[med-svn] [seqan2] branch master updated (0ea7aaa -> aed10f8)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 14 17:54:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository seqan2.
from 0ea7aaa Drop Soeren Sonnenburg from Uploaders
adds 275acf8 Try patch from upstream to fix kfreebsd/hurd builds
adds d45d8d2 bump version
adds a7057cf switch to upstream's patch
adds 52afd09 Restrict archs for now.
adds 6f07e3e New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
adds 922aa9c Merge tag 'upstream/2.3.0_0.20161011_73a5aaf+dfsg' into debian-experimental
adds 91b2729 test upstream's develop branch
adds 97da30d New upstream version 2.3.0~0.20161019~af07bc1+dfsg
adds d35474a Merge tag 'upstream/2.3.0_0.20161019_af07bc1+dfsg' into debian-experimental
adds cdca0c6 New test build
adds 3a1fd65 fix typo
adds b9be45d Work around GNU Hurd TANDEM problem
adds 89ff8db remove some archs, save memory on others
adds a58b2c3 New upstream version 2.3.0~1.20161019~af07bc1+dfsg
adds 2dbbfd5 Merge tag 'upstream/2.3.0_1.20161019_af07bc1+dfsg' into debian-experimental
adds 35fb99e tweak version due to earlier misversioning
adds f63d320 Fix recursive variable expansion error.
adds 2ec4e20 Skip unneeded build for -indep.
adds b839e38 Fix architecture detection logic
adds 9460525 Another typo fix from upstream
adds d5c2144 Try out -O3 for many architectures as that is upstream's default.
adds 20af6c2 Try to save more memory on kfreebsd-*
adds 8327bef New upstream version 2.3.1+dfsg
adds 7fcf128 Merge tag 'upstream/2.3.1+dfsg' into debian-experimental
adds 2dc4b73 new upstream release
adds a38b519 Remove archs with failing builds: armhf mips mipsel
adds 0b4e43e Only the seqan-config CMAKE is needed.
adds aa1ade6 disable git based revision
new 7b71c29 Merge branch 'debian-experimental'
new 2b11f68 Update changelog, patch description
new aed10f8 spelling fix, skip empy CMAKE directive
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CHANGELOG.rst | 99 ++
CMakeLists.txt | 7 +
CONTRIBUTING.rst | 7 +-
README.rst | 5 +-
apps/alf/CMakeLists.txt | 6 +-
apps/bs_tools/CMakeLists.txt | 10 +-
apps/bs_tools/casbar.cpp | 1 +
apps/bs_tools/casbar.h | 14 +-
apps/bs_tools/casbar_score.h | 2 +
apps/bs_tools/tests/run_tests.py | 6 +-
apps/dfi/CMakeLists.txt | 6 +-
apps/dfi/dfi.cpp | 2 +
apps/fiona/CMakeLists.txt | 12 +-
apps/fiona/compute_gain.cpp | 4 +-
apps/fiona/error_rate_from_sam.cpp | 4 +-
apps/fiona/fiona.cpp | 10 +-
apps/fiona/index_qgram_parallel.h | 44 +-
apps/fx_tools/CMakeLists.txt | 6 +-
apps/gustaf/CMakeLists.txt | 6 +-
apps/gustaf/msplazer.h | 6 +-
apps/gustaf/msplazer_algorithms.h | 2 +-
apps/gustaf/msplazer_main.h | 2 +-
apps/gustaf/msplazer_out.h | 6 +-
apps/gustaf/tests/pairedEnd_st1_l30.stdout | 2 +-
apps/gustaf/tests/reference2_st1_l30.stdout | 2 +-
apps/gustaf/tests/st1_l30.stdout | 2 +-
apps/gustaf/tests/st1_l30_gth3.stdout | 2 +-
apps/gustaf/tests/st1_l30_ith5.stdout | 2 +-
apps/gustaf/tests/st1_l30_m.stdout | 2 +-
apps/gustaf/tests/st2_l100.stdout | 2 +-
apps/insegt/CMakeLists.txt | 6 +-
apps/mason2/CMakeLists.txt | 10 +-
apps/mason2/README.mason_splicing | 2 +-
apps/mason2/mason_options.cpp | 8 +-
apps/micro_razers/CMakeLists.txt | 6 +-
apps/ngs_roi/CMakeLists.txt | 8 +-
apps/ngs_roi/project_spliced.h | 2 +-
apps/pair_align/CMakeLists.txt | 6 +-
apps/pair_align/pair_align.cpp | 2 +-
apps/param_chooser/CMakeLists.txt | 6 +-
apps/rabema/CMakeLists.txt | 8 +-
apps/rabema/README | 4 +-
apps/rabema/rabema_build_gold_standard.cpp | 2 +-
apps/rabema/rabema_evaluate.cpp | 10 +-
apps/rabema/ref_id_mapping.h | 2 +-
apps/razers/CMakeLists.txt | 6 +-
apps/razers/razers.h | 2 +-
apps/razers/razers_matepairs.h | 2 +-
apps/razers/readSimulator.h | 2 +
apps/razers3/CMakeLists.txt | 12 +-
apps/razers3/razers.cpp | 2 +-
apps/razers3/razers.h | 2 +-
apps/razers3/razers_match_filter.h | 8 +-
apps/razers3/razers_matepairs.h | 2 +-
apps/razers3/razers_matepairs_parallel.h | 2 +-
apps/razers3/razers_parallel.h | 2 +-
apps/razers3/readSimulator.h | 2 +
apps/rep_sep/CMakeLists.txt | 6 +-
apps/rep_sep/rep_sep.cpp | 2 +-
apps/sak/CMakeLists.txt | 6 +-
apps/sak/README | 2 +-
apps/sam2matrix/CMakeLists.txt | 6 +-
apps/samcat/CMakeLists.txt | 10 +-
apps/samcat/README | 2 +-
apps/samcat/README.md | 2 +-
apps/samcat/samcat.cpp | 2 +-
apps/searchjoin/CMakeLists.txt | 8 +-
apps/seqan_tcoffee/CMakeLists.txt | 6 +-
apps/seqcons2/CMakeLists.txt | 8 +-
apps/seqcons2/seqcons.cpp | 2 +-
apps/seqcons2/seqcons_options.cpp | 4 +-
apps/seqcons2/seqcons_options.h | 2 +-
.../tests/alns1.contig_consensus.sam.stderr | 2 +-
.../tests/alns1.contig_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.txt.stderr | 2 +-
.../tests/alns1.overlap_consensus.sam.stderr | 2 +-
.../tests/alns1.overlap_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.txt.stderr | 2 +-
apps/seqcons2/tests/seqs1.align_consensus.stderr | 2 +-
apps/seqcons2/tests/seqs1.nop.stderr | 2 +-
apps/seqcons2/tests/seqs1.overlap_consensus.stderr | 2 +-
.../tests/seqs2.align_consensus.sam.stderr | 2 +-
.../tests/seqs2.align_consensus.txt.stderr | 2 +-
apps/sgip/CMakeLists.txt | 6 +-
apps/sgip/sgip.cpp | 24 +-
apps/snp_store/CMakeLists.txt | 10 +-
apps/splazers/CMakeLists.txt | 6 +-
apps/splazers/readSimulator.h | 2 +
apps/stellar/CMakeLists.txt | 6 +-
apps/stellar/README | 2 +-
apps/stellar/stellar.cpp | 2 +-
apps/tree_recon/CMakeLists.txt | 6 +-
apps/yara/CMakeLists.txt | 12 +-
debian/changelog | 55 +
debian/control | 6 +-
debian/libseqan2-dev.install | 6 +-
debian/patches/boost1.62.patch | 16 -
debian/patches/pthread-linking | 34 -
debian/patches/series | 7 +-
debian/patches/skip-SEQAN_PKGCFG_CFLAGS | 11 +
debian/patches/skip-seqan-revision | 29 +
debian/patches/spelling | 24 +
debian/patches/spelling.patch | 1155 --------------------
debian/rules | 32 +-
demos/tutorial/basics/strings.cpp | 4 +-
demos/tutorial/blast_io/write_assignment.cpp | 2 +-
.../index_iterators/UNUSED_index_assignment3.cpp | 26 -
.../UNUSED_index_assignment3.cpp.stdout | 16 -
.../index_iterators/index_assignment4.cpp.stdout | 14 -
.../index_iterators/index_bidirectional_search.cpp | 36 +
.../index_bidirectional_search.cpp.stdout | 4 +
.../index_iterators/iterator_assignment2.cpp | 2 +-
.../index_iterators/iterator_solution2.cpp | 2 +-
.../index_iterators/iterator_solution2.cpp.stdout | 31 +-
...ndex_assignment4.cpp => iterator_solution3.cpp} | 2 +-
.../index_iterators/iterator_solution3.cpp.stdout | 17 +
demos/tutorial/indices/fm_index.cpp | 29 +
.../tutorial/indices/fm_index.stdout | 0
.../tutorial_file_io/solution3.cpp | 4 +-
dox/CMakeLists.txt | 47 +-
dox/dox_only.sh | 4 +-
dox/images/docs2/position_vs_id.png | Bin 0 -> 175321 bytes
dox/pages/index.dox | 2 +-
dox/pages/language_entities.dox | 2 +-
dox/pages/suffix_array.dox | 2 +-
dox/run.sh | 4 +-
include/seqan/align.h | 2 +-
include/seqan/align/align_interface_wrapper.h | 2 +-
include/seqan/align/dp_align_simd_helper.h | 2 +-
include/seqan/align/gaps_base.h | 2 +-
include/seqan/align/gaps_iterator_array.h | 4 +-
include/seqan/align/gaps_iterator_base.h | 2 +-
.../align/global_alignment_myers_hirschberg_impl.h | 1 -
include/seqan/align/global_alignment_unbanded.h | 4 +-
include/seqan/align/local_alignment_unbanded.h | 2 +-
include/seqan/arg_parse.h | 5 +
include/seqan/arg_parse/arg_parse_argument.h | 189 +++-
include/seqan/arg_parse/arg_parse_ctd_support.h | 34 +-
include/seqan/arg_parse/arg_parse_doc.h | 229 +++-
include/seqan/arg_parse/arg_parse_option.h | 14 +-
include/seqan/arg_parse/arg_parse_parse.h | 25 +-
include/seqan/arg_parse/arg_parse_type_support.h | 62 +-
include/seqan/arg_parse/arg_parse_version_check.h | 474 ++++++++
include/seqan/arg_parse/argument_parser.h | 41 +-
include/seqan/arg_parse/tool_doc.h | 61 +-
include/seqan/bam_io/bam_alignment_record_util.h | 2 +-
include/seqan/bam_io/bam_file.h | 7 +-
include/seqan/bam_io/bam_header_record.h | 4 +-
include/seqan/bam_io/cigar.h | 19 +-
include/seqan/bam_io/write_bam.h | 51 +-
include/seqan/bam_io/write_sam.h | 14 +-
include/seqan/basic/aggregate_concept.h | 5 +-
include/seqan/basic/basic_allocator.h | 1 -
include/seqan/basic/basic_simd_vector.h | 48 +-
include/seqan/basic/fundamental_tags.h | 56 +
include/seqan/basic/iterator_zip.h | 2 +-
include/seqan/basic/metaprogramming_enable_if.h | 8 +-
include/seqan/basic/metaprogramming_type.h | 2 +-
include/seqan/basic/tuple_bit_compressed.h | 38 +-
include/seqan/blast/blast_record.h | 99 +-
include/seqan/blast/blast_report_out.h | 18 +-
include/seqan/blast/blast_tabular.h | 144 +--
include/seqan/blast/blast_tabular_in.h | 74 +-
include/seqan/blast/blast_tabular_out.h | 145 ++-
include/seqan/file/file_page.h | 42 +-
include/seqan/file/string_external.h | 200 ++--
include/seqan/find/find_base.h | 4 +-
include/seqan/find/find_begin.h | 2 +-
include/seqan/gff_io/gff_io_base.h | 3 +
include/seqan/graph_algorithms.h | 2 +
.../seqan/graph_algorithms/depth_first_search.h | 101 +-
.../strongly_connected_compnents.h | 29 +
include/seqan/graph_align/graph_impl_align.h | 12 +
include/seqan/graph_msa/graph_align_tcoffee_io.h | 2 +-
.../seqan/graph_msa/graph_align_tcoffee_library.h | 71 +-
include/seqan/graph_types/graph_impl_automaton.h | 55 +
include/seqan/graph_types/graph_impl_directed.h | 64 +-
include/seqan/graph_types/graph_impl_hmm.h | 12 +
include/seqan/graph_types/graph_impl_tree.h | 12 +
include/seqan/graph_types/graph_impl_undirected.h | 50 +
include/seqan/graph_types/graph_interface.h | 14 +
include/seqan/index/find_index.h | 1 +
include/seqan/index/index_bidirectional.h | 41 +-
include/seqan/index/index_bidirectional_stree.h | 153 ++-
include/seqan/index/index_bifm.h | 2 +
include/seqan/index/index_bifm_stree.h | 4 +-
include/seqan/index/index_esa_algs_multi.h | 22 +-
include/seqan/index/index_esa_base.h | 5 +-
include/seqan/index/index_esa_stree.h | 2 +-
include/seqan/index/index_fm.h | 64 +-
include/seqan/index/index_fm_dox.h | 2 +-
include/seqan/index/index_fm_lf_table.h | 36 +-
.../seqan/index/index_fm_rank_dictionary_base.h | 10 +-
.../seqan/index/index_fm_rank_dictionary_levels.h | 727 ++++++++----
include/seqan/index/index_fm_rank_dictionary_wt.h | 21 +-
include/seqan/index/index_sa_qsort.h | 5 +-
include/seqan/index/index_sa_stree.h | 4 +-
include/seqan/index/index_wotd.h | 2 +-
include/seqan/index/pump_extender7.h | 24 +-
include/seqan/index/shape_threshold.h | 2 +
include/seqan/journaled_set/score_biaffine.h | 31 +-
include/seqan/misc/bit_twiddling.h | 4 +-
include/seqan/modifier/modifier_padding.h | 12 +
include/seqan/parallel/parallel_lock.h | 22 +-
include/seqan/parallel/parallel_splitting.h | 2 +-
include/seqan/pipe/pipe_edit_environment.h | 4 +-
include/seqan/platform.h | 17 +-
include/seqan/{arg_parse.h => rna_io.h} | 51 +-
include/seqan/rna_io/bpseq_read_write.h | 240 ++++
include/seqan/rna_io/connect_read_write.h | 302 +++++
include/seqan/rna_io/dot_bracket_read_write.h | 409 +++++++
include/seqan/rna_io/ebpseq_read_write.h | 672 ++++++++++++
.../seqan/rna_io/rna_header.h | 144 +--
.../rna_io_context.h} | 151 ++-
include/seqan/rna_io/rna_record.h | 279 +++++
include/seqan/rna_io/rna_struct_file.h | 347 ++++++
include/seqan/rna_io/stockholm_read_write.h | 339 ++++++
include/seqan/rna_io/vienna_read_write.h | 280 +++++
include/seqan/score.h | 2 +-
include/seqan/seeds/banded_chain_alignment.h | 2 +-
include/seqan/seeds/banded_chain_alignment_impl.h | 19 +-
include/seqan/seq_io.h | 1 +
include/seqan/seq_io/bam_sam.h | 554 ++++++++++
include/seqan/seq_io/fai_index.h | 2 +-
include/seqan/seq_io/fasta_fastq.h | 123 +--
include/seqan/seq_io/read_embl.h | 8 +-
include/seqan/seq_io/read_genbank.h | 8 +-
include/seqan/seq_io/sequence_file.h | 246 ++++-
include/seqan/sequence/sequence_interface.h | 2 +-
include/seqan/sequence/string_cstyle.h | 12 +-
include/seqan/sequence/string_set_base.h | 15 +-
.../seqan/sequence/string_set_dependent_generous.h | 29 +
.../seqan/sequence/string_set_dependent_tight.h | 55 +-
include/seqan/statistics/statistics_base.h | 8 +-
include/seqan/store/store_io_gff.h | 6 +-
include/seqan/stream/file_stream.h | 28 +-
include/seqan/stream/formatted_file.h | 20 +
include/seqan/stream/stream_base.h | 11 +-
include/seqan/stream/tokenization.h | 45 +-
include/seqan/tabix_io/tabix_index_tbi.h | 5 +-
include/seqan/vcf_io/read_vcf.h | 48 +-
include/seqan/version.h | 4 +-
manual/attic/Tutorial/IndicesOld.rst | 2 +-
.../Infrastructure/Contribute/GitWorkflow.rst | 70 +-
.../Infrastructure/Use/CustomBuildSystem.rst | 36 +
.../source/Infrastructure/Use/FindSeqAnCMake.rst | 29 +-
manual/source/Infrastructure/Use/Install.rst | 44 +-
manual/source/Intel-Logo-300x198.jpg | Bin 0 -> 41926 bytes
.../Alignment/PairwiseSequenceAlignment.rst | 2 +-
.../Tutorial/DataStructures/Indices/FMIndex.rst | 93 ++
.../DataStructures/Indices/IndexIterators.rst | 52 +-
.../DataStructures/Indices/StringIndices.rst | 6 +-
.../Tutorial/DataStructures/Indices/index.rst | 1 +
.../Tutorial/DataStructures/Indices/preOrder.png | Bin 0 -> 35567 bytes
.../GettingStarted/BackgroundAndMotivation.rst | 6 +-
.../Tutorial/Workflows/GenerateKnimeNodes.rst | 12 +-
.../Tutorial/Workflows/KnimeReadySeqAnApp.rst | 4 +-
.../Tutorial/Workflows/UseSeqAnNodesInKnime.rst | 10 +-
manual/source/deNBI_Logo_rgb.jpg | Bin 0 -> 110243 bytes
manual/source/index.rst | 20 +-
tests/align/CMakeLists.txt | 4 +-
tests/align_extend/CMakeLists.txt | 4 +-
tests/align_profile/CMakeLists.txt | 4 +-
tests/align_split/CMakeLists.txt | 4 +-
tests/alignment_free/CMakeLists.txt | 4 +-
tests/arg_parse/CMakeLists.txt | 24 +-
tests/arg_parse/test_app.ctd | 14 +-
tests/arg_parse/test_arg_parse.cpp | 17 +-
tests/arg_parse/test_arg_parse.h | 51 +
tests/arg_parse/test_arg_parse_argument.h | 94 +-
.../test_arg_parse_version_check.cpp} | 53 +-
tests/arg_parse/test_arg_parse_version_check.h | 278 +++++
tests/bam_io/CMakeLists.txt | 6 +-
tests/bam_io/test_bam_file.h | 42 +
tests/bam_io/test_bam_io.cpp | 4 +
tests/basic/CMakeLists.txt | 4 +-
tests/basic/test_basic_allocator.h | 2 +-
tests/basic/test_basic_simd_vector.cpp | 6 +-
tests/basic/test_basic_simd_vector.h | 7 +-
tests/bed_io/CMakeLists.txt | 4 +-
tests/bed_io/test_bed_io.cpp | 42 +
tests/blast/CMakeLists.txt | 4 +-
tests/consensus/CMakeLists.txt | 4 +-
tests/consensus/test_consensus_realign.h | 2 +-
tests/consensus_v2/CMakeLists.txt | 4 +-
tests/find/CMakeLists.txt | 4 +-
tests/gff_io/CMakeLists.txt | 4 +-
tests/gff_io/test_gff_io.cpp | 4 +
tests/gff_io/test_gff_io.h | 38 +
tests/graph_algorithms/CMakeLists.txt | 4 +-
tests/graph_align/CMakeLists.txt | 4 +-
tests/graph_align/test_graph_impl_align.h | 10 +
tests/graph_msa/CMakeLists.txt | 4 +-
tests/graph_msa/test_graph_tcoffee.h | 2 +-
tests/graph_types/CMakeLists.txt | 4 +-
tests/graph_types/test_graph_types_types.cpp | 58 +-
tests/index/CMakeLists.txt | 6 +-
tests/index/test_index_bifm.cpp | 58 +-
tests/index/test_index_finder.cpp | 2 +-
tests/index/test_index_fm_rank_dictionary.cpp | 14 +-
tests/journaled_set/CMakeLists.txt | 4 +-
tests/journaled_string_tree/CMakeLists.txt | 6 +-
tests/journaled_string_tree/test_delta_store.h | 8 +-
tests/map/CMakeLists.txt | 4 +-
tests/misc/CMakeLists.txt | 4 +-
tests/modifier/CMakeLists.txt | 4 +-
tests/modifier/test_modifier_view.h | 2 +-
tests/modifier_cyclic_shape/CMakeLists.txt | 4 +-
tests/multiple_translation_units/CMakeLists.txt | 4 +-
tests/parallel/CMakeLists.txt | 6 +-
tests/parse_lm/CMakeLists.txt | 4 +-
tests/pipe/CMakeLists.txt | 4 +-
tests/platform/CMakeLists.txt | 4 +-
tests/random/CMakeLists.txt | 4 +-
tests/realign/CMakeLists.txt | 4 +-
tests/realign/test_realign.cpp | 2 +-
tests/reduced_aminoacid/CMakeLists.txt | 4 +-
tests/{roi_io => rna_io}/CMakeLists.txt | 17 +-
tests/rna_io/example.bpseq | 52 +
tests/rna_io/example.ct | 74 ++
tests/rna_io/example.dbn | 3 +
tests/rna_io/example.dbv | 9 +
tests/rna_io/example.ebpseq | 39 +
tests/rna_io/example.sth | 20 +
.../test_vcf_io.cpp => rna_io/test_rna_io.cpp} | 27 +-
tests/rna_io/test_rna_io.h | 472 ++++++++
tests/roi_io/CMakeLists.txt | 4 +-
tests/roi_io/test_roi_io.cpp | 42 +
tests/score/CMakeLists.txt | 4 +-
tests/seeds/CMakeLists.txt | 4 +-
tests/seeds/test_align_banded_chain_impl.cpp | 18 +
tests/seq_io/CMakeLists.txt | 13 +-
tests/seq_io/small_sequences.bam | Bin 0 -> 214 bytes
tests/seq_io/small_sequences.sam | 5 +
tests/seq_io/test_genbank.gbk | 90 ++
tests/seq_io/test_read_bam.h | 135 +++
tests/seq_io/test_seq_io.cpp | 25 +
tests/seq_io/test_sequence_file.h | 42 +
tests/seq_io/test_tag_select_intersect.h | 108 ++
tests/seq_io/test_write_bam.h | 144 +++
tests/sequence/CMakeLists.txt | 4 +-
tests/sequence_journaled/CMakeLists.txt | 4 +-
tests/simple_intervals_io/CMakeLists.txt | 4 +-
tests/statistics/CMakeLists.txt | 4 +-
tests/store/CMakeLists.txt | 6 +-
tests/stream/CMakeLists.txt | 8 +-
tests/swift_local/CMakeLists.txt | 4 +-
tests/tabix_io/CMakeLists.txt | 6 +-
tests/translation/CMakeLists.txt | 6 +-
tests/ucsc_io/CMakeLists.txt | 4 +-
tests/vcf_io/CMakeLists.txt | 4 +-
tests/vcf_io/test_vcf_io.cpp | 3 +
tests/vcf_io/test_vcf_io.h | 38 +
util/cmake/SeqAnBuildSystem.cmake | 115 +-
util/cmake/SetCPackSystemName.cmake | 2 +
util/cmake/package.cmake | 8 +-
util/cmake/{FindSeqAn.cmake => seqan-config.cmake} | 30 +-
util/pkgconfig/seqan.pc.in | 3 +-
util/raw_cmake_project/CMakeLists.txt | 2 +-
363 files changed, 10230 insertions(+), 3188 deletions(-)
delete mode 100644 debian/patches/boost1.62.patch
delete mode 100644 debian/patches/pthread-linking
create mode 100644 debian/patches/skip-SEQAN_PKGCFG_CFLAGS
create mode 100644 debian/patches/skip-seqan-revision
create mode 100644 debian/patches/spelling
delete mode 100644 debian/patches/spelling.patch
delete mode 100644 demos/tutorial/index_iterators/UNUSED_index_assignment3.cpp
delete mode 100644 demos/tutorial/index_iterators/UNUSED_index_assignment3.cpp.stdout
delete mode 100644 demos/tutorial/index_iterators/index_assignment4.cpp.stdout
create mode 100644 demos/tutorial/index_iterators/index_bidirectional_search.cpp
create mode 100644 demos/tutorial/index_iterators/index_bidirectional_search.cpp.stdout
rename demos/tutorial/index_iterators/{index_assignment4.cpp => iterator_solution3.cpp} (95%)
create mode 100644 demos/tutorial/index_iterators/iterator_solution3.cpp.stdout
create mode 100644 demos/tutorial/indices/fm_index.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/indices/fm_index.stdout (100%)
create mode 100644 dox/images/docs2/position_vs_id.png
create mode 100644 include/seqan/arg_parse/arg_parse_version_check.h
copy include/seqan/{arg_parse.h => rna_io.h} (72%)
create mode 100644 include/seqan/rna_io/bpseq_read_write.h
create mode 100644 include/seqan/rna_io/connect_read_write.h
create mode 100644 include/seqan/rna_io/dot_bracket_read_write.h
create mode 100644 include/seqan/rna_io/ebpseq_read_write.h
copy tests/index/test_index_finder.cpp => include/seqan/rna_io/rna_header.h (54%)
copy include/seqan/{basic/aggregate_concept.h => rna_io/rna_io_context.h} (52%)
create mode 100644 include/seqan/rna_io/rna_record.h
create mode 100644 include/seqan/rna_io/rna_struct_file.h
create mode 100644 include/seqan/rna_io/stockholm_read_write.h
create mode 100644 include/seqan/rna_io/vienna_read_write.h
create mode 100644 include/seqan/seq_io/bam_sam.h
create mode 100644 manual/source/Intel-Logo-300x198.jpg
create mode 100644 manual/source/Tutorial/DataStructures/Indices/FMIndex.rst
create mode 100644 manual/source/Tutorial/DataStructures/Indices/preOrder.png
create mode 100644 manual/source/deNBI_Logo_rgb.jpg
copy tests/{gff_io/test_gff_io.cpp => arg_parse/test_arg_parse_version_check.cpp} (58%)
create mode 100644 tests/arg_parse/test_arg_parse_version_check.h
copy tests/{roi_io => rna_io}/CMakeLists.txt (78%)
create mode 100644 tests/rna_io/example.bpseq
create mode 100644 tests/rna_io/example.ct
create mode 100644 tests/rna_io/example.dbn
create mode 100644 tests/rna_io/example.dbv
create mode 100644 tests/rna_io/example.ebpseq
create mode 100644 tests/rna_io/example.sth
copy tests/{vcf_io/test_vcf_io.cpp => rna_io/test_rna_io.cpp} (73%)
create mode 100644 tests/rna_io/test_rna_io.h
create mode 100644 tests/seq_io/small_sequences.bam
create mode 100644 tests/seq_io/small_sequences.sam
create mode 100644 tests/seq_io/test_genbank.gbk
create mode 100644 tests/seq_io/test_read_bam.h
create mode 100644 tests/seq_io/test_tag_select_intersect.h
create mode 100644 tests/seq_io/test_write_bam.h
rename util/cmake/{FindSeqAn.cmake => seqan-config.cmake} (94%)
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