Attachment 164374 Details for Bug 204127 – QA'd Updated patch

[patch] QA'd Updated patch

seqan-2.0.1.patch (text/plain), 190.74 KB, created by Jason Unovitch on 2015-12-19 01:37:41 UTC

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Description:

Filename:

MIME Type:

Creator: Jason Unovitch

Created: 2015-12-19 01:37:41 UTC

Size: 190.74 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 403996)
>+++ Makefile	(working copy)
>@@ -2,33 +2,29 @@
> # $FreeBSD$
> 
> PORTNAME=	seqan
>-PORTVERSION=	1.3.1
>-PORTREVISION=	3
>+PORTVERSION=	2.0.1
> 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=${WRKSRC}/apps/LICENSE
>+USES=		tar:bz2
>+NO_BUILD=	yes
> 
>-USES=		cmake:outsource python:build zip
>-CMAKE_SOURCE_PATH=${WRKSRC}/cmake
>-MAKE_JOB_SAFE=	yes
>+OPTIONS_DEFINE=	DOCS
>+DOCS_DESC=	Install official API documentation (html)
> 
>-SUB_FILES=	pkg-message
>-PKG_MESSAGE=	${WRKDIR}/pkg-message
>+do-install:
>+	${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME}
>+	cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
> 
>-USE_GCC=	4.8
>+post-install:
>+	${MKDIR} ${STAGEDIR}${DOCSDIR}
>+	cd ${WRKSRC}/share/doc/ && ${COPYTREE_SHARE} ./seqan/ ${STAGEDIR}${DOCSDIR}/../
> 
>-# 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
>-
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 403996)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
>-SIZE (seqan-1.3.1.zip) = 8787521
>+SHA256 (seqan-library-2.0.1.tar.bz2) = 7226160b2403429011702a02ba676b165c47cfb232f2d4d0b81c415eda8886de
>+SIZE (seqan-library-2.0.1.tar.bz2) = 7044538
>Index: files/patch-cmake-CMakeLists.txt
>===================================================================
>--- files/patch-cmake-CMakeLists.txt	(revision 403996)
>+++ files/patch-cmake-CMakeLists.txt	(nonexistent)
>@@ -1,13 +0,0 @@
>---- cmake/CMakeLists.txt.orig	2012-05-04 12:56:23.000000000 +0800
>-+++ cmake/CMakeLists.txt	2012-05-04 13:00:03.000000000 +0800
>-@@ -146,6 +146,10 @@
>-             COMPONENT headers)
>-     #message("install(FILES ${HEADER} RENAME seqan${NEW_PATH} DESTINATION include COMPONENT headers)")
>- endforeach()
>-+#seqan.h
>-+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../seqan.h
>-+	DESTINATION include
>-+	COMPONENT headers)
>- 
>- ################################################################################
>- # Set Compiler Flags
>
>Property changes on: files/patch-cmake-CMakeLists.txt
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: files/patch-cmake-apps-CMakeLists.txt
>===================================================================
>--- files/patch-cmake-apps-CMakeLists.txt	(revision 403996)
>+++ files/patch-cmake-apps-CMakeLists.txt	(nonexistent)
>@@ -1,8 +0,0 @@
>---- cmake/apps/CMakeLists.txt.orig	2012-05-04 11:12:35.000000000 +0800
>-+++ cmake/apps/CMakeLists.txt	2012-05-04 11:23:26.000000000 +0800
>-@@ -108,4 +108,4 @@
>- 
>- # Install RazerS gapped parameters.
>- install(DIRECTORY ${SEQAN_LIBRARY}/apps/razers2/gapped_params
>--        DESTINATION bin)
>-+        DESTINATION share/seqan)
>
>Property changes on: files/patch-cmake-apps-CMakeLists.txt
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(revision 403996)
>+++ pkg-descr	(working copy)
>@@ -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/
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 403996)
>+++ pkg-plist	(working copy)
>@@ -1,169 +1,216 @@
>-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/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/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/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/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 +220,9 @@
> 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 +236,42 @@
> 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 +282,6 @@
> 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 +289,6 @@
> 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
>@@ -266,19 +303,30 @@
> 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_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
>@@ -285,25 +333,43 @@
> 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
>@@ -319,35 +385,54 @@
> 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/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/sse2.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_reverse.h
> include/seqan/modifier/modifier_shortcuts.h
>@@ -354,10 +439,23 @@
> 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 +463,6 @@
> 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
>@@ -378,14 +475,18 @@
> 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_icc.h
> include/seqan/platform/platform_mingw.h
>+include/seqan/platform/platform_nvcc.h
>+include/seqan/platform/platform_pgi.h
> include/seqan/platform/platform_solaris.h
> include/seqan/platform/platform_windows.h
>+include/seqan/platform/windows_stdint.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_beta.h
>+include/seqan/random/random_beta_kfunc.h
> include/seqan/random/random_geometric.h
> include/seqan/random/random_lognormal.h
> include/seqan/random/random_mt19937.h
>@@ -393,79 +494,77 @@
> 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/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_thrust_vector.h
>+include/seqan/sequence/container_view.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
>@@ -472,24 +571,26 @@
> 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
>@@ -498,10 +599,8 @@
> 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
>@@ -508,1604 +607,1244 @@
> 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
>+include/seqan/stream/iostream_zip.h
>+include/seqan/stream/iostream_zip_impl.h
>+include/seqan/stream/iostream_zutil.h
>+include/seqan/stream/iter_stream.h
>+include/seqan/stream/lexical_cast.h
>+include/seqan/stream/stream_base.h
>+include/seqan/stream/stream_compressor.h
>+include/seqan/stream/tokenization.h
>+include/seqan/stream/virtual_stream.h
> include/seqan/system.h
> include/seqan/system/file_async.h
> include/seqan/system/file_directory.h
>-include/seqan/system/file_manual_forwards.h
>+include/seqan/system/file_forwards.h
> include/seqan/system/file_sync.h
> include/seqan/system/system_base.h
>+include/seqan/system/system_condition.h
>+include/seqan/system/system_critical_section.h
> include/seqan/system/system_event.h
>-include/seqan/system/system_generated_forwards.h
>-include/seqan/system/system_manual_forwards.h
>+include/seqan/system/system_forwards.h
> include/seqan/system/system_mutex.h
>-include/seqan/system/system_sema.h
> include/seqan/system/system_thread.h
>+include/seqan/translation.h
>+include/seqan/translation/translation.h
>+include/seqan/translation/translation_tables.h
>+include/seqan/ucsc_io.h
>+include/seqan/ucsc_io/ucsc_file.h
>+include/seqan/ucsc_io/ucsc_io.h
>+include/seqan/ucsc_io/ucsc_record.h
>+include/seqan/vcf_io.h
>+include/seqan/vcf_io/read_vcf.h
>+include/seqan/vcf_io/vcf_file.h
>+include/seqan/vcf_io/vcf_header.h
>+include/seqan/vcf_io/vcf_header_record.h
>+include/seqan/vcf_io/vcf_io_context.h
>+include/seqan/vcf_io/vcf_record.h
>+include/seqan/vcf_io/write_vcf.h
> include/seqan/version.h
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>-%%DATADIR%%/docs/DEMO_Allocators.html
>-%%DATADIR%%/docs/DEMO_Alphabets.html
>-%%DATADIR%%/docs/DEMO_Approximate+_Searching.html
>-%%DATADIR%%/docs/DEMO_Bellman-_Ford+_Algorithm.html
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>-%%DATADIR%%/docs/DEMO_Breadth-_First+_Search.html
>-%%DATADIR%%/docs/DEMO_Constraint+_Iterator.html
>-%%DATADIR%%/docs/DEMO_Depth-_First+_Search.html
>-%%DATADIR%%/docs/DEMO_Dijkstras+_Algorithm.html
>-%%DATADIR%%/docs/DEMO_Exact+_Searching.html
>-%%DATADIR%%/docs/DEMO_File+_Format+_I_2f_O.html
>-%%DATADIR%%/docs/DEMO_Floyd-_Warshall+_Algorithm.html
>-%%DATADIR%%/docs/DEMO_Global+_Alignments.html
>-%%DATADIR%%/docs/DEMO_H_M_M+_Silent+_States.html
>-%%DATADIR%%/docs/DEMO_H_M_M.html
>-%%DATADIR%%/docs/DEMO_Heaviest+_Increasing+_Subsequence.html
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>-%%DATADIR%%/docs/DEMO_Shortest+_Path+in+_D_A_Gs.html
>-%%DATADIR%%/docs/DEMO_String+_Basics.html
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>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OracleMultiBfamPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OutEdgeIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OutputStreamIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OwnerStringSet.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedPair.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedString.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedTriple.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PexPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PigeonholeFinder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PigeonholePattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliIndex.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliString.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfig.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfigSize.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolSpec.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PositionIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PrefixSegment.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PriorityHeap.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqFracScore.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqScore.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ReducedAminoAcid.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RightArrayBinaryTreeIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna5.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RngFunctor.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileIn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileOut.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Sampler.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileIn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileOut.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SetHorspoolPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftAndPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftOrPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Shifter.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleAllocator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleHolder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileIn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileInOut.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimplePattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleScore.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleSeed.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleShape.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SinglePoolAllocator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Skiplist.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfig.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfigSize.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterSpec.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Source.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StdAdaptorIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StoreIntervalsIntervalTreeNode.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StorePointsOnlyIntervalTreeNode.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StreamIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuffixSegment.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsFastIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftFinder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalFinder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalFinder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SyncFile.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TightDependentStringSet.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownHistoryIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tree.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TrieBfamPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TristateHolder.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tupler.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TwoLevelRankDictionary.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileIn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileOut.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnbandedLocalAlignmentEnumerator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UndirectedGraph.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UngappedShape.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UniformPdf.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VSTreeIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileIn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileOut.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VectorSet.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VertexIterator.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WaveletTree.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WildShiftAndPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WordGraph.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WuManberPattern.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Default.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_DotDrawing.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_EditDistance.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_GeneticCode.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_HammingDistance.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_LevenshteinDistance.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Move.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Murphy10.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Nothing.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/variable_LibraryStoreElementstd.html

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Attachments on bug 204127: 162571 | 164374 | 165571 | 165572 | 169191 | 169192 | 169193 | 169671 | 169674