity_workflow/workflow_kmer.py
- src/test/teamcity/teamcity_workflow/workflow_smoke.py → assembler/src/test/teamcity/teamcity_workflow/workflow_smoke.py
- src/test/teamcity/test.sh → assembler/src/test/teamcity/test.sh
- src/test/teamcity/update_threshold.py → assembler/src/test/teamcity/update_threshold.py
- + assembler/src/tools/IlluminaTech/demultiplex.py
- + assembler/src/tools/IlluminaTech/generate_variations.py
- + assembler/src/tools/IlluminaTech/landmark_gen.py
- + assembler/src/tools/IlluminaTech/tru_quast.py
- + assembler/src/tools/IlluminaTech/variation_parser.py
- + assembler/src/tools/blast-fasta/blast_fasta.py
- + assembler/src/tools/clean_contaminations/16SrRNA/README
- + assembler/src/tools/clean_contaminations/16SrRNA/parse_tax_from_bowtie.py
- + assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.py
- + assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh
- + assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh
- + assembler/src/tools/clean_contaminations/README
- + assembler/src/tools/clean_contaminations/blast_contigs_and_process_output.sh
- + assembler/src/tools/clean_contaminations/build_index_for_multifasta.py
- + assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh
- + assembler/src/tools/clean_contaminations/process_blast_output.py
- + assembler/src/tools/clean_contaminations/read_fasta_using_index.py
- + assembler/src/tools/cleancontigs/cleancontigs.py
- + assembler/src/tools/cleancontigs/sort_contigs.py
- src/tools/contig_analysis/analyze_sinks.py → assembler/src/tools/contig_analysis/analyze_sinks.py
- src/tools/contig_analysis/break_scaffolds_into_contigs.py → assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py
- src/tools/contig_analysis/compare_fasta.py → assembler/src/tools/contig_analysis/compare_fasta.py
- src/tools/contig_analysis/compare_gaps.py → assembler/src/tools/contig_analysis/compare_gaps.py
- src/tools/contig_analysis/compare_gaps_pos.py → assembler/src/tools/contig_analysis/compare_gaps_pos.py
- src/tools/contig_analysis/compare_runs.sh → assembler/src/tools/contig_analysis/compare_runs.sh
- src/tools/contig_analysis/compare_used_snps.py → assembler/src/tools/contig_analysis/compare_used_snps.py
- src/tools/contig_analysis/contigs_concatenator.py → assembler/src/tools/contig_analysis/contigs_concatenator.py
- + assembler/src/tools/contig_analysis/fastaparser.py
- src/tools/contig_analysis/gap_finder.py → assembler/src/tools/contig_analysis/gap_finder.py
- src/tools/contig_analysis/get_misassembled_contigs.py → assembler/src/tools/contig_analysis/get_misassembled_contigs.py
- src/tools/contig_analysis/real_misassembly_counter.py → assembler/src/tools/contig_analysis/real_misassembly_counter.py
- src/tools/contig_analysis/texify_results.py → assembler/src/tools/contig_analysis/texify_results.py
- src/tools/contig_analysis/visualizer/arcs.py → assembler/src/tools/contig_analysis/visualizer/arcs.py
- + assembler/src/tools/contig_analysis/visualizer/main.py
- src/tools/contig_analysis/visualizer/mis_parser.py → assembler/src/tools/contig_analysis/visualizer/mis_parser.py
- src/tools/contig_analysis/visualizer/misassemblies.py → assembler/src/tools/contig_analysis/visualizer/misassemblies.py
- src/tools/contig_analysis/visualizer/misassemblies_old.py → assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py
- src/tools/contig_analysis/visualizer/miss_nocov.py → assembler/src/tools/contig_analysis/visualizer/miss_nocov.py
- src/tools/contig_analysis/visualizer/parser.py → assembler/src/tools/contig_analysis/visualizer/parser.py
- src/tools/contig_analysis/visualizer/run_parser.sh → assembler/src/tools/contig_analysis/visualizer/run_parser.sh
- src/tools/contig_analysis/visualizer/run_viz.sh → assembler/src/tools/contig_analysis/visualizer/run_viz.sh
- + assembler/src/tools/copy_ungzip.sh
- + assembler/src/tools/correctionEvaluator/README
- + assembler/src/tools/correctionEvaluator/bowtieOutputTranslator.py
- + assembler/src/tools/correctionEvaluator/common.py
- + assembler/src/tools/correctionEvaluator/comparator.py
- src/tools/correctionEvaluatorIon/Makefile → assembler/src/tools/correctionEvaluatorIon/Makefile
- src/tools/correctionEvaluatorIon/README → assembler/src/tools/correctionEvaluatorIon/README
- src/tools/correctionEvaluatorIon/bam2fastq.d → assembler/src/tools/correctionEvaluatorIon/bam2fastq.d
- + assembler/src/tools/correctionEvaluatorIon/cgce/CMakeLists.txt
- src/tools/correctionEvaluatorIon/cgce/cgce.cpp → assembler/src/tools/correctionEvaluatorIon/cgce/cgce.cpp
- src/tools/correctionEvaluatorIon/cluster_summaries.d → assembler/src/tools/correctionEvaluatorIon/cluster_summaries.d
- src/tools/correctionEvaluatorIon/comparator.d → assembler/src/tools/correctionEvaluatorIon/comparator.d
- src/tools/correctionEvaluatorIon/compile.sh → assembler/src/tools/correctionEvaluatorIon/compile.sh
- src/tools/correctionEvaluatorIon/error_sites.d → assembler/src/tools/correctionEvaluatorIon/error_sites.d
- src/tools/correctionEvaluatorIon/evaluate.sh → assembler/src/tools/correctionEvaluatorIon/evaluate.sh
- + assembler/src/tools/correctionEvaluatorIon/evaluate_kmers/CMakeLists.txt
- + assembler/src/tools/correctionEvaluatorIon/evaluate_kmers/kmer_evaluator.cpp
- src/tools/correctionEvaluatorIon/fasta_slice.d → assembler/src/tools/correctionEvaluatorIon/fasta_slice.d
- src/tools/correctionEvaluatorIon/ion_dist_table.d → assembler/src/tools/correctionEvaluatorIon/ion_dist_table.d
- src/tools/correctionEvaluatorIon/singletons.d → assembler/src/tools/correctionEvaluatorIon/singletons.d
- + assembler/src/tools/correctionEvaluatorIon/test_distance/CMakeLists.txt
- src/tools/correctionEvaluatorIon/test_distance/test_distance.cpp → assembler/src/tools/correctionEvaluatorIon/test_distance/test_distance.cpp
- + assembler/src/tools/coverage_based_rr/coverage.py
- + assembler/src/tools/cuckoo_test/cuckoo_test.cpp
- + assembler/src/tools/cuckoo_test/cuckoo_test.sh
- + assembler/src/tools/cuckoo_test/diagrams.gnu
- + assembler/src/tools/cuckoo_test/makefile
- + assembler/src/tools/dataset.py
- + assembler/src/tools/dataset_check
- + assembler/src/tools/dataset_hammer
- + assembler/src/tools/dataset_md5
- + assembler/src/tools/dataset_tar
- + assembler/src/tools/de_quality/.gitignore
- + assembler/src/tools/de_quality/README
- + assembler/src/tools/de_quality/alignment/align.sh
- + assembler/src/tools/de_quality/build.xml
- + assembler/src/tools/de_quality/cpfiles.sh
- + assembler/src/tools/de_quality/genFalse.sh
- + assembler/src/tools/de_quality/genPics.sh
- + assembler/src/tools/de_quality/genPlot.sh
- + assembler/src/tools/de_quality/genScaf.sh
- + assembler/src/tools/de_quality/lookAtPics.sh
- + assembler/src/tools/de_quality/src/GenStartStats.java
- + assembler/src/tools/de_quality/src/GetErrors.java
- + assembler/src/tools/de_quality/src/PlotFPR.java
- + assembler/src/tools/de_quality/src/utils/MyScanner.java
- + assembler/src/tools/divide_fastq/divide_fastq.py
- src/tools/dot_conv.sh → assembler/src/tools/dot_conv.sh
- + assembler/src/tools/estimation/run_real.sh
- + assembler/src/tools/estimation_deprecated/Nx_plot.py
- + assembler/src/tools/estimation_deprecated/README
- + assembler/src/tools/estimation_deprecated/assemblathon/README
- + assembler/src/tools/estimation_deprecated/assemblathon/assess_assembly.pl
- + assembler/src/tools/estimation_deprecated/cumulative.py
- + assembler/src/tools/estimation_deprecated/fastaparser.py
- + assembler/src/tools/estimation_deprecated/real_cumulative.py
- + assembler/src/tools/fastafix/fastafix.py
- + assembler/src/tools/fastaparser.py
- + assembler/src/tools/filter/filter.cpp
- + assembler/src/tools/filter/makefile
- + assembler/src/tools/kmersongenome/Debug/makefile
- + assembler/src/tools/kmersongenome/Debug/objects.mk
- + assembler/src/tools/kmersongenome/Debug/sources.mk
- + assembler/src/tools/kmersongenome/Debug/src/subdir.mk
- + assembler/src/tools/kmersongenome/Release/makefile
- + assembler/src/tools/kmersongenome/Release/objects.mk
- + assembler/src/tools/kmersongenome/Release/sources.mk
- + assembler/src/tools/kmersongenome/Release/src/subdir.mk
- + assembler/src/tools/kmersongenome/drawplot.pl
- + assembler/src/tools/kmersongenome/kmercov.tex
- + assembler/src/tools/kmersongenome/kmercoverage.pl
- + assembler/src/tools/kmersongenome/runjelly.pl
- + assembler/src/tools/kmersongenome/runqcount.pl
- + assembler/src/tools/kmersongenome/src/libtrie/Exception.cpp
- + assembler/src/tools/kmersongenome/src/libtrie/Exception.h
- + assembler/src/tools/kmersongenome/src/libtrie/Trie.h
- + assembler/src/tools/kmersongenome/src/libtrie/Trie.hxx
- + assembler/src/tools/kmersongenome/src/libtrie/TrieFactory.h
- + assembler/src/tools/kmersongenome/src/libtrie/TrieFactory.hxx
- + assembler/src/tools/kmersongenome/src/libtrie/TrieNode.h
- + assembler/src/tools/kmersongenome/src/libtrie/TrieNode.hxx
- + assembler/src/tools/kmersongenome/src/processjelly.cpp
- + assembler/src/tools/kmerstats/AdditionalFunction.cpp
- + assembler/src/tools/kmerstats/AdditionalFunction.h
- + assembler/src/tools/kmerstats/README
- + assembler/src/tools/kmerstats/algoritms/CountMinSketch.cpp
- + assembler/src/tools/kmerstats/algoritms/CountMinSketch.h
- + assembler/src/tools/kmerstats/algoritms/DistinctElements.cpp
- + assembler/src/tools/kmerstats/algoritms/DistinctElements.h
- + assembler/src/tools/kmerstats/algoritms/Frequent.cpp
- + assembler/src/tools/kmerstats/algoritms/Frequent.h
- + assembler/src/tools/kmerstats/algoritms/LossyCounting.cpp
- + assembler/src/tools/kmerstats/algoritms/LossyCounting.h
- + assembler/src/tools/kmerstats/algoritms/SpaceSaving.cpp
- + assembler/src/tools/kmerstats/algoritms/SpaceSaving.h
- + assembler/src/tools/kmerstats/analyses.cpp
- + assembler/src/tools/kmerstats/analyses.h
- + assembler/src/tools/kmerstats/commandline.cpp
- + assembler/src/tools/kmerstats/commandline.h
- + assembler/src/tools/kmerstats/file.gnu
- + assembler/src/tools/kmerstats/kmerstats.pro
- + assembler/src/tools/kmerstats/main.cpp
- + assembler/src/tools/loc_pic.py
- + assembler/src/tools/mail_sender/message.html
- + assembler/src/tools/mail_sender/message_3.6.1.html
- + assembler/src/tools/mapreads/mapreads.py
- + assembler/src/tools/maps_test/diagrams.gnu
- + assembler/src/tools/maps_test/filter.cpp
- + assembler/src/tools/maps_test/makefile
- + assembler/src/tools/maps_test/maps_test.sh
- + assembler/src/tools/mauve_assembly_align.sh
- + assembler/src/tools/misc/assembler_runner/CABOG_assemble.sh
- + assembler/src/tools/misc/assembler_runner/CABOG_config.txt
- + assembler/src/tools/misc/assembler_runner/CABOG_mp_assemble.sh
- + assembler/src/tools/misc/assembler_runner/MIRA_config.txt
- + assembler/src/tools/misc/assembler_runner/MIRA_mp_config.txt
- + assembler/src/tools/misc/assembler_runner/MSRCA_config.txt
- + assembler/src/tools/misc/assembler_runner/MSRCA_mp_config.txt
- + assembler/src/tools/misc/assembler_runner/SGA_assemble.sh
- + assembler/src/tools/misc/assembler_runner/SGA_assemble_cor.sh
- + assembler/src/tools/misc/assembler_runner/SGA_mp_assemble.sh
- + assembler/src/tools/misc/assembler_runner/SGA_mp_assemble_cor.sh
- + assembler/src/tools/misc/assembler_runner/SOAP_assemble.sh
- + assembler/src/tools/misc/assembler_runner/SOAP_config.txt
- + assembler/src/tools/misc/assembler_runner/SOAP_mp_config.txt
- + assembler/src/tools/misc/assembler_runner/VELVETSC_assemble.sh
- + assembler/src/tools/misc/assembler_runner/VELVETSC_mp_assemble.sh
- + assembler/src/tools/misc/assembler_runner/VELVET_assemble.sh
- + assembler/src/tools/misc/assembler_runner/VELVET_mp_assemble.sh
- + assembler/src/tools/misc/assembler_runner/ideal_assembler_chain
- + assembler/src/tools/misc/assembler_runner/ideal_assembler_runner.py
- + assembler/src/tools/misc/assembler_runner/runner.py
- + assembler/src/tools/misc/clean_python_tmp.sh
- + assembler/src/tools/misc/copyrighter.py
- src/tools/misc/datasets_converter.py → assembler/src/tools/misc/datasets_converter.py
- src/tools/misc/datasets_info2yaml_converter.py → assembler/src/tools/misc/datasets_info2yaml_converter.py
- src/tools/misc/datasets_info_cleaner.py → assembler/src/tools/misc/datasets_info_cleaner.py
- src/tools/misc/gcc_version_check.py → assembler/src/tools/misc/gcc_version_check.py
- src/tools/misc/markdown_to_github_html.py → assembler/src/tools/misc/markdown_to_github_html.py
- src/tools/misc/sam_analysis_sorter.py → assembler/src/tools/misc/sam_analysis_sorter.py
- src/tools/misc/sam_analyzer.py → assembler/src/tools/misc/sam_analyzer.py
- src/tools/misc/sam_analyzer_2.py → assembler/src/tools/misc/sam_analyzer_2.py
- src/tools/misc/sra_download.py → assembler/src/tools/misc/sra_download.py
- src/tools/misc/sv_simulator.py → assembler/src/tools/misc/sv_simulator.py
- src/tools/misc/txt2gff.py → assembler/src/tools/misc/txt2gff.py
- + assembler/src/tools/multi_hist.r
- + assembler/src/tools/nucmer_tool/makefile
- + assembler/src/tools/nucmer_tool/nucmer_coords_tool.cpp
- + assembler/src/tools/nucmer_tool/nucmer_coords_tool.hpp
- + assembler/src/tools/nucmer_tool/nucmer_tool_test.cpp
- + assembler/src/tools/prolonger/.gitignore
- + assembler/src/tools/quake-correct/.gitignore
- + assembler/src/tools/quake-correct/Makefile
- + assembler/src/tools/quake-correct/Read.cpp
- + assembler/src/tools/quake-correct/Read.h
- + assembler/src/tools/quake-correct/bithash.cpp
- + assembler/src/tools/quake-correct/bithash.h
- + assembler/src/tools/quake-correct/correct.cpp
- + assembler/src/tools/quake-correct/edit.cpp
- + assembler/src/tools/quake-correct/edit.h
- + assembler/src/tools/quake-correct/gzstream.C
- + assembler/src/tools/quake-correct/gzstream.h
- + assembler/src/tools/readsReformatter.hpp
- src/tools/reads_utils/conversion/broken_fastq_filter.py → assembler/src/tools/reads_utils/conversion/broken_fastq_filter.py
- src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py → assembler/src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py
- src/tools/reads_utils/conversion/fasta_to_fastq.py → assembler/src/tools/reads_utils/conversion/fasta_to_fastq.py
- + assembler/src/tools/reads_utils/conversion/fastaparser.py
- src/tools/reads_utils/conversion/fastq_crop_read_length.py → assembler/src/tools/reads_utils/conversion/fastq_crop_read_length.py
- src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py → assembler/src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py
- src/tools/reads_utils/conversion/join.py → assembler/src/tools/reads_utils/conversion/join.py
- src/tools/reads_utils/conversion/meraculus_to_fastq.py → assembler/src/tools/reads_utils/conversion/meraculus_to_fastq.py
- src/tools/reads_utils/conversion/multiline_to_oneline_reads.py → assembler/src/tools/reads_utils/conversion/multiline_to_oneline_reads.py
- + assembler/src/tools/reads_utils/conversion/rf_to_fr.py
- src/tools/reads_utils/conversion/single_fastq_to_paired.py → assembler/src/tools/reads_utils/conversion/single_fastq_to_paired.py
- src/tools/reads_utils/conversion/split_2_fasts_any_format.py → assembler/src/tools/reads_utils/conversion/split_2_fasts_any_format.py
- src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py → assembler/src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py
- src/tools/reads_utils/conversion/split_fastq.py → assembler/src/tools/reads_utils/conversion/split_fastq.py
- src/tools/reads_utils/conversion/to_meraculus.py → assembler/src/tools/reads_utils/conversion/to_meraculus.py
- src/tools/reads_utils/conversion/trim_ns.py → assembler/src/tools/reads_utils/conversion/trim_ns.py
- src/tools/reads_utils/crop/crop_bfaecium.py → assembler/src/tools/reads_utils/crop/crop_bfaecium.py
- src/tools/reads_utils/crop/crop_ecoli.py → assembler/src/tools/reads_utils/crop/crop_ecoli.py
- src/tools/reads_utils/crop/crop_genome.py → assembler/src/tools/reads_utils/crop/crop_genome.py
- src/tools/reads_utils/crop/crop_reads.py → assembler/src/tools/reads_utils/crop/crop_reads.py
- src/tools/reads_utils/crop/paired_crop.py → assembler/src/tools/reads_utils/crop/paired_crop.py
- src/tools/reads_utils/crop/single_crop.py → assembler/src/tools/reads_utils/crop/single_crop.py
- src/tools/reads_utils/filter/filter_contigs.py → assembler/src/tools/reads_utils/filter/filter_contigs.py
- src/tools/reads_utils/filter/filter_reads.py → assembler/src/tools/reads_utils/filter/filter_reads.py
- src/tools/reads_utils/filter/filter_reads_by_fastq.py → assembler/src/tools/reads_utils/filter/filter_reads_by_fastq.py
- src/tools/reads_utils/filter/filter_reads_by_paired.py → assembler/src/tools/reads_utils/filter/filter_reads_by_paired.py
- src/tools/reads_utils/filter/filter_single_reads.py → assembler/src/tools/reads_utils/filter/filter_single_reads.py
- src/tools/reads_utils/ideal_by_fasta.py → assembler/src/tools/reads_utils/ideal_by_fasta.py
- src/tools/reads_utils/ideal_sim.py → assembler/src/tools/reads_utils/ideal_sim.py
- src/tools/reads_utils/identical_contigs_stats.py → assembler/src/tools/reads_utils/identical_contigs_stats.py
- src/tools/reads_utils/meta/mixin_contamination.py → assembler/src/tools/reads_utils/meta/mixin_contamination.py
- src/tools/reads_utils/paired_reads_quality.py → assembler/src/tools/reads_utils/paired_reads_quality.py
- src/tools/reads_utils/read_stat.py → assembler/src/tools/reads_utils/read_stat.py
- src/tools/reads_utils/reads_quality.py → assembler/src/tools/reads_utils/reads_quality.py
- src/tools/reads_utils/report_maker.py → assembler/src/tools/reads_utils/report_maker.py
- src/tools/reads_utils/scaf_to_cont.pl → assembler/src/tools/reads_utils/scaf_to_cont.pl
- src/tools/reads_utils/simulate_ideal_by_dataset.py → assembler/src/tools/reads_utils/simulate_ideal_by_dataset.py
- src/tools/reads_utils/simulate_ideal_by_fasta.py → assembler/src/tools/reads_utils/simulate_ideal_by_fasta.py
- src/tools/reads_utils/stat/coverage_hist.py → assembler/src/tools/reads_utils/stat/coverage_hist.py
- src/tools/reads_utils/stat/gc.py → assembler/src/tools/reads_utils/stat/gc.py
- src/tools/reads_utils/stat/is.py → assembler/src/tools/reads_utils/stat/is.py
- src/tools/reads_utils/stat/is_from_single_log.py → assembler/src/tools/reads_utils/stat/is_from_single_log.py
- src/tools/reads_utils/stat/is_genome.py → assembler/src/tools/reads_utils/stat/is_genome.py
- src/tools/reads_utils/stat/mean_is.py → assembler/src/tools/reads_utils/stat/mean_is.py
- src/tools/reads_utils/stat/overlaps.py → assembler/src/tools/reads_utils/stat/overlaps.py
- src/tools/reads_utils/stat/raw.py → assembler/src/tools/reads_utils/stat/raw.py
- src/tools/reads_utils/stat/raw_single.py → assembler/src/tools/reads_utils/stat/raw_single.py
- src/tools/reads_utils/stat/raw_w_gc.py → assembler/src/tools/reads_utils/stat/raw_w_gc.py
- src/tools/reads_utils/stat/raws_w_orientation.py → assembler/src/tools/reads_utils/stat/raws_w_orientation.py
- src/tools/reads_utils/stat/read_coverage.py → assembler/src/tools/reads_utils/stat/read_coverage.py
- src/tools/reads_utils/stat/reads_length.py → assembler/src/tools/reads_utils/stat/reads_length.py
- + assembler/src/tools/reads_utils/stat/rf_to_fr.py
- src/tools/reads_utils/stat/shift.py → assembler/src/tools/reads_utils/stat/shift.py
- src/tools/reads_utils/stat/single_log_to_paired.py → assembler/src/tools/reads_utils/stat/single_log_to_paired.py
- src/tools/reads_utils/stat/trim.py → assembler/src/tools/reads_utils/stat/trim.py
- src/tools/res_counter/README → assembler/src/tools/res_counter/README
- src/tools/res_counter/measure_all.sh → assembler/src/tools/res_counter/measure_all.sh
- src/tools/res_counter/mem_checker.py → assembler/src/tools/res_counter/mem_checker.py
- src/tools/res_counter/pstree.c → assembler/src/tools/res_counter/pstree.c
- src/tools/res_counter/result_saver.sh → assembler/src/tools/res_counter/result_saver.sh
- src/tools/res_counter/run.pl → assembler/src/tools/res_counter/run.pl
- src/tools/res_counter/spades_pipeline_measurer.sh → assembler/src/tools/res_counter/spades_pipeline_measurer.sh
- src/tools/res_counter/stats_counter.py → assembler/src/tools/res_counter/stats_counter.py
- + assembler/src/tools/run_velvet2.sh
- + assembler/src/tools/run_velvet_unpaired.sh
- + assembler/src/tools/seq_filter.hpp
- + assembler/src/tools/seq_filter_stat.hpp
- + assembler/src/tools/sequenceDistanceMeter/main.py
- + assembler/src/tools/sequenceDistanceMeter/sequenceDistanceMeter.py
- + assembler/src/tools/sequenceDistanceMeter/sequenceDistanceMeter_test.py
- + assembler/src/tools/spades_build/bug-fix.version
- + assembler/src/tools/spades_build/tag-bug-fix.sh
- + assembler/src/tools/spades_download_stats/filter.py
- + assembler/src/tools/spades_download_stats/grep_stat.sh
- + assembler/src/tools/spades_download_stats/grep_stat_old.sh
- + assembler/src/tools/spades_download_stats/grep_stat_old221.sh
- + assembler/src/tools/spades_download_stats/grep_stat_rpm.sh
- + assembler/src/tools/spades_download_stats/grep_stat_veryold.sh
- + assembler/src/tools/spades_download_stats/readme.txt
- + assembler/src/tools/spades_download_stats/stat.sh
- + assembler/src/tools/spades_download_stats/stat_all.sh
- src/tools/spades_holybox_compile.sh → assembler/src/tools/spades_holybox_compile.sh
- + assembler/src/tools/spades_pipeline/spades_download_binary.py
- src/tools/stash_cfg → assembler/src/tools/stash_cfg
- + assembler/src/tools/truseq/quast_all.py
- + assembler/src/tools/truseq/quast_all.sh
- + assembler/src/tools/ukonnen/ukonnen.py
- src/projects/spades/test_dataset/ecoli_1K_1.fq.gz → assembler/test_dataset/ecoli_1K_1.fq.gz
- src/projects/spades/test_dataset/ecoli_1K_2.fq.gz → assembler/test_dataset/ecoli_1K_2.fq.gz
- src/projects/spades/test_dataset/genes_1K.gff → assembler/test_dataset/genes_1K.gff
- src/projects/spades/test_dataset/genes_1K.txt → assembler/test_dataset/genes_1K.txt
- src/projects/spades/test_dataset/operons_1K.gff → assembler/test_dataset/operons_1K.gff
- src/projects/spades/test_dataset/operons_1K.txt → assembler/test_dataset/operons_1K.txt
- src/projects/spades/test_dataset/reference_1K.fa.gz → assembler/test_dataset/reference_1K.fa.gz
- src/projects/spades/test_dataset_plasmid/pl1.fq.gz → assembler/test_dataset_plasmid/pl1.fq.gz
- src/projects/spades/test_dataset_plasmid/pl2.fq.gz → assembler/test_dataset_plasmid/pl2.fq.gz
- + assembler/test_dataset_truspades/A_R1.fastq.gz
- + assembler/test_dataset_truspades/A_R2.fastq.gz
- + assembler/test_dataset_truspades/B_R1.fastq.gz
- + assembler/test_dataset_truspades/B_R2.fastq.gz
- + assembler/truspades.py
- + assembler/truspades_manual.html
- − changelog.md
- + dnanexus/Makefile
- + dnanexus/Readme.md
- + dnanexus/dxapp.json
- + dnanexus/src/spades-dnanexus.sh
- − docs/binspreader.md
- − docs/citation.md
- − docs/datatypes.md
- − docs/feedback.md
- − docs/getting-started.md
- − docs/getversion.py
- − docs/hmm.md
- − docs/hybrid.md
- − docs/index.md
- − docs/input.md
- − docs/installation.md
- − docs/output.md
- − docs/pHMM_with_frameshifts.svg
- − docs/pathracer.md
- − docs/rna.md
- − docs/running.md
- − docs/spades.png
- − docs/spaligner.md
- − docs/standalone.md
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- − ext/include/blaze/blaze/Math.h
- − ext/include/blaze/blaze/Tutorial.h
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- − ext/include/blaze/blaze/math/constraints/Shrinkable.h
- − ext/include/blaze/blaze/math/constraints/SolveExpr.h
- − ext/include/blaze/blaze/math/constraints/SparseElement.h
- − ext/include/blaze/blaze/math/constraints/SparseMatrix.h
- − ext/include/blaze/blaze/math/constraints/SparseVector.h
- − ext/include/blaze/blaze/math/constraints/Square.h
- − ext/include/blaze/blaze/math/constraints/Static.h
- − ext/include/blaze/blaze/math/constraints/StorageOrder.h
- − ext/include/blaze/blaze/math/constraints/StrictlyLower.h
- − ext/include/blaze/blaze/math/constraints/StrictlyTriangular.h
- − ext/include/blaze/blaze/math/constraints/StrictlyUpper.h
- − ext/include/blaze/blaze/math/constraints/SubExpr.h
- − ext/include/blaze/blaze/math/constraints/Submatrix.h
- − ext/include/blaze/blaze/math/constraints/Subvector.h
- − ext/include/blaze/blaze/math/constraints/Symmetric.h
- − ext/include/blaze/blaze/math/constraints/TVecMatMultExpr.h
- − ext/include/blaze/blaze/math/constraints/TransExpr.h
- − ext/include/blaze/blaze/math/constraints/Transformation.h
- − ext/include/blaze/blaze/math/constraints/TransposeFlag.h
- − ext/include/blaze/blaze/math/constraints/Triangular.h
- − ext/include/blaze/blaze/math/constraints/UnaryMapExpr.h
- − ext/include/blaze/blaze/math/constraints/UniLower.h
- − ext/include/blaze/blaze/math/constraints/UniTriangular.h
- − ext/include/blaze/blaze/math/constraints/UniUpper.h
- − ext/include/blaze/blaze/math/constraints/Uniform.h
- − ext/include/blaze/blaze/math/constraints/Upper.h
- − ext/include/blaze/blaze/math/constraints/VecEvalExpr.h
- − ext/include/blaze/blaze/math/constraints/VecExpandExpr.h
- − ext/include/blaze/blaze/math/constraints/VecGenExpr.h
- − ext/include/blaze/blaze/math/constraints/VecMapExpr.h
- − ext/include/blaze/blaze/math/constraints/VecNoAliasExpr.h
- − ext/include/blaze/blaze/math/constraints/VecNoSIMDExpr.h
- − ext/include/blaze/blaze/math/constraints/VecRepeatExpr.h
- − ext/include/blaze/blaze/math/constraints/VecScalarDivExpr.h
- − ext/include/blaze/blaze/math/constraints/VecScalarMultExpr.h
- − ext/include/blaze/blaze/math/constraints/VecSerialExpr.h
- − ext/include/blaze/blaze/math/constraints/VecTVecMapExpr.h
- − ext/include/blaze/blaze/math/constraints/VecTVecMultExpr.h
- − ext/include/blaze/blaze/math/constraints/VecTransExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecAddExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecDivExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecKronExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecMapExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecMultExpr.h
- − ext/include/blaze/blaze/math/constraints/VecVecSubExpr.h
- − ext/include/blaze/blaze/math/constraints/Vector.h
- − ext/include/blaze/blaze/math/constraints/View.h
- − ext/include/blaze/blaze/math/constraints/Zero.h
- − ext/include/blaze/blaze/math/dense/CustomMatrix.h
- − ext/include/blaze/blaze/math/dense/CustomVector.h
- − ext/include/blaze/blaze/math/dense/DenseIterator.h
- − ext/include/blaze/blaze/math/dense/DenseMatrix.h
- − ext/include/blaze/blaze/math/dense/DenseVector.h
- − ext/include/blaze/blaze/math/dense/DynamicMatrix.h
- − ext/include/blaze/blaze/math/dense/DynamicVector.h
- − ext/include/blaze/blaze/math/dense/Eigen.h
- − ext/include/blaze/blaze/math/dense/Forward.h
- − ext/include/blaze/blaze/math/dense/HybridMatrix.h
- − ext/include/blaze/blaze/math/dense/HybridVector.h
- − ext/include/blaze/blaze/math/dense/InitializerIterator.h
- − ext/include/blaze/blaze/math/dense/InitializerMatrix.h
- − ext/include/blaze/blaze/math/dense/InitializerVector.h
- − ext/include/blaze/blaze/math/dense/Inversion.h
- − ext/include/blaze/blaze/math/dense/LLH.h
- − ext/include/blaze/blaze/math/dense/LQ.h
- − ext/include/blaze/blaze/math/dense/LSE.h
- − ext/include/blaze/blaze/math/dense/LU.h
- − ext/include/blaze/blaze/math/dense/MMM.h
- − ext/include/blaze/blaze/math/dense/QL.h
- − ext/include/blaze/blaze/math/dense/QR.h
- − ext/include/blaze/blaze/math/dense/RQ.h
- − ext/include/blaze/blaze/math/dense/SVD.h
- − ext/include/blaze/blaze/math/dense/StaticMatrix.h
- − ext/include/blaze/blaze/math/dense/StaticVector.h
- − ext/include/blaze/blaze/math/dense/UniformIterator.h
- − ext/include/blaze/blaze/math/dense/UniformMatrix.h
- − ext/include/blaze/blaze/math/dense/UniformVector.h
- − ext/include/blaze/blaze/math/expressions/AddExpr.h
- − ext/include/blaze/blaze/math/expressions/BinaryMapExpr.h
- − ext/include/blaze/blaze/math/expressions/Computation.h
- − ext/include/blaze/blaze/math/expressions/CrossExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatSolveExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDVecSolveExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclDiagExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclHermExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclStrLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclStrUppExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclSymExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclUniLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclUniUppExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDeclUppExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatDetExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatEigenExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatExpExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatGenExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatInvExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatMeanExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatNoAliasExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatNoSIMDExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatNormExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatReduceExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSVDExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatSoftmaxExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatStdDevExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTDMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTDMatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTDMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTDMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTransExpr.h
- − ext/include/blaze/blaze/math/expressions/DMatTransposer.h
- − ext/include/blaze/blaze/math/expressions/DMatVarExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecCrossExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecDivExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecInnerExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecKronExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecOuterExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecDVecSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecExpandExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecGenExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecMeanExpr.h
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- − ext/include/blaze/blaze/math/expressions/DVecReduceExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecAddExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecCrossExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecInnerExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecKronExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSVecMultExpr.h
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- − ext/include/blaze/blaze/math/expressions/DVecSVecSubExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecSoftmaxExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecStdDevExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecTransExpr.h
- − ext/include/blaze/blaze/math/expressions/DVecTransposer.h
- − ext/include/blaze/blaze/math/expressions/DVecVarExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclDiagExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclHermExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclStrLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclStrUppExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclSymExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclUniLowExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclUniUppExpr.h
- − ext/include/blaze/blaze/math/expressions/DeclUppExpr.h
- − ext/include/blaze/blaze/math/expressions/Declaration.h
- − ext/include/blaze/blaze/math/expressions/DenseMatrix.h
- − ext/include/blaze/blaze/math/expressions/DenseVector.h
- − ext/include/blaze/blaze/math/expressions/DivExpr.h
- − ext/include/blaze/blaze/math/expressions/EigenExpr.h
- − ext/include/blaze/blaze/math/expressions/EvalExpr.h
- − ext/include/blaze/blaze/math/expressions/ExpandExpr.h
- − ext/include/blaze/blaze/math/expressions/ExpandExprData.h
- − ext/include/blaze/blaze/math/expressions/Expression.h
- − ext/include/blaze/blaze/math/expressions/Forward.h
- − ext/include/blaze/blaze/math/expressions/GenExpr.h
- − ext/include/blaze/blaze/math/expressions/KronExpr.h
- − ext/include/blaze/blaze/math/expressions/MatEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/MatExpExpr.h
- − ext/include/blaze/blaze/math/expressions/MatGenExpr.h
- − ext/include/blaze/blaze/math/expressions/MatInvExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatSolveExpr.h
- − ext/include/blaze/blaze/math/expressions/MatMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/MatNoAliasExpr.h
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- − ext/include/blaze/blaze/math/expressions/MatRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/MatScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/MatScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/MatSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/MatTransExpr.h
- − ext/include/blaze/blaze/math/expressions/MatVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/MatVecSolveExpr.h
- − ext/include/blaze/blaze/math/expressions/Matrix.h
- − ext/include/blaze/blaze/math/expressions/Modification.h
- − ext/include/blaze/blaze/math/expressions/MultExpr.h
- − ext/include/blaze/blaze/math/expressions/NoAliasExpr.h
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- − ext/include/blaze/blaze/math/expressions/Operation.h
- − ext/include/blaze/blaze/math/expressions/ReduceExpr.h
- − ext/include/blaze/blaze/math/expressions/RepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/RepeatExprData.h
- − ext/include/blaze/blaze/math/expressions/SMatDMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclDiagExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclHermExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclLowExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclStrLowExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclStrUppExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclSymExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclUniLowExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclUniUppExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatDeclUppExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatMapExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatMeanExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatNoAliasExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatNoSIMDExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatNormExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatReduceExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatStdDevExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTDMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTSMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTransExpr.h
- − ext/include/blaze/blaze/math/expressions/SMatTransposer.h
- − ext/include/blaze/blaze/math/expressions/SMatVarExpr.h
- − ext/include/blaze/blaze/math/expressions/SVDExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecDVecCrossExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecDVecDivExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecDVecInnerExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecDVecKronExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecDVecMultExpr.h
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- − ext/include/blaze/blaze/math/expressions/SVecDVecSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecExpandExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecMeanExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecNoAliasExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecNoSIMDExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecNormExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecReduceExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecAddExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecCrossExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecEqualExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecInnerExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecKronExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecOuterExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSVecSubExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecStdDevExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecTransExpr.h
- − ext/include/blaze/blaze/math/expressions/SVecTransposer.h
- − ext/include/blaze/blaze/math/expressions/SVecVarExpr.h
- − ext/include/blaze/blaze/math/expressions/SchurExpr.h
- − ext/include/blaze/blaze/math/expressions/SerialExpr.h
- − ext/include/blaze/blaze/math/expressions/SolveExpr.h
- − ext/include/blaze/blaze/math/expressions/SparseMatrix.h
- − ext/include/blaze/blaze/math/expressions/SparseVector.h
- − ext/include/blaze/blaze/math/expressions/SubExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatDVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatSVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDMatTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDVecDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDVecSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDVecTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TDVecTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatDMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatDMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatDVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatSMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatSVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTSMatAddExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTSMatKronExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTSMatSchurExpr.h
- − ext/include/blaze/blaze/math/expressions/TSMatTSMatSubExpr.h
- − ext/include/blaze/blaze/math/expressions/TSVecDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSVecSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSVecTDMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TSVecTSMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TVecMatMultExpr.h
- − ext/include/blaze/blaze/math/expressions/TransExpr.h
- − ext/include/blaze/blaze/math/expressions/Transformation.h
- − ext/include/blaze/blaze/math/expressions/UnaryMapExpr.h
- − ext/include/blaze/blaze/math/expressions/VecEvalExpr.h
- − ext/include/blaze/blaze/math/expressions/VecExpandExpr.h
- − ext/include/blaze/blaze/math/expressions/VecGenExpr.h
- − ext/include/blaze/blaze/math/expressions/VecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/VecNoAliasExpr.h
- − ext/include/blaze/blaze/math/expressions/VecNoSIMDExpr.h
- − ext/include/blaze/blaze/math/expressions/VecRepeatExpr.h
- − ext/include/blaze/blaze/math/expressions/VecScalarDivExpr.h
- − ext/include/blaze/blaze/math/expressions/VecScalarMultExpr.h
- − ext/include/blaze/blaze/math/expressions/VecSerialExpr.h
- − ext/include/blaze/blaze/math/expressions/VecTVecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/VecTVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/VecTransExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecAddExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecDivExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecKronExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecMapExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecMultExpr.h
- − ext/include/blaze/blaze/math/expressions/VecVecSubExpr.h
- − ext/include/blaze/blaze/math/expressions/Vector.h
- − ext/include/blaze/blaze/math/expressions/View.h
- − ext/include/blaze/blaze/math/functors/Abs.h
- − ext/include/blaze/blaze/math/functors/Acos.h
- − ext/include/blaze/blaze/math/functors/Acosh.h
- − ext/include/blaze/blaze/math/functors/Add.h
- − ext/include/blaze/blaze/math/functors/AddAssign.h
- − ext/include/blaze/blaze/math/functors/And.h
- − ext/include/blaze/blaze/math/functors/AndAssign.h
- − ext/include/blaze/blaze/math/functors/Arg.h
- − ext/include/blaze/blaze/math/functors/Asin.h
- − ext/include/blaze/blaze/math/functors/Asinh.h
- − ext/include/blaze/blaze/math/functors/Assign.h
- − ext/include/blaze/blaze/math/functors/Atan.h
- − ext/include/blaze/blaze/math/functors/Atan2.h
- − ext/include/blaze/blaze/math/functors/Atanh.h
- − ext/include/blaze/blaze/math/functors/Bind1st.h
- − ext/include/blaze/blaze/math/functors/Bind2nd.h
- − ext/include/blaze/blaze/math/functors/Bind3rd.h
- − ext/include/blaze/blaze/math/functors/Bitand.h
- − ext/include/blaze/blaze/math/functors/Bitor.h
- − ext/include/blaze/blaze/math/functors/Bitxor.h
- − ext/include/blaze/blaze/math/functors/CTrans.h
- − ext/include/blaze/blaze/math/functors/Cbrt.h
- − ext/include/blaze/blaze/math/functors/Ceil.h
- − ext/include/blaze/blaze/math/functors/Clamp.h
- − ext/include/blaze/blaze/math/functors/Clear.h
- − ext/include/blaze/blaze/math/functors/Conj.h
- − ext/include/blaze/blaze/math/functors/Cos.h
- − ext/include/blaze/blaze/math/functors/Cosh.h
- − ext/include/blaze/blaze/math/functors/DeclDiag.h
- − ext/include/blaze/blaze/math/functors/DeclHerm.h
- − ext/include/blaze/blaze/math/functors/DeclId.h
- − ext/include/blaze/blaze/math/functors/DeclLow.h
- − ext/include/blaze/blaze/math/functors/DeclStrLow.h
- − ext/include/blaze/blaze/math/functors/DeclStrUpp.h
- − ext/include/blaze/blaze/math/functors/DeclSym.h
- − ext/include/blaze/blaze/math/functors/DeclUniLow.h
- − ext/include/blaze/blaze/math/functors/DeclUniUpp.h
- − ext/include/blaze/blaze/math/functors/DeclUpp.h
- − ext/include/blaze/blaze/math/functors/DeclZero.h
- − ext/include/blaze/blaze/math/functors/Div.h
- − ext/include/blaze/blaze/math/functors/DivAssign.h
- − ext/include/blaze/blaze/math/functors/Erf.h
- − ext/include/blaze/blaze/math/functors/Erfc.h
- − ext/include/blaze/blaze/math/functors/Eval.h
- − ext/include/blaze/blaze/math/functors/Exp.h
- − ext/include/blaze/blaze/math/functors/Exp10.h
- − ext/include/blaze/blaze/math/functors/Exp2.h
- − ext/include/blaze/blaze/math/functors/Floor.h
- − ext/include/blaze/blaze/math/functors/Forward.h
- − ext/include/blaze/blaze/math/functors/Functors.h
- − ext/include/blaze/blaze/math/functors/Greater.h
- − ext/include/blaze/blaze/math/functors/Hypot.h
- − ext/include/blaze/blaze/math/functors/Imag.h
- − ext/include/blaze/blaze/math/functors/Inv.h
- − ext/include/blaze/blaze/math/functors/InvAdd.h
- − ext/include/blaze/blaze/math/functors/InvCbrt.h
- − ext/include/blaze/blaze/math/functors/InvSqrt.h
- − ext/include/blaze/blaze/math/functors/Join.h
- − ext/include/blaze/blaze/math/functors/Kron.h
- − ext/include/blaze/blaze/math/functors/L1Norm.h
- − ext/include/blaze/blaze/math/functors/L2Norm.h
- − ext/include/blaze/blaze/math/functors/L3Norm.h
- − ext/include/blaze/blaze/math/functors/L4Norm.h
- − ext/include/blaze/blaze/math/functors/LGamma.h
- − ext/include/blaze/blaze/math/functors/LeftShiftAssign.h
- − ext/include/blaze/blaze/math/functors/Less.h
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- − ext/include/blaze/blaze/math/functors/Log10.h
- − ext/include/blaze/blaze/math/functors/Log1p.h
- − ext/include/blaze/blaze/math/functors/Log2.h
- − ext/include/blaze/blaze/math/functors/LpNorm.h
- − ext/include/blaze/blaze/math/functors/MAC.h
- − ext/include/blaze/blaze/math/functors/MakePair.h
- − ext/include/blaze/blaze/math/functors/Max.h
- − ext/include/blaze/blaze/math/functors/Min.h
- − ext/include/blaze/blaze/math/functors/Minmax.h
- − ext/include/blaze/blaze/math/functors/ModuloAssign.h
- − ext/include/blaze/blaze/math/functors/Mult.h
- − ext/include/blaze/blaze/math/functors/MultAssign.h
- − ext/include/blaze/blaze/math/functors/NoAlias.h
- − ext/include/blaze/blaze/math/functors/NoSIMD.h
- − ext/include/blaze/blaze/math/functors/Noop.h
- − ext/include/blaze/blaze/math/functors/Not.h
- − ext/include/blaze/blaze/math/functors/Or.h
- − ext/include/blaze/blaze/math/functors/OrAssign.h
- − ext/include/blaze/blaze/math/functors/Pow.h
- − ext/include/blaze/blaze/math/functors/Pow2.h
- − ext/include/blaze/blaze/math/functors/Pow3.h
- − ext/include/blaze/blaze/math/functors/Pow4.h
- − ext/include/blaze/blaze/math/functors/Qdrt.h
- − ext/include/blaze/blaze/math/functors/Real.h
- − ext/include/blaze/blaze/math/functors/Reset.h
- − ext/include/blaze/blaze/math/functors/RightShiftAssign.h
- − ext/include/blaze/blaze/math/functors/Round.h
- − ext/include/blaze/blaze/math/functors/Schur.h
- − ext/include/blaze/blaze/math/functors/Serial.h
- − ext/include/blaze/blaze/math/functors/ShiftLI.h
- − ext/include/blaze/blaze/math/functors/ShiftLV.h
- − ext/include/blaze/blaze/math/functors/ShiftRI.h
- − ext/include/blaze/blaze/math/functors/ShiftRV.h
- − ext/include/blaze/blaze/math/functors/Sign.h
- − ext/include/blaze/blaze/math/functors/Sin.h
- − ext/include/blaze/blaze/math/functors/Sinh.h
- − ext/include/blaze/blaze/math/functors/SqrAbs.h
- − ext/include/blaze/blaze/math/functors/Sqrt.h
- − ext/include/blaze/blaze/math/functors/Sub.h
- − ext/include/blaze/blaze/math/functors/SubAssign.h
- − ext/include/blaze/blaze/math/functors/Tan.h
- − ext/include/blaze/blaze/math/functors/Tanh.h
- − ext/include/blaze/blaze/math/functors/Trans.h
- − ext/include/blaze/blaze/math/functors/Trunc.h
- − ext/include/blaze/blaze/math/functors/XorAssign.h
- − ext/include/blaze/blaze/math/lapack/LAPACK.h
- − ext/include/blaze/blaze/math/lapack/clapack/geev.h
- − ext/include/blaze/blaze/math/lapack/clapack/gelqf.h
- − ext/include/blaze/blaze/math/lapack/clapack/geqlf.h
- − ext/include/blaze/blaze/math/lapack/clapack/geqp3.h
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- − ext/include/blaze/blaze/math/lapack/clapack/gerqf.h
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- − ext/include/blaze/blaze/math/lapack/geqp3.h
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- − ext/include/blaze/blaze/math/proxy/DenseVectorProxy.h
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- − ext/include/blaze/blaze/math/proxy/Proxy.h
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- − ext/include/blaze/blaze/math/proxy/SparseVectorProxy.h
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- − ext/include/blaze/blaze/math/shims/Arg.h
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- − ext/include/blaze/blaze/math/shims/Digits.h
- − ext/include/blaze/blaze/math/shims/Equal.h
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- − ext/include/blaze/blaze/math/shims/Hypot.h
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- − ext/include/blaze/blaze/math/shims/IsDefault.h
- − ext/include/blaze/blaze/math/shims/IsDivisor.h
- − ext/include/blaze/blaze/math/shims/IsFinite.h
- − ext/include/blaze/blaze/math/shims/IsInf.h
- − ext/include/blaze/blaze/math/shims/IsNaN.h
- − ext/include/blaze/blaze/math/shims/IsOne.h
- − ext/include/blaze/blaze/math/shims/IsReal.h
- − ext/include/blaze/blaze/math/shims/IsZero.h
- − ext/include/blaze/blaze/math/shims/LGamma.h
- − ext/include/blaze/blaze/math/shims/Less.h
- − ext/include/blaze/blaze/math/shims/Log.h
- − ext/include/blaze/blaze/math/shims/Log10.h
- − ext/include/blaze/blaze/math/shims/Log1p.h
- − ext/include/blaze/blaze/math/shims/Log2.h
- − ext/include/blaze/blaze/math/shims/NextMultiple.h
- − ext/include/blaze/blaze/math/shims/Pow.h
- − ext/include/blaze/blaze/math/shims/Pow2.h
- − ext/include/blaze/blaze/math/shims/Pow3.h
- − ext/include/blaze/blaze/math/shims/Pow4.h
- − ext/include/blaze/blaze/math/shims/PrevMultiple.h
- − ext/include/blaze/blaze/math/shims/Qdrt.h
- − ext/include/blaze/blaze/math/shims/Real.h
- − ext/include/blaze/blaze/math/shims/Reset.h
- − ext/include/blaze/blaze/math/shims/Round.h
- − ext/include/blaze/blaze/math/shims/Serial.h
- − ext/include/blaze/blaze/math/shims/Shims.h
- − ext/include/blaze/blaze/math/shims/Sign.h
- − ext/include/blaze/blaze/math/shims/Sin.h
- − ext/include/blaze/blaze/math/shims/Sinh.h
- − ext/include/blaze/blaze/math/shims/Sqrt.h
- − ext/include/blaze/blaze/math/shims/Tan.h
- − ext/include/blaze/blaze/math/shims/Tanh.h
- − ext/include/blaze/blaze/math/shims/Trunc.h
- − ext/include/blaze/blaze/math/simd/Abs.h
- − ext/include/blaze/blaze/math/simd/Acos.h
- − ext/include/blaze/blaze/math/simd/Acosh.h
- − ext/include/blaze/blaze/math/simd/Add.h
- − ext/include/blaze/blaze/math/simd/Asin.h
- − ext/include/blaze/blaze/math/simd/Asinh.h
- − ext/include/blaze/blaze/math/simd/Atan.h
- − ext/include/blaze/blaze/math/simd/Atan2.h
- − ext/include/blaze/blaze/math/simd/Atanh.h
- − ext/include/blaze/blaze/math/simd/BasicTypes.h
- − ext/include/blaze/blaze/math/simd/Bitand.h
- − ext/include/blaze/blaze/math/simd/Bitor.h
- − ext/include/blaze/blaze/math/simd/Bitxor.h
- − ext/include/blaze/blaze/math/simd/Cbrt.h
- − ext/include/blaze/blaze/math/simd/Ceil.h
- − ext/include/blaze/blaze/math/simd/Conj.h
- − ext/include/blaze/blaze/math/simd/Cos.h
- − ext/include/blaze/blaze/math/simd/Cosh.h
- − ext/include/blaze/blaze/math/simd/DerivedTypes.h
- − ext/include/blaze/blaze/math/simd/Div.h
- − ext/include/blaze/blaze/math/simd/Equal.h
- − ext/include/blaze/blaze/math/simd/Erf.h
- − ext/include/blaze/blaze/math/simd/Erfc.h
- − ext/include/blaze/blaze/math/simd/Exp.h
- − ext/include/blaze/blaze/math/simd/Exp10.h
- − ext/include/blaze/blaze/math/simd/Exp2.h
- − ext/include/blaze/blaze/math/simd/FMA.h
- − ext/include/blaze/blaze/math/simd/Floor.h
- − ext/include/blaze/blaze/math/simd/Functions.h
- − ext/include/blaze/blaze/math/simd/Hypot.h
- − ext/include/blaze/blaze/math/simd/InvCbrt.h
- − ext/include/blaze/blaze/math/simd/InvSqrt.h
- − ext/include/blaze/blaze/math/simd/LGamma.h
- − ext/include/blaze/blaze/math/simd/Loada.h
- − ext/include/blaze/blaze/math/simd/Loadu.h
- − ext/include/blaze/blaze/math/simd/Log.h
- − ext/include/blaze/blaze/math/simd/Log10.h
- − ext/include/blaze/blaze/math/simd/Log1p.h
- − ext/include/blaze/blaze/math/simd/Log2.h
- − ext/include/blaze/blaze/math/simd/Max.h
- − ext/include/blaze/blaze/math/simd/Min.h
- − ext/include/blaze/blaze/math/simd/Mult.h
- − ext/include/blaze/blaze/math/simd/Pow.h
- − ext/include/blaze/blaze/math/simd/Prod.h
- − ext/include/blaze/blaze/math/simd/Reduce.h
- − ext/include/blaze/blaze/math/simd/Round.h
- − ext/include/blaze/blaze/math/simd/SIMD.h
- − ext/include/blaze/blaze/math/simd/SIMDPack.h
- − ext/include/blaze/blaze/math/simd/SIMDTrait.h
- − ext/include/blaze/blaze/math/simd/Set.h
- − ext/include/blaze/blaze/math/simd/Setzero.h
- − ext/include/blaze/blaze/math/simd/ShiftLI.h
- − ext/include/blaze/blaze/math/simd/ShiftLV.h
- − ext/include/blaze/blaze/math/simd/ShiftRI.h
- − ext/include/blaze/blaze/math/simd/ShiftRV.h
- − ext/include/blaze/blaze/math/simd/Sign.h
- − ext/include/blaze/blaze/math/simd/Sin.h
- − ext/include/blaze/blaze/math/simd/Sinh.h
- − ext/include/blaze/blaze/math/simd/Sqrt.h
- − ext/include/blaze/blaze/math/simd/Storea.h
- − ext/include/blaze/blaze/math/simd/Storeu.h
- − ext/include/blaze/blaze/math/simd/Stream.h
- − ext/include/blaze/blaze/math/simd/Sub.h
- − ext/include/blaze/blaze/math/simd/Sum.h
- − ext/include/blaze/blaze/math/simd/Tan.h
- − ext/include/blaze/blaze/math/simd/Tanh.h
- − ext/include/blaze/blaze/math/simd/Trunc.h
- − ext/include/blaze/blaze/math/smp/DenseMatrix.h
- − ext/include/blaze/blaze/math/smp/DenseVector.h
- − ext/include/blaze/blaze/math/smp/Functions.h
- − ext/include/blaze/blaze/math/smp/ParallelSection.h
- − ext/include/blaze/blaze/math/smp/SMP.h
- − ext/include/blaze/blaze/math/smp/SerialSection.h
- − ext/include/blaze/blaze/math/smp/SparseMatrix.h
- − ext/include/blaze/blaze/math/smp/SparseVector.h
- − ext/include/blaze/blaze/math/smp/ThreadMapping.h
- − ext/include/blaze/blaze/math/smp/default/DenseMatrix.h
- − ext/include/blaze/blaze/math/smp/default/DenseVector.h
- − ext/include/blaze/blaze/math/smp/default/Functions.h
- − ext/include/blaze/blaze/math/smp/default/SparseMatrix.h
- − ext/include/blaze/blaze/math/smp/default/SparseVector.h
- − ext/include/blaze/blaze/math/smp/hpx/DenseMatrix.h
- − ext/include/blaze/blaze/math/smp/hpx/DenseVector.h
- − ext/include/blaze/blaze/math/smp/hpx/Functions.h
- − ext/include/blaze/blaze/math/smp/openmp/DenseMatrix.h
- − ext/include/blaze/blaze/math/smp/openmp/DenseVector.h
- − ext/include/blaze/blaze/math/smp/openmp/Functions.h
- − ext/include/blaze/blaze/math/smp/threads/DenseMatrix.h
- − ext/include/blaze/blaze/math/smp/threads/DenseVector.h
- − ext/include/blaze/blaze/math/smp/threads/Functions.h
- − ext/include/blaze/blaze/math/smp/threads/ThreadBackend.h
- − ext/include/blaze/blaze/math/sparse/CompressedMatrix.h
- − ext/include/blaze/blaze/math/sparse/CompressedVector.h
- − ext/include/blaze/blaze/math/sparse/Forward.h
- − ext/include/blaze/blaze/math/sparse/IdentityMatrix.h
- − ext/include/blaze/blaze/math/sparse/MatrixAccessProxy.h
- − ext/include/blaze/blaze/math/sparse/SparseElement.h
- − ext/include/blaze/blaze/math/sparse/SparseMatrix.h
- − ext/include/blaze/blaze/math/sparse/SparseVector.h
- − ext/include/blaze/blaze/math/sparse/ValueIndexPair.h
- − ext/include/blaze/blaze/math/sparse/VectorAccessProxy.h
- − ext/include/blaze/blaze/math/sparse/ZeroMatrix.h
- − ext/include/blaze/blaze/math/sparse/ZeroVector.h
- − ext/include/blaze/blaze/math/traits/AddTrait.h
- − ext/include/blaze/blaze/math/traits/BandTrait.h
- − ext/include/blaze/blaze/math/traits/ColumnTrait.h
- − ext/include/blaze/blaze/math/traits/ColumnsTrait.h
- − ext/include/blaze/blaze/math/traits/CrossTrait.h
- − ext/include/blaze/blaze/math/traits/DeclDiagTrait.h
- − ext/include/blaze/blaze/math/traits/DeclHermTrait.h
- − ext/include/blaze/blaze/math/traits/DeclIdTrait.h
- − ext/include/blaze/blaze/math/traits/DeclLowTrait.h
- − ext/include/blaze/blaze/math/traits/DeclStrLowTrait.h
- − ext/include/blaze/blaze/math/traits/DeclStrUppTrait.h
- − ext/include/blaze/blaze/math/traits/DeclSymTrait.h
- − ext/include/blaze/blaze/math/traits/DeclUniLowTrait.h
- − ext/include/blaze/blaze/math/traits/DeclUniUppTrait.h
- − ext/include/blaze/blaze/math/traits/DeclUppTrait.h
- − ext/include/blaze/blaze/math/traits/DeclZeroTrait.h
- − ext/include/blaze/blaze/math/traits/DerestrictTrait.h
- − ext/include/blaze/blaze/math/traits/DivTrait.h
- − ext/include/blaze/blaze/math/traits/ElementsTrait.h
- − ext/include/blaze/blaze/math/traits/EvaluateTrait.h
- − ext/include/blaze/blaze/math/traits/ExpandTrait.h
- − ext/include/blaze/blaze/math/traits/KronTrait.h
- − ext/include/blaze/blaze/math/traits/MapTrait.h
- − ext/include/blaze/blaze/math/traits/MultTrait.h
- − ext/include/blaze/blaze/math/traits/ReduceTrait.h
- − ext/include/blaze/blaze/math/traits/RepeatTrait.h
- − ext/include/blaze/blaze/math/traits/RowTrait.h
- − ext/include/blaze/blaze/math/traits/RowsTrait.h
- − ext/include/blaze/blaze/math/traits/SchurTrait.h
- − ext/include/blaze/blaze/math/traits/SolveTrait.h
- − ext/include/blaze/blaze/math/traits/SubTrait.h
- − ext/include/blaze/blaze/math/traits/SubmatrixTrait.h
- − ext/include/blaze/blaze/math/traits/SubvectorTrait.h
- − ext/include/blaze/blaze/math/traits/Traits.h
- − ext/include/blaze/blaze/math/typetraits/CustomOppositeType.h
- − ext/include/blaze/blaze/math/typetraits/CustomTransposeType.h
- − ext/include/blaze/blaze/math/typetraits/DynamicAllocator.h
- − ext/include/blaze/blaze/math/typetraits/GetAllocator.h
- − ext/include/blaze/blaze/math/typetraits/HasAbs.h
- − ext/include/blaze/blaze/math/typetraits/HasAcos.h
- − ext/include/blaze/blaze/math/typetraits/HasAcosh.h
- − ext/include/blaze/blaze/math/typetraits/HasAdd.h
- − ext/include/blaze/blaze/math/typetraits/HasAsin.h
- − ext/include/blaze/blaze/math/typetraits/HasAsinh.h
- − ext/include/blaze/blaze/math/typetraits/HasAtan.h
- − ext/include/blaze/blaze/math/typetraits/HasAtan2.h
- − ext/include/blaze/blaze/math/typetraits/HasAtanh.h
- − ext/include/blaze/blaze/math/typetraits/HasCbrt.h
- − ext/include/blaze/blaze/math/typetraits/HasCeil.h
- − ext/include/blaze/blaze/math/typetraits/HasClamp.h
- − ext/include/blaze/blaze/math/typetraits/HasCompositeType.h
- − ext/include/blaze/blaze/math/typetraits/HasConj.h
- − ext/include/blaze/blaze/math/typetraits/HasConstDataAccess.h
- − ext/include/blaze/blaze/math/typetraits/HasCos.h
- − ext/include/blaze/blaze/math/typetraits/HasCosh.h
- − ext/include/blaze/blaze/math/typetraits/HasDiv.h
- − ext/include/blaze/blaze/math/typetraits/HasErf.h
- − ext/include/blaze/blaze/math/typetraits/HasErfc.h
- − ext/include/blaze/blaze/math/typetraits/HasExp.h
- − ext/include/blaze/blaze/math/typetraits/HasExp10.h
- − ext/include/blaze/blaze/math/typetraits/HasExp2.h
- − ext/include/blaze/blaze/math/typetraits/HasFloor.h
- − ext/include/blaze/blaze/math/typetraits/HasHypot.h
- − ext/include/blaze/blaze/math/typetraits/HasImag.h
- − ext/include/blaze/blaze/math/typetraits/HasInvCbrt.h
- − ext/include/blaze/blaze/math/typetraits/HasInvSqrt.h
- − ext/include/blaze/blaze/math/typetraits/HasLGamma.h
- − ext/include/blaze/blaze/math/typetraits/HasLoad.h
- − ext/include/blaze/blaze/math/typetraits/HasLog.h
- − ext/include/blaze/blaze/math/typetraits/HasLog10.h
- − ext/include/blaze/blaze/math/typetraits/HasLog1p.h
- − ext/include/blaze/blaze/math/typetraits/HasLog2.h
- − ext/include/blaze/blaze/math/typetraits/HasMax.h
- − ext/include/blaze/blaze/math/typetraits/HasMin.h
- − ext/include/blaze/blaze/math/typetraits/HasMult.h
- − ext/include/blaze/blaze/math/typetraits/HasMutableDataAccess.h
- − ext/include/blaze/blaze/math/typetraits/HasPow.h
- − ext/include/blaze/blaze/math/typetraits/HasReal.h
- − ext/include/blaze/blaze/math/typetraits/HasResultType.h
- − ext/include/blaze/blaze/math/typetraits/HasRound.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAbs.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAcos.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAcosh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAdd.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAsin.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAsinh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAtan.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAtan2.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDAtanh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDBitand.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDBitor.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDBitxor.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDCbrt.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDCeil.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDConj.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDCos.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDCosh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDDiv.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDEqual.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDErf.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDErfc.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDExp.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDExp10.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDExp2.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDFloor.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDHypot.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDInvCbrt.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDInvSqrt.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDLGamma.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDLog.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDLog10.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDLog1p.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDLog2.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDMax.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDMin.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDMult.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDPow.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDRound.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDShiftLI.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDShiftLV.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDShiftRI.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDShiftRV.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDSign.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDSin.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDSinh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDSqrt.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDSub.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDTan.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDTanh.h
- − ext/include/blaze/blaze/math/typetraits/HasSIMDTrunc.h
- − ext/include/blaze/blaze/math/typetraits/HasSign.h
- − ext/include/blaze/blaze/math/typetraits/HasSin.h
- − ext/include/blaze/blaze/math/typetraits/HasSinh.h
- − ext/include/blaze/blaze/math/typetraits/HasSqrt.h
- − ext/include/blaze/blaze/math/typetraits/HasSub.h
- − ext/include/blaze/blaze/math/typetraits/HasTan.h
- − ext/include/blaze/blaze/math/typetraits/HasTanh.h
- − ext/include/blaze/blaze/math/typetraits/HasTrunc.h
- − ext/include/blaze/blaze/math/typetraits/HighType.h
- − ext/include/blaze/blaze/math/typetraits/IsAdaptor.h
- − ext/include/blaze/blaze/math/typetraits/IsAddExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsAligned.h
- − ext/include/blaze/blaze/math/typetraits/IsBLASCompatible.h
- − ext/include/blaze/blaze/math/typetraits/IsBand.h
- − ext/include/blaze/blaze/math/typetraits/IsBinaryMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsCUDAAssignable.h
- − ext/include/blaze/blaze/math/typetraits/IsColumn.h
- − ext/include/blaze/blaze/math/typetraits/IsColumnMajorMatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsColumnVector.h
- − ext/include/blaze/blaze/math/typetraits/IsColumns.h
- − ext/include/blaze/blaze/math/typetraits/IsCommutative.h
- − ext/include/blaze/blaze/math/typetraits/IsComputation.h
- − ext/include/blaze/blaze/math/typetraits/IsContiguous.h
- − ext/include/blaze/blaze/math/typetraits/IsCrossExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsCustom.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclDiagExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclHermExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclLowExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclStrLowExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclStrUppExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclSymExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclUniLowExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclUniUppExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclUppExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsDeclaration.h
- − ext/include/blaze/blaze/math/typetraits/IsDenseMatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsDenseVector.h
- − ext/include/blaze/blaze/math/typetraits/IsDiagonal.h
- − ext/include/blaze/blaze/math/typetraits/IsDivExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsEigenExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsElements.h
- − ext/include/blaze/blaze/math/typetraits/IsEvalExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsExpandExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsExpression.h
- − ext/include/blaze/blaze/math/typetraits/IsGenExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsGeneral.h
- − ext/include/blaze/blaze/math/typetraits/IsHermitian.h
- − ext/include/blaze/blaze/math/typetraits/IsIdentity.h
- − ext/include/blaze/blaze/math/typetraits/IsInitializer.h
- − ext/include/blaze/blaze/math/typetraits/IsInvertible.h
- − ext/include/blaze/blaze/math/typetraits/IsKronExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsLower.h
- − ext/include/blaze/blaze/math/typetraits/IsMatEvalExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatExpExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatGenExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatInvExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatAddExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatKronExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatSolveExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatMatSubExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatNoAliasExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatNoSIMDExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatReduceExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatRepeatExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatScalarDivExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatScalarMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatSerialExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatTransExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatVecMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatVecSolveExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsMatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsModification.h
- − ext/include/blaze/blaze/math/typetraits/IsMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsNoAliasExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsNoSIMDExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsOperation.h
- − ext/include/blaze/blaze/math/typetraits/IsOpposedView.h
- − ext/include/blaze/blaze/math/typetraits/IsPadded.h
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- − ext/include/blaze/blaze/math/typetraits/IsProxy.h
- − ext/include/blaze/blaze/math/typetraits/IsReduceExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsRepeatExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsResizable.h
- − ext/include/blaze/blaze/math/typetraits/IsRestricted.h
- − ext/include/blaze/blaze/math/typetraits/IsRow.h
- − ext/include/blaze/blaze/math/typetraits/IsRowMajorMatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsRowVector.h
- − ext/include/blaze/blaze/math/typetraits/IsRows.h
- − ext/include/blaze/blaze/math/typetraits/IsSIMDCombinable.h
- − ext/include/blaze/blaze/math/typetraits/IsSIMDEnabled.h
- − ext/include/blaze/blaze/math/typetraits/IsSIMDPack.h
- − ext/include/blaze/blaze/math/typetraits/IsSMPAssignable.h
- − ext/include/blaze/blaze/math/typetraits/IsSVDExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsScalar.h
- − ext/include/blaze/blaze/math/typetraits/IsSchurExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsSerialExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsShrinkable.h
- − ext/include/blaze/blaze/math/typetraits/IsSolveExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsSparseElement.h
- − ext/include/blaze/blaze/math/typetraits/IsSparseMatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsSparseVector.h
- − ext/include/blaze/blaze/math/typetraits/IsSquare.h
- − ext/include/blaze/blaze/math/typetraits/IsStatic.h
- − ext/include/blaze/blaze/math/typetraits/IsStrictlyLower.h
- − ext/include/blaze/blaze/math/typetraits/IsStrictlyTriangular.h
- − ext/include/blaze/blaze/math/typetraits/IsStrictlyUpper.h
- − ext/include/blaze/blaze/math/typetraits/IsSubExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsSubmatrix.h
- − ext/include/blaze/blaze/math/typetraits/IsSubvector.h
- − ext/include/blaze/blaze/math/typetraits/IsSymmetric.h
- − ext/include/blaze/blaze/math/typetraits/IsTVecMatMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsTemporary.h
- − ext/include/blaze/blaze/math/typetraits/IsTransExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsTransformation.h
- − ext/include/blaze/blaze/math/typetraits/IsTriangular.h
- − ext/include/blaze/blaze/math/typetraits/IsUnaryMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsUniLower.h
- − ext/include/blaze/blaze/math/typetraits/IsUniTriangular.h
- − ext/include/blaze/blaze/math/typetraits/IsUniUpper.h
- − ext/include/blaze/blaze/math/typetraits/IsUniform.h
- − ext/include/blaze/blaze/math/typetraits/IsUpper.h
- − ext/include/blaze/blaze/math/typetraits/IsVecEvalExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecExpandExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecGenExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecNoAliasExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecNoSIMDExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecRepeatExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecScalarDivExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecScalarMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecSerialExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecTVecMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecTVecMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecTransExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecAddExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecDivExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecKronExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecMapExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecMultExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVecVecSubExpr.h
- − ext/include/blaze/blaze/math/typetraits/IsVector.h
- − ext/include/blaze/blaze/math/typetraits/IsView.h
- − ext/include/blaze/blaze/math/typetraits/IsZero.h
- − ext/include/blaze/blaze/math/typetraits/LowType.h
- − ext/include/blaze/blaze/math/typetraits/MakeComplex.h
- − ext/include/blaze/blaze/math/typetraits/MaxSize.h
- − ext/include/blaze/blaze/math/typetraits/RemoveAdaptor.h
- − ext/include/blaze/blaze/math/typetraits/RequiresEvaluation.h
- − ext/include/blaze/blaze/math/typetraits/Size.h
- − ext/include/blaze/blaze/math/typetraits/StorageOrder.h
- − ext/include/blaze/blaze/math/typetraits/TransposeFlag.h
- − ext/include/blaze/blaze/math/typetraits/TypeTraits.h
- − ext/include/blaze/blaze/math/typetraits/UnderlyingBuiltin.h
- − ext/include/blaze/blaze/math/typetraits/UnderlyingElement.h
- − ext/include/blaze/blaze/math/typetraits/UnderlyingNumeric.h
- − ext/include/blaze/blaze/math/typetraits/UnderlyingScalar.h
- − ext/include/blaze/blaze/math/typetraits/YieldsDiagonal.h
- − ext/include/blaze/blaze/math/typetraits/YieldsHermitian.h
- − ext/include/blaze/blaze/math/typetraits/YieldsIdentity.h
- − ext/include/blaze/blaze/math/typetraits/YieldsLower.h
- − ext/include/blaze/blaze/math/typetraits/YieldsStrictlyLower.h
- − ext/include/blaze/blaze/math/typetraits/YieldsStrictlyTriangular.h
- − ext/include/blaze/blaze/math/typetraits/YieldsStrictlyUpper.h
- − ext/include/blaze/blaze/math/typetraits/YieldsSymmetric.h
- − ext/include/blaze/blaze/math/typetraits/YieldsTriangular.h
- − ext/include/blaze/blaze/math/typetraits/YieldsUniLower.h
- − ext/include/blaze/blaze/math/typetraits/YieldsUniTriangular.h
- − ext/include/blaze/blaze/math/typetraits/YieldsUniUpper.h
- − ext/include/blaze/blaze/math/typetraits/YieldsUniform.h
- − ext/include/blaze/blaze/math/typetraits/YieldsUpper.h
- − ext/include/blaze/blaze/math/typetraits/YieldsZero.h
- − ext/include/blaze/blaze/math/views/Band.h
- − ext/include/blaze/blaze/math/views/Check.h
- − ext/include/blaze/blaze/math/views/Column.h
- − ext/include/blaze/blaze/math/views/Columns.h
- − ext/include/blaze/blaze/math/views/Elements.h
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- − ext/include/blaze/blaze/math/views/Subvector.h
- − ext/include/blaze/blaze/math/views/Views.h
- − ext/include/blaze/blaze/math/views/band/Band.h
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- − ext/include/blaze/blaze/math/views/band/Dense.h
- − ext/include/blaze/blaze/math/views/band/Sparse.h
- − ext/include/blaze/blaze/math/views/column/BaseTemplate.h
- − ext/include/blaze/blaze/math/views/column/Column.h
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- − ext/include/blaze/blaze/math/views/column/Dense.h
- − ext/include/blaze/blaze/math/views/column/Sparse.h
- − ext/include/blaze/blaze/math/views/columns/BaseTemplate.h
- − ext/include/blaze/blaze/math/views/columns/Columns.h
- − ext/include/blaze/blaze/math/views/columns/ColumnsData.h
- − ext/include/blaze/blaze/math/views/columns/Dense.h
- − ext/include/blaze/blaze/math/views/columns/Sparse.h
- − ext/include/blaze/blaze/math/views/elements/BaseTemplate.h
- − ext/include/blaze/blaze/math/views/elements/Dense.h
- − ext/include/blaze/blaze/math/views/elements/Elements.h
- − ext/include/blaze/blaze/math/views/elements/ElementsData.h
- − ext/include/blaze/blaze/math/views/elements/Sparse.h
- − ext/include/blaze/blaze/math/views/row/BaseTemplate.h
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- − ext/include/blaze/blaze/math/views/row/Row.h
- − ext/include/blaze/blaze/math/views/row/RowData.h
- − ext/include/blaze/blaze/math/views/row/Sparse.h
- − ext/include/blaze/blaze/math/views/rows/BaseTemplate.h
- − ext/include/blaze/blaze/math/views/rows/Dense.h
- − ext/include/blaze/blaze/math/views/rows/Rows.h
- − ext/include/blaze/blaze/math/views/rows/RowsData.h
- − ext/include/blaze/blaze/math/views/rows/Sparse.h
- − ext/include/blaze/blaze/math/views/submatrix/BaseTemplate.h
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- − ext/include/blaze/blaze/math/views/submatrix/Sparse.h
- − ext/include/blaze/blaze/math/views/submatrix/Submatrix.h
- − ext/include/blaze/blaze/math/views/submatrix/SubmatrixData.h
- − ext/include/blaze/blaze/math/views/subvector/BaseTemplate.h
- − ext/include/blaze/blaze/math/views/subvector/Dense.h
- − ext/include/blaze/blaze/math/views/subvector/Sparse.h
- − ext/include/blaze/blaze/math/views/subvector/Subvector.h
- − ext/include/blaze/blaze/math/views/subvector/SubvectorData.h
- − ext/include/blaze/blaze/system/Alignment.h
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- − ext/include/blaze/blaze/system/System.h
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- − ext/include/blaze/blaze/system/TransposeFlag.h
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- − ext/include/blaze/blaze/util/Algorithms.h
- − ext/include/blaze/blaze/util/AlignedAllocator.h
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- − ext/include/blaze/blaze/util/constraints/GreaterThan.h
- − ext/include/blaze/blaze/util/constraints/Integer.h
- − ext/include/blaze/blaze/util/constraints/Integral.h
- − ext/include/blaze/blaze/util/constraints/LValueReference.h
- − ext/include/blaze/blaze/util/constraints/LessThan.h
- − ext/include/blaze/blaze/util/constraints/Long.h
- − ext/include/blaze/blaze/util/constraints/LongDouble.h
- − ext/include/blaze/blaze/util/constraints/Numeric.h
- − ext/include/blaze/blaze/util/constraints/Object.h
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- − ext/include/blaze/blaze/util/constraints/RValueReference.h
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- − ext/include/blaze/blaze/util/constraints/Size.h
- − ext/include/blaze/blaze/util/constraints/Subscriptable.h
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- − ext/include/blaze/blaze/util/constraints/Valid.h
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- − ext/include/blaze/blaze/util/constraints/Volatile.h
- − ext/include/blaze/blaze/util/functiontrace/FunctionTrace.h
- − ext/include/blaze/blaze/util/mpl/And.h
- − ext/include/blaze/blaze/util/mpl/Bools.h
- − ext/include/blaze/blaze/util/mpl/Equal.h
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- − ext/include/blaze/blaze/util/mpl/MPL.h
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- − ext/include/blaze/blaze/util/mpl/Min.h
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- − ext/include/blaze/blaze/util/mpl/Nand.h
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- − ext/include/blaze/blaze/util/mpl/Times.h
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- − ext/include/blaze/blaze/util/policies/ArrayDelete.h
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- − ext/include/blaze/blaze/util/smallarray/SmallArrayData.h
- − ext/include/blaze/blaze/util/threadpool/Task.h
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- − ext/include/blaze/blaze/util/threadpool/ThreadPool.h
- − ext/include/blaze/blaze/util/timing/CpuPolicy.h
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- − ext/include/blaze/blaze/util/timing/Timing.h
- − ext/include/blaze/blaze/util/timing/WcPolicy.h
- − ext/include/blaze/blaze/util/timing/WcTimer.h
- − ext/include/blaze/blaze/util/typelist/Append.h
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- − ext/include/blaze/blaze/util/typelist/IndexOf.h
- − ext/include/blaze/blaze/util/typelist/Length.h
- − ext/include/blaze/blaze/util/typelist/TypeAt.h
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- − ext/include/blaze/blaze/util/typetraits/AddCV.h
- − ext/include/blaze/blaze/util/typetraits/AddConst.h
- − ext/include/blaze/blaze/util/typetraits/AddLValueReference.h
- − ext/include/blaze/blaze/util/typetraits/AddPointer.h
- − ext/include/blaze/blaze/util/typetraits/AddRValueReference.h
- − ext/include/blaze/blaze/util/typetraits/AddVolatile.h
- − ext/include/blaze/blaze/util/typetraits/AlignmentOf.h
- − ext/include/blaze/blaze/util/typetraits/All.h
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- − ext/include/blaze/blaze/util/typetraits/Any.h
- − ext/include/blaze/blaze/util/typetraits/CommonType.h
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- − ext/include/blaze/blaze/util/typetraits/GetMemberType.h
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