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864e413d06
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
1984 lines
96 KiB
Plaintext
1984 lines
96 KiB
Plaintext
include/seqan.h
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include/seqan/LICENSE
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include/seqan/align.h
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include/seqan/align/align_algorithms.h
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include/seqan/align/align_base.h
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include/seqan/align/align_cols_base.h
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include/seqan/align/align_dynprog.h
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include/seqan/align/align_generated_forwards.h
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include/seqan/align/align_hirschberg.h
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include/seqan/align/align_iterator_base.h
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include/seqan/align/align_local_dynprog.h
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include/seqan/align/align_local_dynprog_banded.h
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include/seqan/align/align_myers.h
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include/seqan/align/align_trace.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_base.h
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include/seqan/align/gaps_sumlist.h
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include/seqan/align/hirschberg_set.h
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include/seqan/align/matrix_base.h
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include/seqan/basic.h
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include/seqan/basic/basic_aggregates.h
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include/seqan/basic/basic_allocator_chunkpool.h
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include/seqan/basic/basic_allocator_interface.h
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include/seqan/basic/basic_allocator_multipool.h
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include/seqan/basic/basic_allocator_simple.h
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include/seqan/basic/basic_allocator_singlepool.h
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include/seqan/basic/basic_allocator_to_std.h
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include/seqan/basic/basic_alphabet_interface.h
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include/seqan/basic/basic_alphabet_interface2.h
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include/seqan/basic/basic_alphabet_simple.h
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include/seqan/basic/basic_alphabet_simple_tabs.h
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include/seqan/basic/basic_alphabet_trait_basic.h
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include/seqan/basic/basic_compare.h
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include/seqan/basic/basic_converter.h
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include/seqan/basic/basic_counted_ptr.h
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include/seqan/basic/basic_debug.h
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include/seqan/basic/basic_definition.h
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include/seqan/basic/basic_forwards.h
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include/seqan/basic/basic_generated_forwards.h
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include/seqan/basic/basic_holder.h
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include/seqan/basic/basic_holder_dynamic.h
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include/seqan/basic/basic_host.h
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include/seqan/basic/basic_iterator.h
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include/seqan/basic/basic_iterator_adapt_std.h
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include/seqan/basic/basic_iterator_adaptor.h
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include/seqan/basic/basic_iterator_base.h
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include/seqan/basic/basic_iterator_position.h
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include/seqan/basic/basic_iterator_simple.h
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include/seqan/basic/basic_logvalue.h
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include/seqan/basic/basic_metaprogramming.h
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include/seqan/basic/basic_operator.h
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include/seqan/basic/basic_parallelism.h
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include/seqan/basic/basic_pointer.h
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include/seqan/basic/basic_profchar.h
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include/seqan/basic/basic_profile.h
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include/seqan/basic/basic_proxy.h
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include/seqan/basic/basic_sse2.h
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include/seqan/basic/basic_tag.h
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include/seqan/basic/basic_testing.h
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include/seqan/basic/basic_transport.h
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include/seqan/basic/basic_type.h
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include/seqan/basic/basic_volatile_ptr.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_generated_forwards.h
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include/seqan/blast/blast_hit.h
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include/seqan/blast/blast_hit_iterator.h
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include/seqan/blast/blast_hsp.h
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include/seqan/blast/blast_hsp_iterator.h
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include/seqan/blast/blast_iterator.h
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include/seqan/blast/blast_parsing.h
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include/seqan/blast/blast_report.h
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include/seqan/blast/blast_run.h
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include/seqan/blast/blast_stream_hit.h
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include/seqan/blast/blast_stream_hit_iterator.h
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include/seqan/blast/blast_stream_hsp_iterator.h
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include/seqan/blast/blast_stream_report.h
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include/seqan/chaining.h
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include/seqan/chaining/chain_base.h
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include/seqan/chaining/chain_generic.h
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include/seqan/chaining/chain_meta_fragment.h
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include/seqan/chaining/chain_point.h
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include/seqan/chaining/chain_wrapper_point.h
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include/seqan/chaining/chaining_generated_forwards.h
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include/seqan/chaining/fragment.h
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include/seqan/chaining/geom_distribution.h
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include/seqan/chaining/range_max_tree.h
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include/seqan/chaining/range_tree.h
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include/seqan/chaining/rmt_base.h
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include/seqan/chaining/rmt_common_algos.h
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include/seqan/chaining/rmt_compl_algos.h
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include/seqan/chaining/rmt_def_algos.h
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include/seqan/chaining/rmt_skip_base_element.h
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include/seqan/chaining/rmt_skip_element.h
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include/seqan/chaining/rt_base.h
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include/seqan/chaining/rt_common_algos.h
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include/seqan/chaining/rt_impl.h
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include/seqan/chaining/rt_skip_base_element.h
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include/seqan/chaining/rt_skip_element.h
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include/seqan/chaining/rt_sl_base.h
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include/seqan/chaining/rt_sl_compl_algos.h
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include/seqan/chaining/rt_sl_def_algos.h
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include/seqan/chaining/rt_sl_impl.h
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include/seqan/chaining/score_chain.h
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include/seqan/chaining/score_chain_sop.h
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include/seqan/chaining/score_manhattan.h
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include/seqan/chaining/score_zero.h
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include/seqan/chaining/skip_base_element.h
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include/seqan/chaining/skip_element.h
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include/seqan/chaining/skip_list.h
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include/seqan/chaining/skip_list_base.h
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include/seqan/chaining/skip_list_dynamic.h
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include/seqan/chaining/skip_list_impl.h
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include/seqan/chaining/skip_list_iterator.h
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include/seqan/chaining/skip_list_type.h
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include/seqan/chaining/skip_pool_alloc.h
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include/seqan/chaining/tree_chain.h
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include/seqan/chaining/tree_chain_sop.h
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include/seqan/chaining/tree_chain_utils.h
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include/seqan/consensus.h
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include/seqan/consensus/consensus_base.h
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include/seqan/consensus/consensus_generated_forwards.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/file.h
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include/seqan/file/chunk_collector.h
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include/seqan/file/cstream.h
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include/seqan/file/file_array.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_filereader.h
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include/seqan/file/file_filereaderiterator.h
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include/seqan/file/file_format.h
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include/seqan/file/file_format_cgviz.h
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include/seqan/file/file_format_embl.h
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include/seqan/file/file_format_fasta.h
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include/seqan/file/file_format_fasta_align.h
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include/seqan/file/file_format_genbank.h
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include/seqan/file/file_format_guess.h
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include/seqan/file/file_format_mmap.h
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include/seqan/file/file_format_raw.h
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include/seqan/file/file_forwards.h
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include/seqan/file/file_generated_forwards.h
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include/seqan/file/file_page.h
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include/seqan/file/file_page_raid0.h
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include/seqan/file/meta.h
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include/seqan/file/stream.h
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include/seqan/file/stream_algorithms.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_generated_forwards.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_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/find2.h
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include/seqan/find2/find2_generated_forwards.h
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include/seqan/find2/find_approx_dpsearch.h
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include/seqan/find2/find_approx_find_begin.h
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include/seqan/find2/find_base.h
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include/seqan/find2/find_exact_shiftand.h
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include/seqan/find2/find_exact_simple.h
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include/seqan/find2/find_finder_default.h
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include/seqan/find2/find_hamming_simple.h
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include/seqan/find2/find_multiple_exact_simple.h
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include/seqan/find2/find_pattern_wild_shiftand.h
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include/seqan/find_motif.h
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include/seqan/find_motif/em_algorithm.h
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include/seqan/find_motif/find_motif_base.h
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include/seqan/find_motif/find_motif_epatternbranching.h
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include/seqan/find_motif/find_motif_generated_forwards.h
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include/seqan/find_motif/find_motif_pms1.h
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include/seqan/find_motif/find_motif_pmsp.h
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include/seqan/find_motif/find_motif_projection.h
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include/seqan/find_motif/frequency_distribution.h
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include/seqan/find_motif/profile.h
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include/seqan/find_motif/pseudocount_base.h
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include/seqan/find_motif/pseudocount_mode_c.h
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include/seqan/find_motif/pseudocount_mode_p.h
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include/seqan/find_motif/sequence_model_types.h
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include/seqan/graph_algorithms.h
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include/seqan/graph_algorithms/graph_algorithm.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/graph_algorithms_generated_forwards.h
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include/seqan/graph_align.h
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include/seqan/graph_align/graph_align_banded_gotoh.h
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include/seqan/graph_align/graph_align_banded_needleman_wunsch.h
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include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h
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include/seqan/graph_align/graph_align_base.h
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include/seqan/graph_align/graph_align_config.h
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include/seqan/graph_align/graph_align_generated_forwards.h
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include/seqan/graph_align/graph_align_gotoh.h
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include/seqan/graph_align/graph_align_hirschberg.h
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include/seqan/graph_align/graph_align_interface.h
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include/seqan/graph_align/graph_align_needleman_wunsch.h
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include/seqan/graph_align/graph_align_smith_waterman.h
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include/seqan/graph_align/graph_align_smith_waterman_clump.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_msa/graph_msa_generated_forwards.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_fragment.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_property.h
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include/seqan/graph_types/graph_types_generated_forwards.h
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include/seqan/graph_types/graph_utility_parsing.h
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include/seqan/index.h
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include/seqan/index/find_index.h
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include/seqan/index/find_index_approx.h
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include/seqan/index/find_index_esa.h
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include/seqan/index/find_index_qgram.h
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include/seqan/index/find_quasar.h
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include/seqan/index/find_swift.h
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include/seqan/index/index_base.h
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include/seqan/index/index_bwt.h
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include/seqan/index/index_childtab.h
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include/seqan/index/index_dfi.h
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include/seqan/index/index_esa_algs.h
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include/seqan/index/index_esa_algs_multi.h
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include/seqan/index/index_esa_base.h
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include/seqan/index/index_esa_drawing.h
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include/seqan/index/index_esa_stree.h
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include/seqan/index/index_generated_forwards.h
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include/seqan/index/index_lcp.h
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include/seqan/index/index_lcp_tree.h
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include/seqan/index/index_manual_forwards.h
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include/seqan/index/index_pizzachili.h
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include/seqan/index/index_pizzachili_find.h
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include/seqan/index/index_pizzachili_string.h
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include/seqan/index/index_qgram.h
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include/seqan/index/index_qgram_openaddressing.h
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include/seqan/index/index_sa_btree.h
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include/seqan/index/index_sa_bwtwalk.h
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include/seqan/index/index_sa_lss.h
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include/seqan/index/index_sa_mm.h
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include/seqan/index/index_sa_qsort.h
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include/seqan/index/index_shawarma.h
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include/seqan/index/index_shims.h
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include/seqan/index/index_skew3.h
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include/seqan/index/index_skew7.h
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include/seqan/index/index_skew7_multi.h
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include/seqan/index/index_wotd.h
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include/seqan/index/pipe_merger3.h
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include/seqan/index/pipe_merger7.h
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include/seqan/index/pizzachili_api.h
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include/seqan/index/pump_extender3.h
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include/seqan/index/pump_extender7.h
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include/seqan/index/pump_lcp_core.h
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include/seqan/index/pump_separator7.h
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include/seqan/index/radix.h
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include/seqan/index/repeat_base.h
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include/seqan/index/shape_base.h
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include/seqan/index/shape_gapped.h
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include/seqan/index/shape_onegapped.h
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include/seqan/index/shape_predefined.h
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include/seqan/index/shape_threshold.h
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include/seqan/map.h
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include/seqan/map/map_adapter_stl.h
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include/seqan/map/map_base.h
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include/seqan/map/map_chooser.h
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include/seqan/map/map_generated_forwards.h
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include/seqan/map/map_skiplist.h
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include/seqan/map/map_vector.h
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include/seqan/map/sumlist.h
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include/seqan/map/sumlist_mini.h
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include/seqan/map/sumlist_skip.h
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include/seqan/misc/edit_environment.h
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include/seqan/misc/misc_base.h
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include/seqan/misc/misc_cmdparser.h
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include/seqan/misc/misc_dequeue.h
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include/seqan/misc/misc_generated_forwards.h
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include/seqan/misc/misc_interval_tree.h
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include/seqan/misc/misc_long_word.h
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include/seqan/misc/misc_map.h
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include/seqan/misc/misc_parsing.h
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include/seqan/misc/misc_random.h
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include/seqan/misc/misc_set.h
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include/seqan/misc/misc_svg.h
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include/seqan/misc/priority_type_base.h
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include/seqan/misc/priority_type_heap.h
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include/seqan/modifier.h
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include/seqan/modifier/modifier_alphabet.h
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include/seqan/modifier/modifier_alphabet_expansion.h
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include/seqan/modifier/modifier_functors.h
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include/seqan/modifier/modifier_generated_forwards.h
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include/seqan/modifier/modifier_iterator.h
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include/seqan/modifier/modifier_reverse.h
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include/seqan/modifier/modifier_shortcuts.h
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include/seqan/modifier/modifier_string.h
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include/seqan/modifier/modifier_view.h
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include/seqan/parallel.h
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include/seqan/parallel/parallel_atomic_misc.h
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include/seqan/parallel/parallel_atomic_primitives.h
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include/seqan/parallel/parallel_generated_forwards.h
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include/seqan/parallel/parallel_macros.h
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include/seqan/pipe.h
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include/seqan/pipe/pipe_base.h
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include/seqan/pipe/pipe_caster.h
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include/seqan/pipe/pipe_counter.h
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include/seqan/pipe/pipe_echoer.h
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include/seqan/pipe/pipe_edit_environment.h
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include/seqan/pipe/pipe_filter.h
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include/seqan/pipe/pipe_generated_forwards.h
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include/seqan/pipe/pipe_iterator.h
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include/seqan/pipe/pipe_joiner.h
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include/seqan/pipe/pipe_namer.h
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include/seqan/pipe/pipe_sampler.h
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include/seqan/pipe/pipe_shifter.h
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include/seqan/pipe/pipe_source.h
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include/seqan/pipe/pipe_tupler.h
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