FreeBSD Bugzilla – Attachment 169671 Details for
Bug 204127
[MAINTAINER] biology/seqan split apps out into biology/seqan-apps
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[patch]
patch for biology/seqan
seqan.patch (text/plain), 192.37 KB, created by
Hannes Hauswedell
on 2016-04-25 10:35:22 UTC
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Description:
patch for biology/seqan
Filename:
MIME Type:
Creator:
Hannes Hauswedell
Created:
2016-04-25 10:35:22 UTC
Size:
192.37 KB
patch
obsolete
>diff -ru seqanORIG/Makefile seqan/Makefile >--- seqanORIG/Makefile 2015-03-21 12:53:27.000000000 +0100 >+++ seqan/Makefile 2016-04-25 12:26:13.635588000 +0200 >@@ -2,33 +2,31 @@ > # $FreeBSD: head/biology/seqan/Makefile 381791 2015-03-21 11:53:27Z marino $ > > PORTNAME= seqan >-PORTVERSION= 1.3.1 >-PORTREVISION= 3 >+PORTVERSION= 2.1.1 > CATEGORIES= biology >-MASTER_SITES= http://ftp.seqan.de/releases/ >+MASTER_SITES= http://packages.seqan.de/seqan-library/ >+DISTNAME= ${PORTNAME}-library-${PORTVERSION} > > MAINTAINER= h2+fbsdports@fsfe.org >-COMMENT= C++ Sequence Analysis Library >+COMMENT= C++ Sequence Analysis Template Library > >-LICENSE= BSD3CLAUSE GPLv3 >-LICENSE_COMB= multi >+LICENSE= BSD3CLAUSE >+LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE > >-LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE >-LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE >+USES= tar:xz >+NO_BUILD= yes > >-USES= cmake:outsource python:build zip >-CMAKE_SOURCE_PATH=${WRKSRC}/cmake >-MAKE_JOB_SAFE= yes >+CONFLICTS= seqan1* > >-SUB_FILES= pkg-message >-PKG_MESSAGE= ${WRKDIR}/pkg-message >+OPTIONS_DEFINE= DOCS >+DOCS_DESC= Install official API documentation (html) > >-USE_GCC= 4.8 >+do-install: >+ ${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME} >+ cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include > >-# unsafe workaround because FreeBSD lacks logl and expl >-# see "BUGS" in `man 3 math` >-post-patch: >- @${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h >- @${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h >+post-install: >+ ${MKDIR} ${STAGEDIR}${DOCSDIR} >+ cd ${WRKSRC}/share/doc/ && ${COPYTREE_SHARE} ./seqan/ ${STAGEDIR}${DOCSDIR}/../ > > .include <bsd.port.mk> >diff -ru seqanORIG/distinfo seqan/distinfo >--- seqanORIG/distinfo 2014-01-22 16:30:13.000000000 +0100 >+++ seqan/distinfo 2016-04-11 16:57:07.941396000 +0200 >@@ -1,2 +1,2 @@ >-SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb >-SIZE (seqan-1.3.1.zip) = 8787521 >+SHA256 (seqan-library-2.1.1.tar.xz) = 8926f91fec5ce57e8efc70ac16cbf041bde0e0be463685b86e0d2e1e6a8169d7 >+SIZE (seqan-library-2.1.1.tar.xz) = 5238884 >diff -ru seqanORIG/pkg-descr seqan/pkg-descr >--- seqanORIG/pkg-descr 2014-01-22 16:44:51.000000000 +0100 >+++ seqan/pkg-descr 2016-04-11 16:55:41.034404000 +0200 >@@ -3,4 +3,7 @@ > focus on biological data. The library is licensed under the > 3-clause BSD license except the applications which are GPL. > >+This port now only contains the header library and API >+documentation. The apps are seperate. >+ > WWW: http://www.seqan.de/ >diff -ru seqanORIG/pkg-plist seqan/pkg-plist >--- seqanORIG/pkg-plist 2014-10-20 09:10:48.000000000 +0200 >+++ seqan/pkg-plist 2016-04-11 16:58:40.365390000 +0200 >@@ -1,169 +1,227 @@ >-bin/dfi >-bin/insegt >-bin/mason >-bin/micro_razers >-bin/pair_align >-bin/param_chooser >-bin/rabema >-bin/razers >-bin/razers2 >-bin/rep_sep >-bin/sak >-bin/seqan_tcoffee >-bin/seqcons >-bin/snp_store >-bin/splazers >-bin/stellar >-bin/tree_recon >-include/seqan.h > include/seqan/align.h >-include/seqan/align/align_algorithms.h > include/seqan/align/align_base.h >-include/seqan/align/align_cols_base.h >-include/seqan/align/align_dynprog.h >-include/seqan/align/align_generated_forwards.h >-include/seqan/align/align_hirschberg.h >+include/seqan/align/align_cols.h >+include/seqan/align/align_config.h > include/seqan/align/align_iterator_base.h >-include/seqan/align/align_local_dynprog.h >-include/seqan/align/align_local_dynprog_banded.h >-include/seqan/align/align_myers.h >-include/seqan/align/align_trace.h >+include/seqan/align/align_metafunctions.h >+include/seqan/align/align_traceback.h >+include/seqan/align/alignment_algorithm_tags.h >+include/seqan/align/alignment_operations.h >+include/seqan/align/dp_algorithm_impl.h >+include/seqan/align/dp_band.h >+include/seqan/align/dp_cell.h >+include/seqan/align/dp_cell_affine.h >+include/seqan/align/dp_cell_dynamic.h >+include/seqan/align/dp_cell_linear.h >+include/seqan/align/dp_context.h >+include/seqan/align/dp_formula.h >+include/seqan/align/dp_formula_affine.h >+include/seqan/align/dp_formula_dynamic.h >+include/seqan/align/dp_formula_linear.h >+include/seqan/align/dp_matrix.h >+include/seqan/align/dp_matrix_navigator.h >+include/seqan/align/dp_matrix_navigator_score_matrix.h >+include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h >+include/seqan/align/dp_matrix_navigator_trace_matrix.h >+include/seqan/align/dp_matrix_sparse.h >+include/seqan/align/dp_meta_info.h >+include/seqan/align/dp_profile.h >+include/seqan/align/dp_scout.h >+include/seqan/align/dp_setup.h >+include/seqan/align/dp_trace_segment.h >+include/seqan/align/dp_traceback_adaptor.h >+include/seqan/align/dp_traceback_impl.h >+include/seqan/align/evaluate_alignment.h >+include/seqan/align/fragment.h >+include/seqan/align/gap_anchor.h >+include/seqan/align/gapped_value_type.h >+include/seqan/align/gaps_anchor.h > include/seqan/align/gaps_array.h > include/seqan/align/gaps_base.h >+include/seqan/align/gaps_iterator_anchor.h >+include/seqan/align/gaps_iterator_array.h > include/seqan/align/gaps_iterator_base.h >-include/seqan/align/gaps_sumlist.h >-include/seqan/align/hirschberg_set.h >+include/seqan/align/global_alignment_banded.h >+include/seqan/align/global_alignment_hirschberg_impl.h >+include/seqan/align/global_alignment_myers_hirschberg_impl.h >+include/seqan/align/global_alignment_myers_impl.h >+include/seqan/align/global_alignment_specialized.h >+include/seqan/align/global_alignment_unbanded.h >+include/seqan/align/local_alignment_banded.h >+include/seqan/align/local_alignment_banded_waterman_eggert_impl.h >+include/seqan/align/local_alignment_enumeration.h >+include/seqan/align/local_alignment_enumeration_banded.h >+include/seqan/align/local_alignment_enumeration_unbanded.h >+include/seqan/align/local_alignment_unbanded.h >+include/seqan/align/local_alignment_waterman_eggert_impl.h > include/seqan/align/matrix_base.h >+include/seqan/align_extend.h >+include/seqan/align_extend/align_extend.h >+include/seqan/align_extend/align_extend_base.h >+include/seqan/align_extend/dp_scout_xdrop.h >+include/seqan/align_profile.h >+include/seqan/align_profile/add_to_profile.h >+include/seqan/align_profile/score_profile_seq.h >+include/seqan/align_split.h >+include/seqan/align_split/align_split_interface.h >+include/seqan/align_split/dp_scout_split.h >+include/seqan/alignment_free.h >+include/seqan/alignment_free/af_d2.h >+include/seqan/alignment_free/af_d2star.h >+include/seqan/alignment_free/af_d2z.h >+include/seqan/alignment_free/af_n2.h >+include/seqan/alignment_free/alignment_free_base.h >+include/seqan/alignment_free/alignment_free_comparison.h >+include/seqan/alignment_free/kmer_functions.h >+include/seqan/arg_parse.h >+include/seqan/arg_parse/arg_parse_argument.h >+include/seqan/arg_parse/arg_parse_ctd_support.h >+include/seqan/arg_parse/arg_parse_doc.h >+include/seqan/arg_parse/arg_parse_exceptions.h >+include/seqan/arg_parse/arg_parse_option.h >+include/seqan/arg_parse/arg_parse_parse.h >+include/seqan/arg_parse/arg_parse_type_support.h >+include/seqan/arg_parse/argument_parser.h >+include/seqan/arg_parse/tool_doc.h >+include/seqan/arg_parse/xml_support.h >+include/seqan/bam_io.h >+include/seqan/bam_io/bam_alignment_record.h >+include/seqan/bam_io/bam_alignment_record_util.h >+include/seqan/bam_io/bam_file.h >+include/seqan/bam_io/bam_header_record.h >+include/seqan/bam_io/bam_index_bai.h >+include/seqan/bam_io/bam_io_context.h >+include/seqan/bam_io/bam_sam_conversion.h >+include/seqan/bam_io/bam_scanner_cache.h >+include/seqan/bam_io/bam_tags_dict.h >+include/seqan/bam_io/cigar.h >+include/seqan/bam_io/read_bam.h >+include/seqan/bam_io/read_sam.h >+include/seqan/bam_io/write_bam.h >+include/seqan/bam_io/write_sam.h > include/seqan/basic.h >-include/seqan/basic/basic_aggregates.h >-include/seqan/basic/basic_allocator_chunkpool.h >-include/seqan/basic/basic_allocator_interface.h >-include/seqan/basic/basic_allocator_multipool.h >-include/seqan/basic/basic_allocator_simple.h >-include/seqan/basic/basic_allocator_singlepool.h >-include/seqan/basic/basic_allocator_to_std.h >-include/seqan/basic/basic_alphabet_interface.h >-include/seqan/basic/basic_alphabet_interface2.h >-include/seqan/basic/basic_alphabet_simple.h >-include/seqan/basic/basic_alphabet_simple_tabs.h >-include/seqan/basic/basic_alphabet_trait_basic.h >-include/seqan/basic/basic_compare.h >-include/seqan/basic/basic_converter.h >-include/seqan/basic/basic_counted_ptr.h >+include/seqan/basic/aggregate_concept.h >+include/seqan/basic/allocator_chunkpool.h >+include/seqan/basic/allocator_interface.h >+include/seqan/basic/allocator_multipool.h >+include/seqan/basic/allocator_simple.h >+include/seqan/basic/allocator_singlepool.h >+include/seqan/basic/allocator_to_std.h >+include/seqan/basic/alphabet_adapt_builtins.h >+include/seqan/basic/alphabet_bio.h >+include/seqan/basic/alphabet_concept.h >+include/seqan/basic/alphabet_math.h >+include/seqan/basic/alphabet_profile.h >+include/seqan/basic/alphabet_qualities.h >+include/seqan/basic/alphabet_residue.h >+include/seqan/basic/alphabet_residue_funcs.h >+include/seqan/basic/alphabet_residue_tabs.h >+include/seqan/basic/alphabet_simple_type.h >+include/seqan/basic/alphabet_storage.h >+include/seqan/basic/array_construct_destruct.h >+include/seqan/basic/basic_aggregate.h >+include/seqan/basic/basic_allocator.h >+include/seqan/basic/basic_alphabet.h >+include/seqan/basic/basic_concept.h >+include/seqan/basic/basic_container.h > include/seqan/basic/basic_debug.h >-include/seqan/basic/basic_definition.h >-include/seqan/basic/basic_forwards.h >-include/seqan/basic/basic_generated_forwards.h >-include/seqan/basic/basic_holder.h >-include/seqan/basic/basic_holder_dynamic.h >-include/seqan/basic/basic_host.h >+include/seqan/basic/basic_device.h >+include/seqan/basic/basic_exception.h >+include/seqan/basic/basic_functors.h >+include/seqan/basic/basic_fundamental.h > include/seqan/basic/basic_iterator.h >-include/seqan/basic/basic_iterator_adapt_std.h >-include/seqan/basic/basic_iterator_adaptor.h >-include/seqan/basic/basic_iterator_base.h >-include/seqan/basic/basic_iterator_position.h >-include/seqan/basic/basic_iterator_simple.h >-include/seqan/basic/basic_logvalue.h >+include/seqan/basic/basic_math.h > include/seqan/basic/basic_metaprogramming.h >-include/seqan/basic/basic_operator.h > include/seqan/basic/basic_parallelism.h >-include/seqan/basic/basic_pointer.h >-include/seqan/basic/basic_profchar.h >-include/seqan/basic/basic_profile.h > include/seqan/basic/basic_proxy.h >-include/seqan/basic/basic_sse2.h >-include/seqan/basic/basic_tag.h >-include/seqan/basic/basic_testing.h >-include/seqan/basic/basic_transport.h >+include/seqan/basic/basic_simd_vector.h >+include/seqan/basic/basic_smart_pointer.h >+include/seqan/basic/basic_stream.h >+include/seqan/basic/basic_tangle.h > include/seqan/basic/basic_type.h >-include/seqan/basic/basic_volatile_ptr.h >+include/seqan/basic/basic_view.h >+include/seqan/basic/boost_preprocessor_subset.h >+include/seqan/basic/builtin_functions.h >+include/seqan/basic/concept_checking.h >+include/seqan/basic/container_concept.h >+include/seqan/basic/debug_helper.h >+include/seqan/basic/debug_test_system.h >+include/seqan/basic/fundamental_chunking.h >+include/seqan/basic/fundamental_comparison.h >+include/seqan/basic/fundamental_concepts.h >+include/seqan/basic/fundamental_conversion.h >+include/seqan/basic/fundamental_metafunctions.h >+include/seqan/basic/fundamental_tags.h >+include/seqan/basic/fundamental_transport.h >+include/seqan/basic/holder_base.h >+include/seqan/basic/holder_simple.h >+include/seqan/basic/holder_tristate.h >+include/seqan/basic/hosted_type_interface.h >+include/seqan/basic/iterator_adapt_pointer.h >+include/seqan/basic/iterator_adapt_std.h >+include/seqan/basic/iterator_adaptor.h >+include/seqan/basic/iterator_base.h >+include/seqan/basic/iterator_concept.h >+include/seqan/basic/iterator_counting.h >+include/seqan/basic/iterator_interface.h >+include/seqan/basic/iterator_position.h >+include/seqan/basic/iterator_range.h >+include/seqan/basic/iterator_zip.h >+include/seqan/basic/macro_deprecated.h >+include/seqan/basic/math_functions.h >+include/seqan/basic/math_log_space_value.h >+include/seqan/basic/metaprogramming_control.h >+include/seqan/basic/metaprogramming_enable_if.h >+include/seqan/basic/metaprogramming_logic.h >+include/seqan/basic/metaprogramming_math.h >+include/seqan/basic/metaprogramming_type.h >+include/seqan/basic/metaprogramming_type_algebra.h >+include/seqan/basic/pair_base.h >+include/seqan/basic/pair_bit_compressed.h >+include/seqan/basic/pair_packed.h >+include/seqan/basic/profiling.h >+include/seqan/basic/property_map_concept.h >+include/seqan/basic/proxy_base.h >+include/seqan/basic/proxy_iterator.h >+include/seqan/basic/test_system.h >+include/seqan/basic/triple_base.h >+include/seqan/basic/triple_packed.h >+include/seqan/basic/tuple_base.h >+include/seqan/basic/tuple_bit_compressed.h >+include/seqan/basic/volatile_ptr.h >+include/seqan/bed_io.h >+include/seqan/bed_io/bed_file.h >+include/seqan/bed_io/bed_record.h >+include/seqan/bed_io/read_bed.h >+include/seqan/bed_io/write_bed.h > include/seqan/blast.h > include/seqan/blast/blast_base.h >-include/seqan/blast/blast_generated_forwards.h >-include/seqan/blast/blast_hit.h >-include/seqan/blast/blast_hit_iterator.h >-include/seqan/blast/blast_hsp.h >-include/seqan/blast/blast_hsp_iterator.h >-include/seqan/blast/blast_iterator.h >-include/seqan/blast/blast_parsing.h >-include/seqan/blast/blast_report.h >-include/seqan/blast/blast_run.h >-include/seqan/blast/blast_stream_hit.h >-include/seqan/blast/blast_stream_hit_iterator.h >-include/seqan/blast/blast_stream_hsp_iterator.h >-include/seqan/blast/blast_stream_report.h >-include/seqan/chaining.h >-include/seqan/chaining/chain_base.h >-include/seqan/chaining/chain_generic.h >-include/seqan/chaining/chain_meta_fragment.h >-include/seqan/chaining/chain_point.h >-include/seqan/chaining/chain_wrapper_point.h >-include/seqan/chaining/chaining_generated_forwards.h >-include/seqan/chaining/fragment.h >-include/seqan/chaining/geom_distribution.h >-include/seqan/chaining/range_max_tree.h >-include/seqan/chaining/range_tree.h >-include/seqan/chaining/rmt_base.h >-include/seqan/chaining/rmt_common_algos.h >-include/seqan/chaining/rmt_compl_algos.h >-include/seqan/chaining/rmt_def_algos.h >-include/seqan/chaining/rmt_skip_base_element.h >-include/seqan/chaining/rmt_skip_element.h >-include/seqan/chaining/rt_base.h >-include/seqan/chaining/rt_common_algos.h >-include/seqan/chaining/rt_impl.h >-include/seqan/chaining/rt_skip_base_element.h >-include/seqan/chaining/rt_skip_element.h >-include/seqan/chaining/rt_sl_base.h >-include/seqan/chaining/rt_sl_compl_algos.h >-include/seqan/chaining/rt_sl_def_algos.h >-include/seqan/chaining/rt_sl_impl.h >-include/seqan/chaining/score_chain.h >-include/seqan/chaining/score_chain_sop.h >-include/seqan/chaining/score_manhattan.h >-include/seqan/chaining/score_zero.h >-include/seqan/chaining/skip_base_element.h >-include/seqan/chaining/skip_element.h >-include/seqan/chaining/skip_list.h >-include/seqan/chaining/skip_list_base.h >-include/seqan/chaining/skip_list_dynamic.h >-include/seqan/chaining/skip_list_impl.h >-include/seqan/chaining/skip_list_iterator.h >-include/seqan/chaining/skip_list_type.h >-include/seqan/chaining/skip_pool_alloc.h >-include/seqan/chaining/tree_chain.h >-include/seqan/chaining/tree_chain_sop.h >-include/seqan/chaining/tree_chain_utils.h >+include/seqan/blast/blast_io_context.h >+include/seqan/blast/blast_record.h >+include/seqan/blast/blast_report_out.h >+include/seqan/blast/blast_statistics.h >+include/seqan/blast/blast_tabular.h >+include/seqan/blast/blast_tabular_in.h >+include/seqan/blast/blast_tabular_lowlevel.h >+include/seqan/blast/blast_tabular_out.h > include/seqan/consensus.h >+include/seqan/consensus/consensus_aligner.h >+include/seqan/consensus/consensus_aligner_interface.h >+include/seqan/consensus/consensus_alignment_options.h > include/seqan/consensus/consensus_base.h >-include/seqan/consensus/consensus_generated_forwards.h >+include/seqan/consensus/consensus_builder.h > include/seqan/consensus/consensus_library.h > include/seqan/consensus/consensus_realign.h > include/seqan/consensus/consensus_score.h >+include/seqan/consensus/overlap_info_computation.h >+include/seqan/consensus/overlapper.h > include/seqan/file.h >-include/seqan/file/chunk_collector.h >-include/seqan/file/cstream.h >-include/seqan/file/file_array.h > include/seqan/file/file_base.h > include/seqan/file/file_cstyle.h >-include/seqan/file/file_filereader.h >-include/seqan/file/file_filereaderiterator.h >-include/seqan/file/file_format.h >-include/seqan/file/file_format_cgviz.h >-include/seqan/file/file_format_embl.h >-include/seqan/file/file_format_fasta.h >-include/seqan/file/file_format_fasta_align.h >-include/seqan/file/file_format_genbank.h >-include/seqan/file/file_format_guess.h >-include/seqan/file/file_format_mmap.h >-include/seqan/file/file_format_raw.h > include/seqan/file/file_forwards.h >-include/seqan/file/file_generated_forwards.h >+include/seqan/file/file_interface.h >+include/seqan/file/file_mapping.h > include/seqan/file/file_page.h >-include/seqan/file/file_page_raid0.h >-include/seqan/file/meta.h >-include/seqan/file/stream.h >-include/seqan/file/stream_algorithms.h > include/seqan/file/string_external.h > include/seqan/file/string_mmap.h > include/seqan/find.h >@@ -173,9 +231,9 @@ > include/seqan/find/find_begin.h > include/seqan/find/find_bndm.h > include/seqan/find/find_bom.h >-include/seqan/find/find_generated_forwards.h > include/seqan/find/find_hamming_simple.h > include/seqan/find/find_horspool.h >+include/seqan/find/find_lambda.h > include/seqan/find/find_multi.h > include/seqan/find/find_multiple_bfam.h > include/seqan/find/find_multiple_shiftand.h >@@ -189,50 +247,42 @@ > include/seqan/find/find_simple.h > include/seqan/find/find_wild_shiftand.h > include/seqan/find/find_wumanber.h >-include/seqan/find2.h >-include/seqan/find2/find2_generated_forwards.h >-include/seqan/find2/find_approx_dpsearch.h >-include/seqan/find2/find_approx_find_begin.h >-include/seqan/find2/find_base.h >-include/seqan/find2/find_exact_shiftand.h >-include/seqan/find2/find_exact_simple.h >-include/seqan/find2/find_finder_default.h >-include/seqan/find2/find_hamming_simple.h >-include/seqan/find2/find_multiple_exact_simple.h >-include/seqan/find2/find_pattern_wild_shiftand.h >-include/seqan/find_motif.h >-include/seqan/find_motif/em_algorithm.h >-include/seqan/find_motif/find_motif_base.h >-include/seqan/find_motif/find_motif_epatternbranching.h >-include/seqan/find_motif/find_motif_generated_forwards.h >-include/seqan/find_motif/find_motif_pms1.h >-include/seqan/find_motif/find_motif_pmsp.h >-include/seqan/find_motif/find_motif_projection.h >-include/seqan/find_motif/frequency_distribution.h >-include/seqan/find_motif/profile.h >-include/seqan/find_motif/pseudocount_base.h >-include/seqan/find_motif/pseudocount_mode_c.h >-include/seqan/find_motif/pseudocount_mode_p.h >-include/seqan/find_motif/sequence_model_types.h >+include/seqan/gff_io.h >+include/seqan/gff_io/gff_file.h >+include/seqan/gff_io/gff_io_base.h > include/seqan/graph_algorithms.h >-include/seqan/graph_algorithms/graph_algorithm.h >+include/seqan/graph_algorithms/all_pairs_shortest_path.h >+include/seqan/graph_algorithms/bellman_ford.h >+include/seqan/graph_algorithms/bipartite_matching.h >+include/seqan/graph_algorithms/breadth_first_search.h >+include/seqan/graph_algorithms/connected_components.h >+include/seqan/graph_algorithms/depth_first_search.h >+include/seqan/graph_algorithms/dijkstra.h >+include/seqan/graph_algorithms/floyd_warshall.h >+include/seqan/graph_algorithms/ford_fulkerson.h > include/seqan/graph_algorithms/graph_algorithm_heap_tree.h > include/seqan/graph_algorithms/graph_algorithm_hmm.h > include/seqan/graph_algorithms/graph_algorithm_lis_his.h >-include/seqan/graph_algorithms/graph_algorithms_generated_forwards.h >+include/seqan/graph_algorithms/kruskal.h >+include/seqan/graph_algorithms/path_growing.h >+include/seqan/graph_algorithms/prim.h >+include/seqan/graph_algorithms/single_source_shortest_path.h >+include/seqan/graph_algorithms/strongly_connected_compnents.h >+include/seqan/graph_algorithms/topological_sort.h >+include/seqan/graph_algorithms/transitive_closure.h >+include/seqan/graph_algorithms/weakly_connected_components.h >+include/seqan/graph_algorithms/weighted_bipartite_matching.h > include/seqan/graph_align.h >-include/seqan/graph_align/graph_align_banded_gotoh.h >-include/seqan/graph_align/graph_align_banded_needleman_wunsch.h >-include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h >-include/seqan/graph_align/graph_align_base.h >-include/seqan/graph_align/graph_align_config.h >-include/seqan/graph_align/graph_align_generated_forwards.h >-include/seqan/graph_align/graph_align_gotoh.h >-include/seqan/graph_align/graph_align_hirschberg.h >-include/seqan/graph_align/graph_align_interface.h >-include/seqan/graph_align/graph_align_needleman_wunsch.h >-include/seqan/graph_align/graph_align_smith_waterman.h >-include/seqan/graph_align/graph_align_smith_waterman_clump.h >+include/seqan/graph_align/graph_algorithm_refine_align.h >+include/seqan/graph_align/graph_algorithm_refine_aligngraph.h >+include/seqan/graph_align/graph_algorithm_refine_annotation.h >+include/seqan/graph_align/graph_algorithm_refine_exact.h >+include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h >+include/seqan/graph_align/graph_algorithm_refine_fragment.h >+include/seqan/graph_align/graph_algorithm_refine_inexact.h >+include/seqan/graph_align/graph_algorithm_refine_scoring.h >+include/seqan/graph_align/graph_impl_align.h >+include/seqan/graph_align/graph_impl_align_adapt.h > include/seqan/graph_msa.h > include/seqan/graph_msa/graph_align_tcoffee_base.h > include/seqan/graph_msa/graph_align_tcoffee_distance.h >@@ -243,7 +293,6 @@ > include/seqan/graph_msa/graph_align_tcoffee_msa.h > include/seqan/graph_msa/graph_align_tcoffee_progressive.h > include/seqan/graph_msa/graph_align_tcoffee_refinement.h >-include/seqan/graph_msa/graph_msa_generated_forwards.h > include/seqan/graph_types.h > include/seqan/graph_types/graph_base.h > include/seqan/graph_types/graph_drawing.h >@@ -251,7 +300,6 @@ > include/seqan/graph_types/graph_idmanager.h > include/seqan/graph_types/graph_impl_automaton.h > include/seqan/graph_types/graph_impl_directed.h >-include/seqan/graph_types/graph_impl_fragment.h > include/seqan/graph_types/graph_impl_hmm.h > include/seqan/graph_types/graph_impl_oracle.h > include/seqan/graph_types/graph_impl_tree.h >@@ -266,44 +314,74 @@ > include/seqan/graph_types/graph_iterator_edge.h > include/seqan/graph_types/graph_iterator_outedge.h > include/seqan/graph_types/graph_iterator_vertex.h >-include/seqan/graph_types/graph_property.h >-include/seqan/graph_types/graph_types_generated_forwards.h > include/seqan/graph_types/graph_utility_parsing.h >+include/seqan/graph_types/property_map_generic.h >+include/seqan/graph_types/property_map_internal.h >+include/seqan/graph_types/property_map_internal_pointer.h > include/seqan/index.h >+include/seqan/index/find2_backtracking.h >+include/seqan/index/find2_base.h >+include/seqan/index/find2_functors.h >+include/seqan/index/find2_index.h >+include/seqan/index/find2_index_multi.h >+include/seqan/index/find2_vstree_factory.h >+include/seqan/index/find_backtracking.h > include/seqan/index/find_index.h > include/seqan/index/find_index_approx.h >+include/seqan/index/find_index_binary.h > include/seqan/index/find_index_esa.h >+include/seqan/index/find_index_lambda.h > include/seqan/index/find_index_qgram.h >+include/seqan/index/find_pigeonhole.h > include/seqan/index/find_quasar.h > include/seqan/index/find_swift.h > include/seqan/index/index_base.h > include/seqan/index/index_bwt.h > include/seqan/index/index_childtab.h >+include/seqan/index/index_device.h > include/seqan/index/index_dfi.h > include/seqan/index/index_esa_algs.h > include/seqan/index/index_esa_algs_multi.h > include/seqan/index/index_esa_base.h > include/seqan/index/index_esa_drawing.h > include/seqan/index/index_esa_stree.h >-include/seqan/index/index_generated_forwards.h >+include/seqan/index/index_fm.h >+include/seqan/index/index_fm_compressed_sa.h >+include/seqan/index/index_fm_compressed_sa_iterator.h >+include/seqan/index/index_fm_device.h >+include/seqan/index/index_fm_dox.h >+include/seqan/index/index_fm_lf_table.h >+include/seqan/index/index_fm_rank_dictionary_base.h >+include/seqan/index/index_fm_rank_dictionary_levels.h >+include/seqan/index/index_fm_rank_dictionary_naive.h >+include/seqan/index/index_fm_rank_dictionary_wt.h >+include/seqan/index/index_fm_right_array_binary_tree.h >+include/seqan/index/index_fm_right_array_binary_tree_iterator.h >+include/seqan/index/index_fm_sparse_string.h >+include/seqan/index/index_fm_stree.h >+include/seqan/index/index_forwards.h > include/seqan/index/index_lcp.h > include/seqan/index/index_lcp_tree.h >-include/seqan/index/index_manual_forwards.h > include/seqan/index/index_pizzachili.h > include/seqan/index/index_pizzachili_find.h > include/seqan/index/index_pizzachili_string.h > include/seqan/index/index_qgram.h >+include/seqan/index/index_qgram_bucketrefinement.h > include/seqan/index/index_qgram_openaddressing.h >+include/seqan/index/index_qgram_stree.h > include/seqan/index/index_sa_btree.h > include/seqan/index/index_sa_bwtwalk.h > include/seqan/index/index_sa_lss.h > include/seqan/index/index_sa_mm.h > include/seqan/index/index_sa_qsort.h >+include/seqan/index/index_sa_stree.h >+include/seqan/index/index_sa_truncated.h > include/seqan/index/index_shawarma.h > include/seqan/index/index_shims.h > include/seqan/index/index_skew3.h > include/seqan/index/index_skew7.h > include/seqan/index/index_skew7_multi.h >+include/seqan/index/index_view.h > include/seqan/index/index_wotd.h > include/seqan/index/pipe_merger3.h > include/seqan/index/pipe_merger7.h >@@ -316,48 +394,99 @@ > include/seqan/index/repeat_base.h > include/seqan/index/shape_base.h > include/seqan/index/shape_gapped.h >+include/seqan/index/shape_minimizer.h > include/seqan/index/shape_onegapped.h > include/seqan/index/shape_predefined.h > include/seqan/index/shape_threshold.h >+include/seqan/journaled_set.h >+include/seqan/journaled_set/journal_alignment_interface.h >+include/seqan/journaled_set/journal_alignment_traceback_adaptor.h >+include/seqan/journaled_set/journaled_set_base.h >+include/seqan/journaled_set/journaled_set_impl.h >+include/seqan/journaled_set/journaled_set_join.h >+include/seqan/journaled_set/journaled_set_join_config.h >+include/seqan/journaled_set/journaled_set_join_global_align_compact.h >+include/seqan/journaled_set/journaled_set_join_global_align_manhatten.h >+include/seqan/journaled_set/journaled_set_journal_trace_descriptor.h >+include/seqan/journaled_set/score_biaffine.h >+include/seqan/journaled_string_tree.h >+include/seqan/journaled_string_tree/delta_map.h >+include/seqan/journaled_string_tree/delta_map_entry.h >+include/seqan/journaled_string_tree/delta_map_iterator.h >+include/seqan/journaled_string_tree/delta_store.h >+include/seqan/journaled_string_tree/journaled_string_tree_base.h >+include/seqan/journaled_string_tree/journaled_string_tree_impl.h >+include/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h >+include/seqan/journaled_string_tree/journaled_string_tree_traverser.h >+include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h >+include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h >+include/seqan/journaled_string_tree/jst_extension_base.h >+include/seqan/journaled_string_tree/jst_extension_horspool.h >+include/seqan/journaled_string_tree/jst_extension_myers_ukkonen.h >+include/seqan/journaled_string_tree/jst_extension_shiftand.h >+include/seqan/journaled_string_tree/jst_extension_shiftor.h >+include/seqan/journaled_string_tree/observable.h >+include/seqan/journaled_string_tree/stack_observer.h > include/seqan/map.h > include/seqan/map/map_adapter_stl.h > include/seqan/map/map_base.h > include/seqan/map/map_chooser.h >-include/seqan/map/map_generated_forwards.h > include/seqan/map/map_skiplist.h > include/seqan/map/map_vector.h > include/seqan/map/sumlist.h > include/seqan/map/sumlist_mini.h > include/seqan/map/sumlist_skip.h >+include/seqan/math.h >+include/seqan/math/math_common_factor.h >+include/seqan/math/math_operators.h >+include/seqan/math/math_rational.h >+include/seqan/misc/accumulators.h >+include/seqan/misc/base.h >+include/seqan/misc/bit_twiddling.h >+include/seqan/misc/bit_twiddling_functors.h >+include/seqan/misc/cuda.h >+include/seqan/misc/dequeue.h > include/seqan/misc/edit_environment.h >-include/seqan/misc/misc_base.h >-include/seqan/misc/misc_cmdparser.h >-include/seqan/misc/misc_dequeue.h >-include/seqan/misc/misc_generated_forwards.h >-include/seqan/misc/misc_interval_tree.h >-include/seqan/misc/misc_long_word.h >-include/seqan/misc/misc_map.h >-include/seqan/misc/misc_parsing.h >-include/seqan/misc/misc_random.h >-include/seqan/misc/misc_set.h >-include/seqan/misc/misc_svg.h >+include/seqan/misc/interval_tree.h >+include/seqan/misc/map.h >+include/seqan/misc/memset.h >+include/seqan/misc/name_store_cache.h > include/seqan/misc/priority_type_base.h > include/seqan/misc/priority_type_heap.h >+include/seqan/misc/set.h >+include/seqan/misc/svg.h >+include/seqan/misc/terminal.h >+include/seqan/misc/union_find.h > include/seqan/modifier.h >+include/seqan/modifier/cyclic_shape.h > include/seqan/modifier/modifier_alphabet.h > include/seqan/modifier/modifier_alphabet_expansion.h >+include/seqan/modifier/modifier_cyclic_shape.h > include/seqan/modifier/modifier_functors.h >-include/seqan/modifier/modifier_generated_forwards.h > include/seqan/modifier/modifier_iterator.h >+include/seqan/modifier/modifier_position.h > include/seqan/modifier/modifier_reverse.h > include/seqan/modifier/modifier_shortcuts.h > include/seqan/modifier/modifier_string.h > include/seqan/modifier/modifier_view.h > include/seqan/parallel.h >+include/seqan/parallel/parallel_algorithms.h > include/seqan/parallel/parallel_atomic_misc.h > include/seqan/parallel/parallel_atomic_primitives.h >-include/seqan/parallel/parallel_generated_forwards.h >+include/seqan/parallel/parallel_lock.h > include/seqan/parallel/parallel_macros.h >+include/seqan/parallel/parallel_queue.h >+include/seqan/parallel/parallel_queue_suspendable.h >+include/seqan/parallel/parallel_resource_pool.h >+include/seqan/parallel/parallel_sequence.h >+include/seqan/parallel/parallel_serializer.h >+include/seqan/parallel/parallel_splitting.h >+include/seqan/parallel/parallel_tags.h >+include/seqan/parse_lm.h >+include/seqan/parse_lm/local_match_store.h >+include/seqan/parse_lm/parse_blastn_tabular.h >+include/seqan/parse_lm/parse_lastz_general.h >+include/seqan/parse_lm/parse_stellar_gff.h > include/seqan/pipe.h > include/seqan/pipe/pipe_base.h > include/seqan/pipe/pipe_caster.h >@@ -365,7 +494,6 @@ > include/seqan/pipe/pipe_echoer.h > include/seqan/pipe/pipe_edit_environment.h > include/seqan/pipe/pipe_filter.h >-include/seqan/pipe/pipe_generated_forwards.h > include/seqan/pipe/pipe_iterator.h > include/seqan/pipe/pipe_joiner.h > include/seqan/pipe/pipe_namer.h >@@ -378,118 +506,109 @@ > include/seqan/pipe/pool_sorter.h > include/seqan/platform.h > include/seqan/platform/platform_gcc.h >-include/seqan/platform/platform_generated_forwards.h >-include/seqan/platform/platform_mingw.h >-include/seqan/platform/platform_solaris.h >+include/seqan/platform/platform_icc.h >+include/seqan/platform/platform_nvcc.h > include/seqan/platform/platform_windows.h > include/seqan/random.h >-include/seqan/random/ext_MersenneTwister.h > include/seqan/random/random_base.h >-include/seqan/random/random_generated_forwards.h >-include/seqan/random/random_geometric.h >-include/seqan/random/random_lognormal.h >-include/seqan/random/random_mt19937.h >-include/seqan/random/random_normal.h >-include/seqan/random/random_rng_functor.h >-include/seqan/random/random_shuffle.h >-include/seqan/random/random_uniform.h >-include/seqan/refinement.h >-include/seqan/refinement/graph_algorithm_refine_align.h >-include/seqan/refinement/graph_algorithm_refine_aligngraph.h >-include/seqan/refinement/graph_algorithm_refine_annotation.h >-include/seqan/refinement/graph_algorithm_refine_exact.h >-include/seqan/refinement/graph_algorithm_refine_exact_iterative.h >-include/seqan/refinement/graph_algorithm_refine_fragment.h >-include/seqan/refinement/graph_algorithm_refine_inexact.h >-include/seqan/refinement/graph_algorithm_refine_scoring.h >-include/seqan/refinement/graph_impl_align.h >-include/seqan/refinement/graph_impl_align_adapt.h >-include/seqan/refinement/refinement_generated_forwards.h >+include/seqan/random/random_beta.h >+include/seqan/random/random_util.h >+include/seqan/realign.h >+include/seqan/realign/realign_base.h >+include/seqan/realign/realign_helper_functions.h >+include/seqan/reduced_aminoacid.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h >+include/seqan/roi_io.h >+include/seqan/roi_io/read_roi.h >+include/seqan/roi_io/roi_file.h >+include/seqan/roi_io/roi_io_context.h >+include/seqan/roi_io/roi_record.h >+include/seqan/roi_io/write_roi.h > include/seqan/score.h > include/seqan/score/score_base.h > include/seqan/score/score_edit.h >-include/seqan/score/score_generated_forwards.h > include/seqan/score/score_matrix.h > include/seqan/score/score_matrix_data.h >+include/seqan/score/score_matrix_io.h > include/seqan/score/score_simple.h > include/seqan/seeds.h >-include/seqan/seeds/banded_align.h >-include/seqan/seeds/banded_chain_align.h >-include/seqan/seeds/banded_chain_align_affine.h >-include/seqan/seeds/global_seed_chain.h >-include/seqan/seeds/memoryManager_base.h >-include/seqan/seeds/memoryManager_int.h >-include/seqan/seeds/propertyMap.h >-include/seqan/seeds/seedHandlingTags.h >-include/seqan/seeds/seedSet_base.h >-include/seqan/seeds/seedSet_iterator.h >-include/seqan/seeds/seedSet_score.h >-include/seqan/seeds/seed_base.h >-include/seqan/seeds/seed_multi.h >-include/seqan/seeds/seeds_generated_forwards.h >-include/seqan/seeds2.h >-include/seqan/seeds2/align_chain_banded.h >-include/seqan/seeds2/align_dynprog_affine.h >-include/seqan/seeds2/align_dynprog_banded_affine.h >-include/seqan/seeds2/align_dynprog_banded_linear.h >-include/seqan/seeds2/align_dynprog_linear.h >-include/seqan/seeds2/basic_iter_indirect.h >-include/seqan/seeds2/seeds2_generated_forwards.h >-include/seqan/seeds2/seeds_base.h >-include/seqan/seeds2/seeds_combination.h >-include/seqan/seeds2/seeds_extension.h >-include/seqan/seeds2/seeds_global_chaining.h >-include/seqan/seeds2/seeds_global_chaining_base.h >-include/seqan/seeds2/seeds_global_chaining_gusfield.h >-include/seqan/seeds2/seeds_seed_base.h >-include/seqan/seeds2/seeds_seed_chained.h >-include/seqan/seeds2/seeds_seed_diagonal.h >-include/seqan/seeds2/seeds_seed_set_base.h >-include/seqan/seeds2/seeds_seed_set_non_scored.h >-include/seqan/seeds2/seeds_seed_set_scored.h >-include/seqan/seeds2/seeds_seed_set_unordered.h >-include/seqan/seeds2/seeds_seed_simple.h >+include/seqan/seeds/banded_chain_alignment.h >+include/seqan/seeds/banded_chain_alignment_impl.h >+include/seqan/seeds/banded_chain_alignment_profile.h >+include/seqan/seeds/banded_chain_alignment_scout.h >+include/seqan/seeds/banded_chain_alignment_traceback.h >+include/seqan/seeds/basic_iter_indirect.h >+include/seqan/seeds/seeds_base.h >+include/seqan/seeds/seeds_combination.h >+include/seqan/seeds/seeds_extension.h >+include/seqan/seeds/seeds_global_chaining.h >+include/seqan/seeds/seeds_global_chaining_base.h >+include/seqan/seeds/seeds_global_chaining_gusfield.h >+include/seqan/seeds/seeds_seed_base.h >+include/seqan/seeds/seeds_seed_chained.h >+include/seqan/seeds/seeds_seed_diagonal.h >+include/seqan/seeds/seeds_seed_set_base.h >+include/seqan/seeds/seeds_seed_set_non_scored.h >+include/seqan/seeds/seeds_seed_set_scored.h >+include/seqan/seeds/seeds_seed_set_unordered.h >+include/seqan/seeds/seeds_seed_simple.h >+include/seqan/seq_io.h >+include/seqan/seq_io/fai_index.h >+include/seqan/seq_io/fasta_fastq.h >+include/seqan/seq_io/genomic_region.h >+include/seqan/seq_io/read_embl.h >+include/seqan/seq_io/read_genbank.h >+include/seqan/seq_io/sequence_file.h > include/seqan/sequence.h > include/seqan/sequence/adapt_array_pointer.h >-include/seqan/sequence/adapt_std_list.h >-include/seqan/sequence/adapt_std_string.h >-include/seqan/sequence/adapt_std_vector.h >+include/seqan/sequence/adapt_stl_container.h >+include/seqan/sequence/adapt_thrust_vector.h >+include/seqan/sequence/container_view.h >+include/seqan/sequence/container_view_zip.h > include/seqan/sequence/iter_concat_virtual.h > include/seqan/sequence/segment_base.h > include/seqan/sequence/segment_infix.h > include/seqan/sequence/segment_prefix.h > include/seqan/sequence/segment_suffix.h >+include/seqan/sequence/segment_utils.h > include/seqan/sequence/sequence_concatenator.h > include/seqan/sequence/sequence_forwards.h >-include/seqan/sequence/sequence_generated_forwards.h > include/seqan/sequence/sequence_interface.h > include/seqan/sequence/sequence_lexical.h > include/seqan/sequence/sequence_shortcuts.h >-include/seqan/sequence/sequence_stream.h > include/seqan/sequence/string_alloc.h > include/seqan/sequence/string_array.h > include/seqan/sequence/string_base.h > include/seqan/sequence/string_block.h > include/seqan/sequence/string_cstyle.h > include/seqan/sequence/string_packed.h >+include/seqan/sequence/string_packed_old.h > include/seqan/sequence/string_set_base.h > include/seqan/sequence/string_set_concat_direct.h > include/seqan/sequence/string_set_dependent_generous.h > include/seqan/sequence/string_set_dependent_tight.h >+include/seqan/sequence/string_set_device.h > include/seqan/sequence/string_set_owner.h >+include/seqan/sequence/string_set_segment.h >+include/seqan/sequence/string_set_view.h > include/seqan/sequence_journaled.h > include/seqan/sequence_journaled/journal_entries_sorted_array.h >-include/seqan/sequence_journaled/journal_entries_unbalanced_tree.h >-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h >-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h > include/seqan/sequence_journaled/journal_entry.h > include/seqan/sequence_journaled/sequence_journaled.h >-include/seqan/sequence_journaled/sequence_journaled_forwards.h >-include/seqan/sequence_journaled/sequence_journaled_generated_forwards.h > include/seqan/sequence_journaled/sequence_journaled_iterator.h >+include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h >+include/seqan/simple_intervals_io.h >+include/seqan/simple_intervals_io/simple_intervals_file.h >+include/seqan/simple_intervals_io/simple_intervals_io.h > include/seqan/statistics.h > include/seqan/statistics/statistics_base.h >-include/seqan/statistics/statistics_generated_forwards.h > include/seqan/statistics/statistics_markov_model.h > include/seqan/store.h > include/seqan/store/store_align.h >@@ -498,1614 +617,1285 @@ > include/seqan/store/store_annotation.h > include/seqan/store/store_base.h > include/seqan/store/store_contig.h >-include/seqan/store/store_generated_forwards.h > include/seqan/store/store_intervaltree.h > include/seqan/store/store_io.h >-include/seqan/store/store_io_bam.h > include/seqan/store/store_io_gff.h > include/seqan/store/store_io_sam.h > include/seqan/store/store_io_ucsc.h > include/seqan/store/store_library.h > include/seqan/store/store_matepair.h > include/seqan/store/store_read.h >+include/seqan/stream.h >+include/seqan/stream/adapt_ios.h >+include/seqan/stream/buffered_stream.h >+include/seqan/stream/file_stream.h >+include/seqan/stream/formatted_file.h >+include/seqan/stream/guess_format.h >+include/seqan/stream/iostream_bgzf.h >+include/seqan/stream/iostream_bzip2.h >+include/seqan/stream/iostream_bzip2_impl.h 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169674