1af9914df9
Port changes for biology/seqan-apps: * Changed to DISTVERSION * Updated COMMENT * Added USES=compiler:openmp * Removed BROKEN_xx (upstream now claims support for these architectures) * Removed USE_GCC * Added SSE4/AVX2/NATIVE SIMD options Port changes for biology/seqan: * Changed to DISTVERSION * Added NO_ARCH * Added PORTDOCS=* * Updated do-install PR: 225682 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Approved by: tcberner (mentor, implicit)
731 lines
30 KiB
Text
731 lines
30 KiB
Text
include/seqan/align.h
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include/seqan/align/align_base.h
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include/seqan/align/align_cols.h
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include/seqan/align/align_config.h
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include/seqan/align/align_interface_wrapper.h
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include/seqan/align/align_iterator_base.h
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include/seqan/align/align_metafunctions.h
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include/seqan/align/align_traceback.h
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include/seqan/align/aligned_sequence_concept.h
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include/seqan/align/alignment_algorithm_tags.h
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include/seqan/align/alignment_operations.h
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include/seqan/align/dp_algorithm_impl.h
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include/seqan/align/dp_align_simd_helper.h
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include/seqan/align/dp_band.h
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include/seqan/align/dp_cell.h
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include/seqan/align/dp_cell_affine.h
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include/seqan/align/dp_cell_dynamic.h
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include/seqan/align/dp_cell_linear.h
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include/seqan/align/dp_context.h
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include/seqan/align/dp_formula.h
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include/seqan/align/dp_formula_affine.h
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include/seqan/align/dp_formula_dynamic.h
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include/seqan/align/dp_formula_linear.h
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include/seqan/align/dp_matrix.h
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include/seqan/align/dp_matrix_navigator.h
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include/seqan/align/dp_matrix_navigator_score_matrix.h
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include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
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include/seqan/align/dp_matrix_navigator_trace_matrix.h
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include/seqan/align/dp_matrix_sparse.h
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include/seqan/align/dp_meta_info.h
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include/seqan/align/dp_profile.h
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include/seqan/align/dp_scout.h
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include/seqan/align/dp_scout_simd.h
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include/seqan/align/dp_setup.h
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include/seqan/align/dp_trace_segment.h
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include/seqan/align/dp_traceback_adaptor.h
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include/seqan/align/dp_traceback_impl.h
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include/seqan/align/evaluate_alignment.h
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include/seqan/align/fragment.h
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include/seqan/align/gap_anchor.h
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include/seqan/align/gapped_value_type.h
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include/seqan/align/gaps_anchor.h
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include/seqan/align/gaps_array.h
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include/seqan/align/gaps_base.h
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include/seqan/align/gaps_iterator_anchor.h
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include/seqan/align/gaps_iterator_array.h
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include/seqan/align/gaps_iterator_base.h
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include/seqan/align/global_alignment_banded.h
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include/seqan/align/global_alignment_hirschberg_impl.h
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include/seqan/align/global_alignment_myers_hirschberg_impl.h
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include/seqan/align/global_alignment_myers_impl.h
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include/seqan/align/global_alignment_specialized.h
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include/seqan/align/global_alignment_unbanded.h
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include/seqan/align/local_alignment_banded.h
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include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
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include/seqan/align/local_alignment_enumeration.h
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include/seqan/align/local_alignment_enumeration_banded.h
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include/seqan/align/local_alignment_enumeration_unbanded.h
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include/seqan/align/local_alignment_unbanded.h
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include/seqan/align/local_alignment_waterman_eggert_impl.h
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include/seqan/align/matrix_base.h
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include/seqan/align_extend.h
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include/seqan/align_extend/align_extend.h
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include/seqan/align_extend/align_extend_base.h
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include/seqan/align_extend/dp_scout_xdrop.h
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include/seqan/align_parallel.h
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include/seqan/align_parallel/async_wave_execution_interface.h
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include/seqan/align_parallel/dp_kernel_adaptor.h
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include/seqan/align_parallel/dp_parallel_execution_policies.h
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include/seqan/align_parallel/dp_parallel_scout.h
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include/seqan/align_parallel/dp_parallel_scout_simd.h
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include/seqan/align_parallel/dp_settings.h
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include/seqan/align_parallel/dp_traits.h
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include/seqan/align_parallel/parallel_align_interface.h
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include/seqan/align_parallel/wavefront_alignment_executor.h
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include/seqan/align_parallel/wavefront_alignment_result.h
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include/seqan/align_parallel/wavefront_alignment_scheduler.h
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include/seqan/align_parallel/wavefront_alignment_task.h
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include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h
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include/seqan/align_parallel/wavefront_task.h
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include/seqan/align_parallel/wavefront_task_event.h
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include/seqan/align_parallel/wavefront_task_executor.h
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include/seqan/align_parallel/wavefront_task_queue.h
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include/seqan/align_parallel/wavefront_task_scheduler.h
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include/seqan/align_parallel/wavefront_task_util.h
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include/seqan/align_profile.h
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include/seqan/align_profile/add_to_profile.h
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include/seqan/align_profile/score_profile_seq.h
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include/seqan/align_split.h
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include/seqan/align_split/align_split_interface.h
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include/seqan/align_split/dp_scout_split.h
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include/seqan/alignment_free.h
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include/seqan/alignment_free/af_d2.h
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include/seqan/alignment_free/af_d2star.h
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include/seqan/alignment_free/af_d2z.h
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include/seqan/alignment_free/af_n2.h
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include/seqan/alignment_free/alignment_free_base.h
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include/seqan/alignment_free/alignment_free_comparison.h
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include/seqan/alignment_free/kmer_functions.h
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include/seqan/arg_parse.h
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include/seqan/arg_parse/arg_parse_argument.h
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include/seqan/arg_parse/arg_parse_ctd_support.h
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include/seqan/arg_parse/arg_parse_doc.h
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include/seqan/arg_parse/arg_parse_exceptions.h
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include/seqan/arg_parse/arg_parse_option.h
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include/seqan/arg_parse/arg_parse_parse.h
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include/seqan/arg_parse/arg_parse_type_support.h
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include/seqan/arg_parse/arg_parse_version_check.h
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include/seqan/arg_parse/argument_parser.h
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include/seqan/arg_parse/tool_doc.h
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include/seqan/arg_parse/xml_support.h
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include/seqan/bam_io.h
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include/seqan/bam_io/bam_alignment_record.h
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include/seqan/bam_io/bam_alignment_record_util.h
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include/seqan/bam_io/bam_file.h
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include/seqan/bam_io/bam_header_record.h
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include/seqan/bam_io/bam_index_bai.h
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include/seqan/bam_io/bam_io_context.h
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include/seqan/bam_io/bam_sam_conversion.h
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include/seqan/bam_io/bam_scanner_cache.h
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include/seqan/bam_io/bam_tags_dict.h
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include/seqan/bam_io/cigar.h
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include/seqan/bam_io/read_bam.h
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include/seqan/bam_io/read_sam.h
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include/seqan/bam_io/write_bam.h
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include/seqan/bam_io/write_sam.h
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include/seqan/basic.h
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include/seqan/basic/aggregate_concept.h
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include/seqan/basic/allocator_chunkpool.h
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include/seqan/basic/allocator_interface.h
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include/seqan/basic/allocator_multipool.h
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include/seqan/basic/allocator_simple.h
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include/seqan/basic/allocator_singlepool.h
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include/seqan/basic/allocator_to_std.h
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include/seqan/basic/alphabet_adapt_builtins.h
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include/seqan/basic/alphabet_bio.h
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include/seqan/basic/alphabet_concept.h
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include/seqan/basic/alphabet_math.h
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include/seqan/basic/alphabet_profile.h
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include/seqan/basic/alphabet_qualities.h
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include/seqan/basic/alphabet_residue.h
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include/seqan/basic/alphabet_residue_funcs.h
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include/seqan/basic/alphabet_residue_tabs.h
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include/seqan/basic/alphabet_simple_type.h
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include/seqan/basic/alphabet_storage.h
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include/seqan/basic/array_construct_destruct.h
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include/seqan/basic/basic_aggregate.h
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include/seqan/basic/basic_allocator.h
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include/seqan/basic/basic_alphabet.h
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include/seqan/basic/basic_concept.h
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include/seqan/basic/basic_container.h
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include/seqan/basic/basic_debug.h
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include/seqan/basic/basic_device.h
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include/seqan/basic/basic_exception.h
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include/seqan/basic/basic_functors.h
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include/seqan/basic/basic_fundamental.h
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include/seqan/basic/basic_iterator.h
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include/seqan/basic/basic_math.h
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include/seqan/basic/basic_metaprogramming.h
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include/seqan/basic/basic_parallelism.h
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include/seqan/basic/basic_proxy.h
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include/seqan/basic/basic_smart_pointer.h
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include/seqan/basic/basic_stream.h
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include/seqan/basic/basic_tangle.h
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include/seqan/basic/basic_type.h
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include/seqan/basic/basic_view.h
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include/seqan/basic/boost_preprocessor_subset.h
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include/seqan/basic/builtin_functions.h
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include/seqan/basic/concept_checking.h
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include/seqan/basic/container_concept.h
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include/seqan/basic/debug_helper.h
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include/seqan/basic/debug_test_system.h
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include/seqan/basic/fundamental_chunking.h
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include/seqan/basic/fundamental_comparison.h
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include/seqan/basic/fundamental_concepts.h
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include/seqan/basic/fundamental_conversion.h
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include/seqan/basic/fundamental_metafunctions.h
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include/seqan/basic/fundamental_tags.h
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include/seqan/basic/fundamental_transport.h
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include/seqan/basic/holder_base.h
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include/seqan/basic/holder_simple.h
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include/seqan/basic/holder_tristate.h
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include/seqan/basic/hosted_type_interface.h
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include/seqan/basic/iterator_adapt_pointer.h
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include/seqan/basic/iterator_adapt_std.h
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include/seqan/basic/iterator_adaptor.h
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include/seqan/basic/iterator_base.h
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include/seqan/basic/iterator_concept.h
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include/seqan/basic/iterator_counting.h
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include/seqan/basic/iterator_interface.h
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include/seqan/basic/iterator_position.h
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include/seqan/basic/iterator_range.h
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include/seqan/basic/iterator_zip.h
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include/seqan/basic/macro_deprecated.h
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include/seqan/basic/math_functions.h
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include/seqan/basic/math_log_space_value.h
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include/seqan/basic/metaprogramming_control.h
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include/seqan/basic/metaprogramming_enable_if.h
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include/seqan/basic/metaprogramming_logic.h
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include/seqan/basic/metaprogramming_math.h
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include/seqan/basic/metaprogramming_type.h
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include/seqan/basic/metaprogramming_type_algebra.h
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include/seqan/basic/pair_base.h
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include/seqan/basic/pair_bit_compressed.h
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include/seqan/basic/pair_packed.h
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include/seqan/basic/profiling.h
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include/seqan/basic/property_map_concept.h
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include/seqan/basic/proxy_base.h
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include/seqan/basic/proxy_iterator.h
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include/seqan/basic/test_system.h
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include/seqan/basic/triple_base.h
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include/seqan/basic/triple_packed.h
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include/seqan/basic/tuple_base.h
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include/seqan/basic/tuple_bit_compressed.h
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include/seqan/basic/volatile_ptr.h
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include/seqan/bed_io.h
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include/seqan/bed_io/bed_file.h
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include/seqan/bed_io/bed_record.h
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include/seqan/bed_io/read_bed.h
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include/seqan/bed_io/write_bed.h
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include/seqan/blast.h
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include/seqan/blast/blast_base.h
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include/seqan/blast/blast_io_context.h
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include/seqan/blast/blast_record.h
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include/seqan/blast/blast_report_out.h
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include/seqan/blast/blast_statistics.h
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include/seqan/blast/blast_tabular.h
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include/seqan/blast/blast_tabular_in.h
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include/seqan/blast/blast_tabular_lowlevel.h
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include/seqan/blast/blast_tabular_out.h
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include/seqan/consensus.h
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include/seqan/consensus/consensus_aligner.h
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include/seqan/consensus/consensus_aligner_interface.h
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include/seqan/consensus/consensus_alignment_options.h
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include/seqan/consensus/consensus_base.h
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include/seqan/consensus/consensus_builder.h
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include/seqan/consensus/consensus_library.h
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include/seqan/consensus/consensus_realign.h
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include/seqan/consensus/consensus_score.h
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include/seqan/consensus/overlap_info_computation.h
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include/seqan/consensus/overlapper.h
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include/seqan/file.h
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include/seqan/file/file_base.h
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include/seqan/file/file_cstyle.h
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include/seqan/file/file_forwards.h
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include/seqan/file/file_interface.h
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include/seqan/file/file_mapping.h
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include/seqan/file/file_page.h
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include/seqan/file/string_external.h
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include/seqan/file/string_mmap.h
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include/seqan/find.h
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include/seqan/find/find_abndm.h
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include/seqan/find/find_ahocorasick.h
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include/seqan/find/find_base.h
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include/seqan/find/find_begin.h
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include/seqan/find/find_bndm.h
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include/seqan/find/find_bom.h
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include/seqan/find/find_hamming_simple.h
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include/seqan/find/find_horspool.h
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include/seqan/find/find_lambda.h
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include/seqan/find/find_multi.h
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include/seqan/find/find_multiple_bfam.h
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include/seqan/find/find_multiple_shiftand.h
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include/seqan/find/find_myers_ukkonen.h
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include/seqan/find/find_pattern_base.h
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include/seqan/find/find_pex.h
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include/seqan/find/find_score.h
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include/seqan/find/find_set_horspool.h
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include/seqan/find/find_shiftand.h
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include/seqan/find/find_shiftor.h
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include/seqan/find/find_simple.h
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include/seqan/find/find_wild_shiftand.h
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include/seqan/find/find_wumanber.h
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include/seqan/gff_io.h
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include/seqan/gff_io/gff_file.h
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include/seqan/gff_io/gff_io_base.h
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include/seqan/graph_algorithms.h
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include/seqan/graph_algorithms/all_pairs_shortest_path.h
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include/seqan/graph_algorithms/bellman_ford.h
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include/seqan/graph_algorithms/bipartite_matching.h
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include/seqan/graph_algorithms/breadth_first_search.h
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include/seqan/graph_algorithms/connected_components.h
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include/seqan/graph_algorithms/depth_first_search.h
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include/seqan/graph_algorithms/dijkstra.h
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include/seqan/graph_algorithms/floyd_warshall.h
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include/seqan/graph_algorithms/ford_fulkerson.h
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include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
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include/seqan/graph_algorithms/graph_algorithm_hmm.h
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include/seqan/graph_algorithms/graph_algorithm_lis_his.h
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include/seqan/graph_algorithms/kruskal.h
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include/seqan/graph_algorithms/maximum_weighted_matching.h
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include/seqan/graph_algorithms/path_growing.h
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include/seqan/graph_algorithms/prim.h
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include/seqan/graph_algorithms/single_source_shortest_path.h
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include/seqan/graph_algorithms/strongly_connected_compnents.h
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include/seqan/graph_algorithms/topological_sort.h
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include/seqan/graph_algorithms/transitive_closure.h
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include/seqan/graph_algorithms/weakly_connected_components.h
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include/seqan/graph_algorithms/weighted_bipartite_matching.h
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include/seqan/graph_align.h
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include/seqan/graph_align/graph_algorithm_refine_align.h
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include/seqan/graph_align/graph_algorithm_refine_aligngraph.h
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include/seqan/graph_align/graph_algorithm_refine_annotation.h
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include/seqan/graph_align/graph_algorithm_refine_exact.h
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include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
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include/seqan/graph_align/graph_algorithm_refine_fragment.h
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include/seqan/graph_align/graph_algorithm_refine_inexact.h
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include/seqan/graph_align/graph_algorithm_refine_scoring.h
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include/seqan/graph_align/graph_impl_align.h
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include/seqan/graph_align/graph_impl_align_adapt.h
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include/seqan/graph_msa.h
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include/seqan/graph_msa/graph_align_tcoffee_base.h
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include/seqan/graph_msa/graph_align_tcoffee_distance.h
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include/seqan/graph_msa/graph_align_tcoffee_guidetree.h
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include/seqan/graph_msa/graph_align_tcoffee_io.h
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include/seqan/graph_msa/graph_align_tcoffee_kmer.h
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include/seqan/graph_msa/graph_align_tcoffee_library.h
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include/seqan/graph_msa/graph_align_tcoffee_msa.h
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include/seqan/graph_msa/graph_align_tcoffee_progressive.h
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include/seqan/graph_msa/graph_align_tcoffee_refinement.h
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include/seqan/graph_types.h
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include/seqan/graph_types/graph_base.h
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include/seqan/graph_types/graph_drawing.h
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include/seqan/graph_types/graph_edgestump.h
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include/seqan/graph_types/graph_idmanager.h
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include/seqan/graph_types/graph_impl_automaton.h
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include/seqan/graph_types/graph_impl_directed.h
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include/seqan/graph_types/graph_impl_hmm.h
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include/seqan/graph_types/graph_impl_oracle.h
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include/seqan/graph_types/graph_impl_tree.h
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include/seqan/graph_types/graph_impl_trie.h
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include/seqan/graph_types/graph_impl_undirected.h
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include/seqan/graph_types/graph_impl_wordgraph.h
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include/seqan/graph_types/graph_interface.h
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include/seqan/graph_types/graph_iterator.h
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include/seqan/graph_types/graph_iterator_adjacency.h
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include/seqan/graph_types/graph_iterator_bfs.h
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include/seqan/graph_types/graph_iterator_dfs.h
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include/seqan/graph_types/graph_iterator_edge.h
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include/seqan/graph_types/graph_iterator_outedge.h
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include/seqan/graph_types/graph_iterator_vertex.h
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include/seqan/graph_types/graph_utility_parsing.h
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include/seqan/graph_types/property_map_generic.h
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include/seqan/graph_types/property_map_internal.h
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include/seqan/graph_types/property_map_internal_pointer.h
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include/seqan/index.h
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include/seqan/index/find2_backtracking.h
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include/seqan/index/find2_base.h
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include/seqan/index/find2_functors.h
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include/seqan/index/find2_index.h
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include/seqan/index/find2_index_approx.h
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include/seqan/system/file_directory.h
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include/seqan/system/file_forwards.h
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include/seqan/system/file_sync.h
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include/seqan/system/system_base.h
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include/seqan/system/system_event_win.h
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include/seqan/system/system_forwards.h
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include/seqan/tabix_io.h
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include/seqan/tabix_io/tabix_index_tbi.h
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include/seqan/translation.h
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include/seqan/translation/translation.h
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include/seqan/translation/translation_tables.h
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include/seqan/ucsc_io.h
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|
include/seqan/ucsc_io/ucsc_file.h
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include/seqan/ucsc_io/ucsc_io.h
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include/seqan/ucsc_io/ucsc_record.h
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include/seqan/vcf_io.h
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include/seqan/vcf_io/read_vcf.h
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include/seqan/vcf_io/vcf_file.h
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include/seqan/vcf_io/vcf_header.h
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include/seqan/vcf_io/vcf_header_record.h
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include/seqan/vcf_io/vcf_io_context.h
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include/seqan/vcf_io/vcf_record.h
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include/seqan/vcf_io/write_vcf.h
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include/seqan/version.h
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lib/cmake/seqan/seqan-config.cmake
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libdata/pkgconfig/seqan-2.pc
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