This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch debian-experimental in repository seqan2.
from d5c2144 Try out -O3 for many architectures as that is upstream's default. new 20af6c2 Try to save more memory on kfreebsd-* new 8327bef New upstream version 2.3.1+dfsg new 7fcf128 Merge tag 'upstream/2.3.1+dfsg' into debian-experimental new 2dc4b73 new upstream release The 4 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 | 5 + README.rst | 5 +- apps/alf/CMakeLists.txt | 4 +- apps/bs_tools/CMakeLists.txt | 4 +- apps/bs_tools/casbar.cpp | 1 + apps/dfi/CMakeLists.txt | 4 +- apps/fiona/CMakeLists.txt | 4 +- apps/fiona/compute_gain.cpp | 4 +- apps/fiona/error_rate_from_sam.cpp | 4 +- apps/fiona/fiona.cpp | 10 +- apps/fx_tools/CMakeLists.txt | 4 +- apps/gustaf/CMakeLists.txt | 4 +- 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 | 4 +- apps/mason2/CMakeLists.txt | 4 +- apps/mason2/README.mason_splicing | 2 +- apps/mason2/mason_options.cpp | 8 +- apps/micro_razers/CMakeLists.txt | 4 +- apps/ngs_roi/CMakeLists.txt | 4 +- apps/ngs_roi/project_spliced.h | 2 +- apps/pair_align/CMakeLists.txt | 4 +- apps/pair_align/pair_align.cpp | 2 +- apps/param_chooser/CMakeLists.txt | 4 +- apps/rabema/CMakeLists.txt | 4 +- 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 | 4 +- apps/razers/razers.h | 2 +- apps/razers/razers_matepairs.h | 2 +- apps/razers3/CMakeLists.txt | 4 +- apps/razers3/razers.cpp | 2 +- apps/razers3/razers.h | 2 +- apps/razers3/razers_matepairs.h | 2 +- apps/razers3/razers_matepairs_parallel.h | 2 +- apps/razers3/razers_parallel.h | 2 +- apps/rep_sep/CMakeLists.txt | 4 +- apps/rep_sep/rep_sep.cpp | 2 +- apps/sak/CMakeLists.txt | 4 +- apps/sak/README | 2 +- apps/sam2matrix/CMakeLists.txt | 4 +- apps/samcat/CMakeLists.txt | 4 +- apps/samcat/README | 2 +- apps/samcat/README.md | 2 +- apps/samcat/samcat.cpp | 2 +- apps/searchjoin/CMakeLists.txt | 4 +- apps/seqan_tcoffee/CMakeLists.txt | 4 +- apps/seqcons2/CMakeLists.txt | 4 +- 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 | 4 +- apps/sgip/sgip.cpp | 24 +- apps/snp_store/CMakeLists.txt | 4 +- apps/splazers/CMakeLists.txt | 4 +- apps/stellar/CMakeLists.txt | 4 +- apps/stellar/README | 2 +- apps/stellar/stellar.cpp | 2 +- apps/tree_recon/CMakeLists.txt | 4 +- apps/yara/CMakeLists.txt | 4 +- debian/changelog | 8 + debian/patches/series | 3 - debian/patches/spelling.patch | 1155 -------------------- debian/patches/tandem-rename | 54 - debian/patches/typo-fix | 22 - debian/rules | 7 +- 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/gaps_base.h | 2 +- include/seqan/align/gaps_iterator_array.h | 4 +- include/seqan/align/gaps_iterator_base.h | 2 +- include/seqan/align/global_alignment_unbanded.h | 4 +- include/seqan/align/local_alignment_unbanded.h | 2 +- include/seqan/arg_parse.h | 1 + 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 | 179 ++- 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/write_bam.h | 51 +- include/seqan/bam_io/write_sam.h | 14 +- include/seqan/basic/aggregate_concept.h | 5 +- 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 | 73 +- include/seqan/blast/blast_tabular_out.h | 145 ++- 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/index/find_index.h | 1 + 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/misc/bit_twiddling.h | 4 +- include/seqan/parallel/parallel_lock.h | 10 +- include/seqan/parallel/parallel_splitting.h | 2 +- include/seqan/pipe/pipe_edit_environment.h | 2 +- include/seqan/platform.h | 4 +- include/seqan/{arg_parse.h => rna_io.h} | 55 +- 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/seeds/banded_chain_alignment.h | 2 +- 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 | 4 +- include/seqan/stream/stream_base.h | 2 +- include/seqan/stream/tokenization.h | 45 +- include/seqan/tabix_io/tabix_index_tbi.h | 2 +- include/seqan/vcf_io/read_vcf.h | 48 +- include/seqan/version.h | 2 +- manual/attic/Tutorial/IndicesOld.rst | 2 +- .../Infrastructure/Contribute/GitWorkflow.rst | 70 +- .../Infrastructure/Use/CustomBuildSystem.rst | 32 + .../source/Infrastructure/Use/FindSeqAnCMake.rst | 29 +- 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 | 18 + tests/arg_parse/CMakeLists.txt | 20 +- 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 +- .../arg_parse/test_arg_parse_version_check.cpp | 75 +- tests/arg_parse/test_arg_parse_version_check.h | 278 +++++ tests/basic/test_basic_allocator.h | 2 +- tests/basic/test_basic_simd_vector.h | 2 +- tests/consensus/test_consensus_realign.h | 2 +- tests/index/test_index_finder.cpp | 2 +- tests/index/test_index_fm_rank_dictionary.cpp | 14 +- tests/journaled_string_tree/test_delta_store.h | 8 +- tests/modifier/test_modifier_view.h | 2 +- tests/realign/test_realign.cpp | 2 +- tests/{arg_parse => rna_io}/CMakeLists.txt | 27 +- 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 + .../version.h => tests/rna_io/test_rna_io.cpp | 34 +- tests/rna_io/test_rna_io.h | 472 ++++++++ tests/seq_io/CMakeLists.txt | 5 +- 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 | 21 + tests/seq_io/test_tag_select_intersect.h | 108 ++ tests/seq_io/test_write_bam.h | 144 +++ util/cmake/SeqAnBuildSystem.cmake | 100 +- util/cmake/SetCPackSystemName.cmake | 2 + util/cmake/package.cmake | 8 +- util/cmake/{FindSeqAn.cmake => seqan-config.cmake} | 8 +- util/pkgconfig/seqan.pc.in | 3 +- util/raw_cmake_project/CMakeLists.txt | 2 +- 255 files changed, 8528 insertions(+), 2737 deletions(-) delete mode 100644 debian/patches/spelling.patch delete mode 100644 debian/patches/tandem-rename delete mode 100644 debian/patches/typo-fix 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 include/seqan/arg_parse.h => tests/arg_parse/test_arg_parse_version_check.cpp (57%) create mode 100644 tests/arg_parse/test_arg_parse_version_check.h copy tests/{arg_parse => rna_io}/CMakeLists.txt (65%) 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 include/seqan/version.h => tests/rna_io/test_rna_io.cpp (70%) 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} (99%) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit