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commit 7b71c29c583d23da2e52430f8940041713910d5f Merge: 0ea7aaa aa1ade6 Author: Michael R. Crusoe <[email protected]> Date: Sat Jan 14 03:53:50 2017 -0800 Merge branch 'debian-experimental' 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 | 52 + debian/control | 6 +- debian/libseqan2-dev.install | 6 +- debian/patches/pthread-linking | 34 - debian/patches/series | 5 +- debian/patches/skip-seqan-revision | 26 + 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 + demos/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 +- 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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 +- 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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 ++++- 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+ 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 +- 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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 +- 360 files changed, 10187 insertions(+), 3172 deletions(-) diff --cc debian/changelog index 93077d8,b7f6356..30c553e --- a/debian/changelog +++ b/debian/changelog @@@ -1,26 -1,55 +1,78 @@@ + seqan2 (2.3.1+dfsg-2) experimental; urgency=medium + + * Remove archs with failing builds: armhf mips mipsel + + -- Michael R. Crusoe <[email protected]> Sat, 14 Jan 2017 00:23:26 -0800 + + seqan2 (2.3.1+dfsg-1) experimental; urgency=medium + + * Try to save more memory on kfreebsd-* + * Fix parallel build disabling to not produce warnings + * New upstream release, three incorporated patched removed + + -- Michael R. Crusoe <[email protected]> Fri, 13 Jan 2017 05:36:28 -0800 + + seqan2 (2.3.0~1.20161019~af07bc1+dfsg-4) experimental; urgency=medium + + * Try out -O3 for many architectures as that is upstream's default. + * Skip unneeded build for -indep. + * Fix architecture detection logic. + * Fix from upstream for another sparc64 related typo. + + -- Michael R. Crusoe <[email protected]> Wed, 26 Oct 2016 03:31:54 -0700 + + seqan2 (2.3.0~1.20161019~af07bc1+dfsg-3) experimental; urgency=medium + + * Fix recursive variable expansion error. + + -- Michael R. Crusoe <[email protected]> Mon, 24 Oct 2016 07:54:44 -0700 + + seqan2 (2.3.0~1.20161019~af07bc1+dfsg-2) experimental; urgency=medium + + * Fix typo from upstream's patch. + * Work around GNU Hurd TANDEM problem + * Skip armel + * Test -O1 for mips[el] + * Test turning off parallel builds for armhf, mips, kfreebsd-* + + -- Michael R. Crusoe <[email protected]> Thu, 20 Oct 2016 04:48:11 -0700 + + seqan2 (2.3.0~0.201610100~af07bc1+dfsg+1) experimental; urgency=medium + + * Second experimental build to test fix for #840030. Source from + https://github.com/seqan/seqan/pull/1887/commits/af07bc19087e662117b70d733e963a1611aa9b9a + + -- Michael R. Crusoe <[email protected]> Thu, 20 Oct 2016 02:06:15 -0700 + + seqan2 (2.3.0~0.20161011~73a5aaf+dfsg-1) experimental; urgency=low + + * Experimental build to test fix for #840030 + + -- Michael R. Crusoe <[email protected]> Tue, 11 Oct 2016 07:08:05 -0700 + +seqan2 (2.2.0+dfsg-6) UNRELEASED; urgency=medium + + * Drop Soeren Sonnenburg from Uploaders + + -- Andreas Tille <[email protected]> Sat, 03 Dec 2016 08:08:51 +0100 + +seqan2 (2.2.0+dfsg-5) unstable; urgency=medium + + * Fix build issue with boost 1.62 (Thanks for the patch to Graham Inggs + <[email protected]>) + Closes: #846617 + * debhelper 10 + * d/watch: version=4 + + -- Andreas Tille <[email protected]> Fri, 02 Dec 2016 19:01:10 +0100 + +seqan2 (2.2.0+dfsg-4) unstable; urgency=medium + + * Restrict to known working archs for now. Closes: #840025 + * Use upstream's patch. Closes: #840030, #840026 + + -- Michael R. Crusoe <[email protected]> Tue, 11 Oct 2016 12:20:59 -0700 + seqan2 (2.2.0+dfsg-3) unstable; urgency=medium * Fix arch specific build. Closes: #840023 diff --cc debian/patches/series index 52f6cc2,a1ed085..18e2946 --- a/debian/patches/series +++ b/debian/patches/series @@@ -1,5 -1,3 +1,2 @@@ - pthread-linking - spelling.patch short-description -- - boost1.62.patch + skip-seqan-revision -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
