[med-svn] [seqan2] branch master updated (003f498 -> 77c2432)
Andreas Tille
tille at debian.org
Wed Aug 3 20:18:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository seqan2.
from 003f498 Disable static compilation of binaries
new df935c6 Fix Vcs-Fields
new 613bfd8 New upstream version
new 7c3e54b Imported Upstream version 2.2.0+dfsg
new 77c2432 Adapt patch
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 | 122 +-
CMakeLists.txt | 44 +-
CONTRIBUTING.rst | 20 +
README.rst | 18 +-
apps/CMakeLists.txt | 1 -
apps/alf/CMakeLists.txt | 2 +-
apps/bs_tools/CMakeLists.txt | 15 +-
apps/bs_tools/casbar.cpp | 4 +-
apps/bs_tools/tests/run_tests.py | 4 +-
apps/dfi/CMakeLists.txt | 2 +-
apps/dfi/tests/run_tests.py | 2 +-
apps/fiona/CMakeLists.txt | 14 +-
apps/fiona/fiona.cpp | 8 +-
apps/fiona/tests/run_tests.py | 2 +-
apps/fx_tools/CMakeLists.txt | 2 +-
apps/gustaf/CMakeLists.txt | 2 +-
apps/gustaf/msplazer_algorithms.h | 16 +-
apps/gustaf/tests/run_tests.py | 2 +-
apps/gustaf/tests/st1_l30.gff | 4 +-
apps/gustaf/tests/st1_l30.vcf | 4 +-
apps/gustaf/tests/st1_l30_gth3.gff | 4 +-
apps/gustaf/tests/st1_l30_gth3.vcf | 4 +-
apps/gustaf/tests/st1_l30_ith5.gff | 2 +-
apps/gustaf/tests/st1_l30_ith5.vcf | 2 +-
apps/gustaf/tests/st1_l30_m.gff | 4 +-
apps/gustaf/tests/st1_l30_m.vcf | 4 +-
apps/insegt/CMakeLists.txt | 2 +-
apps/insegt/LICENSE | 27 +-
apps/insegt/tests/run_tests.py | 2 +-
apps/mason2/CMakeLists.txt | 7 +-
apps/mason2/external_split_merge.cpp | 6 +-
apps/mason2/tests/run_tests.py | 2 +-
apps/mason2/vcf_materialization.cpp | 4 +-
apps/micro_razers/CMakeLists.txt | 2 +-
apps/micro_razers/micro_razers.cpp | 2 +-
apps/micro_razers/tests/run_tests.py | 2 +-
apps/ngs_roi/CMakeLists.txt | 2 +-
apps/ngs_roi/tests/run_tests.py | 2 +-
apps/ngs_roi/tool_shed/ctd2galaxy.py | 2 +-
apps/ngs_roi/tool_shed/ngs_roi/app.py | 2 +-
apps/ngs_roi/tool_shed/ngs_roi/argparse.py | 2 +-
apps/ngs_roi/tool_shed/ngs_roi/io.py | 2 +-
apps/ngs_roi/tool_shed/roi_details.py | 2 +-
apps/ngs_roi/tool_shed/roi_plot_thumbnails.py | 2 +-
apps/ngs_roi/tool_shed/roi_report.py | 2 +-
apps/ngs_roi/tool_shed/roi_table.py | 2 +-
apps/ngs_roi/tool_shed/rois.py | 2 +-
apps/pair_align/CMakeLists.txt | 2 +-
apps/pair_align/lib/CMakeLists.txt | 19 +-
apps/pair_align/tests/run_tests.py | 2 +-
apps/param_chooser/CMakeLists.txt | 2 +-
apps/rabema/CMakeLists.txt | 2 +-
apps/rabema/rabema_stats.h | 6 +-
apps/rabema/tests/run_tests.py | 2 +-
apps/razers/CMakeLists.txt | 2 +-
apps/razers/gapped_params/dat2cpp.py | 2 +-
apps/razers/razers.cpp | 4 +-
apps/razers/tests/run_tests.py | 2 +-
apps/razers3/CMakeLists.txt | 10 +-
apps/razers3/outputFormat.h | 6 +-
apps/razers3/parallel_store.h | 10 +-
apps/razers3/paramChooser.h | 3 +-
apps/razers3/profile_timeline.h | 14 +-
apps/razers3/razers.cpp | 10 +-
.../razers3/tests/pe-adeno-reads100_2-f-tc0.razers | 16 +-
.../tests/pe-adeno-reads100_2-i100-tc1.razers | 42 +-
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.../tests/pe-adeno-reads100_2-of0-tc0.razers | 24 +-
.../tests/pe-adeno-reads100_2-of0-tc1.razers | 8 +-
apps/razers3/tests/pe-adeno-reads100_2-of4-tc0.sam | 2 +-
apps/razers3/tests/pe-adeno-reads100_2-of4-tc1.sam | 2 +-
.../razers3/tests/pe-adeno-reads100_2-r-tc0.razers | 8 +-
.../tests/pe-adeno-reads100_2-so0-tc0.razers | 24 +-
.../tests/pe-adeno-reads100_2-so0-tc1.razers | 8 +-
.../tests/pe-adeno-reads100_2-so1-tc0.razers | 24 +-
.../tests/pe-adeno-reads100_2-so1-tc1.razers | 8 +-
apps/razers3/tests/pe-adeno-reads100_2-tc0.razers | 24 +-
apps/razers3/tests/pe-adeno-reads100_2-tc1.razers | 8 +-
.../tests/pe-adeno-reads36_2-i100-tc1.razers | 118 +-
.../tests/pe-adeno-reads36_2-i90-tc0.razers | 8 +-
.../tests/pe-adeno-reads36_2-i90-tc1.razers | 8 +-
.../tests/pe-adeno-reads36_2-i91-tc0.razers | 8 +-
.../tests/pe-adeno-reads36_2-i91-tc1.razers | 8 +-
.../tests/pe-adeno-reads36_2-i98-tc1.razers | 118 +-
.../tests/pe-adeno-reads36_2-i99-tc1.razers | 118 +-
apps/razers3/tests/pe-adeno-reads36_2-of4-tc0.sam | 2 +-
apps/razers3/tests/pe-adeno-reads36_2-of4-tc1.sam | 2 +-
apps/razers3/tests/run_tests.py | 2 +-
apps/razers3/tests/run_tests_sequential.py | 2 +-
apps/razers3/tests/se-adeno-reads100_1-of4-tc0.sam | 2 +-
apps/razers3/tests/se-adeno-reads100_1-of4-tc1.sam | 2 +-
apps/razers3/tests/se-adeno-reads36_1-of4-tc0.sam | 2 +-
apps/razers3/tests/se-adeno-reads36_1-of4-tc1.sam | 2 +-
apps/rep_sep/CMakeLists.txt | 2 +-
apps/sak/CMakeLists.txt | 2 +-
apps/sak/sak.cpp | 105 +-
apps/sak/tests/adeno.sn.fa | 5 -
apps/sak/tests/run_tests.py | 2 +-
apps/sam2matrix/CMakeLists.txt | 2 +-
apps/sam2matrix/tests/run_tests.py | 2 +-
apps/samcat/CMakeLists.txt | 2 +-
apps/samcat/tests/run_tests.py | 2 +-
apps/searchjoin/CMakeLists.txt | 2 +-
apps/searchjoin/join.cpp | 8 +
apps/searchjoin/search.cpp | 7 +
apps/searchjoin/tests/run_tests.py | 2 +-
apps/seqan_tcoffee/CMakeLists.txt | 2 +-
apps/seqan_tcoffee/tests/run_tests.py | 2 +-
apps/seqcons2/CMakeLists.txt | 2 +-
apps/seqcons2/tests/run_tests.py | 2 +-
apps/sgip/CMakeLists.txt | 2 +-
apps/sgip/tests/run_tests.py | 2 +-
apps/snp_store/CMakeLists.txt | 6 +-
apps/snp_store/snp_store.cpp | 2 +-
apps/snp_store/snp_store.h | 2 +-
apps/snp_store/tests/run_tests.py | 2 +-
apps/splazers/CMakeLists.txt | 2 +-
apps/splazers/splazers.cpp | 2 +-
apps/splazers/tests/run_tests.py | 2 +-
apps/stellar/CMakeLists.txt | 2 +-
apps/stellar/tests/run_tests.py | 2 +-
apps/tree_recon/CMakeLists.txt | 2 +-
apps/tree_recon/tests/run_tests.py | 2 +-
apps/yara/CMakeLists.txt | 39 +-
apps/yara/README.rst | 99 +-
apps/yara/basic_alphabet.h | 2 +-
apps/yara/bits_matches.h | 54 +-
apps/yara/find_extender.h | 35 +-
apps/yara/find_verifier.h | 22 +-
apps/yara/index_fm.h | 63 +-
apps/yara/mapper.cpp | 60 +-
apps/yara/mapper.h | 94 +-
apps/yara/mapper_aligner.h | 4 +-
apps/yara/mapper_writer.h | 69 +-
apps/yara/misc_options.h | 8 +-
apps/yara/misc_tags.h | 10 +
apps/yara/misc_types.h | 20 +-
apps/yara/tests/gold/adeno-reads_1.t1.sam | 1992 +--
apps/yara/tests/run_tests.py | 4 +-
debian/changelog | 3 +-
debian/control | 4 +-
debian/patches/spelling.patch | 554 +-
demos/CMakeLists.txt | 1 -
demos/blast/blast_in_lowlevel.cpp | 2 +-
demos/dox/align/gaps_example.cpp.stdout | 10 +-
demos/dox/graph_algorithms/dijkstra.cpp.stdout | 8 +-
demos/dox/index/open_save.cpp | 4 +
demos/dox/modifier/cyclic_shape.cpp | 4 +-
demos/dox/stream/lexical_cast.cpp | 21 +-
demos/howto/align_gaps_clipping.cpp.stdout | 27 +
demos/howto/filter_similar_sequences.cpp | 5 +-
demos/howto/filter_similar_sequences.cpp.stderr | 1 +
.../howto/filter_similar_sequences.cpp.stdout | 0
demos/howto/scores/init_score.cpp | 2 +-
demos/howto/scores/load_score.cpp.stdout | 12 +-
.../align.cpp | 89 +-
demos/tutorial/alignment/align.cpp.stdout | 74 +
.../align_assignment1.cpp} | 0
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demos/tutorial/alignment/graph.cpp | 59 +
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.../alignment/scoring_scheme_affine_dgs.cpp | 42 +
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.../scoring_scheme_matrix.cpp} | 9 +-
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.../scoring_scheme_simple.cpp} | 11 +-
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.../alignment_representation/align.cpp.stdout | 48 -
demos/tutorial/alignment_representation/graph.cpp | 43 -
demos/tutorial/alphabets/assignment_1_solution.cpp | 2 +-
.../alphabets/assignment_1_solution.cpp.stdout | Bin 183 -> 200 bytes
demos/tutorial/basics/allocator.cpp.stdout | 12 +-
demos/tutorial/bed_io/base.cpp | 20 +-
demos/tutorial/bed_io/example1.cpp.stdout | 5 +
demos/tutorial/bed_io/solution1.cpp.stdout | 5 +
demos/tutorial/{blast => blast_io}/plus_sub.m0 | 0
.../{blast => blast_io}/read_assignment.cpp | 11 +-
demos/tutorial/blast_io/read_assignment.cpp.stderr | 1 +
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demos/tutorial/file_io_overview/example1.cpp | 11 +-
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demos/tutorial/gff_and_gtf_io/base.cpp | 10 +-
demos/tutorial/graph/graph_algo_scc.cpp | 4 +-
demos/tutorial/graph/graph_hmm.cpp | 1 -
demos/tutorial/graph/solution_1.cpp | 3 -
demos/tutorial/index_iterators/index_search.cpp | 2 +-
demos/tutorial/indexed_fasta_io/base.cpp | 2 +-
demos/tutorial/indexed_fasta_io/base.cpp.stdout | 1 -
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demos/tutorial/indices/base.cpp | 15 +-
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util/py_lib/seqan/dox/inc_mgr.py | 2 +-
util/py_lib/seqan/dox/lexer.py | 2 +-
util/py_lib/seqan/dox/migration.py | 2 +-
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util/py_lib/seqan/dox/pure.py | 6 +-
util/py_lib/seqan/dox/raw_doc.py | 6 +-
util/py_lib/seqan/dox/sig_parser.py | 2 +-
util/py_lib/seqan/dox/test/test_dox_parser.py | 2 +-
util/py_lib/seqan/dox/test/test_file_mgr.py | 2 +-
util/py_lib/seqan/dox/test/test_inc_mgr.py | 2 +-
util/py_lib/seqan/dox/test/test_lexer.py | 2 +-
util/py_lib/seqan/dox/test/test_proc_doc.py | 4 +-
util/py_lib/seqan/dox/test/test_raw_doc.py | 2 +-
util/py_lib/seqan/dox/test/test_sig_parser.py | 2 +-
util/py_lib/seqan/dox/tpl/css/full_list.css | 13 +-
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util/py_lib/seqan/dox/tpl/list.html | 14708 ++++++++++++++++++-
util/py_lib/seqan/dox/validation.py | 2 +-
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util/py_lib/seqan/fixgcov/__init__.py | 2 +-
util/py_lib/seqan/fixgcov/app.py | 2 +-
util/py_lib/seqan/one_package.html | 175 -
util/py_lib/seqan/paths.py | 2 +-
util/py_lib/seqan/pyclangcheck/__init__.py | 2 +-
util/py_lib/seqan/pyclangcheck/app.py | 2 +-
util/py_lib/seqan/pyclangcheck/rules.py | 2 +-
util/py_lib/seqan/pyclangcheck/simple_checks.py | 2 +-
util/py_lib/seqan/pyclangcheck/suppressions.py | 2 +-
util/py_lib/seqan/pyclangcheck/violations.py | 2 +-
util/py_lib/seqan/release_page.html | 215 -
util/py_lib/seqan/release_page.py | 250 -
util/py_lib/seqan/skel.py | 2 +-
util/skel/app_tests_template/run_tests.py | 2 +-
util/uncrustify/uncrustify.cfg | 4 +-
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create mode 100644 tests/index/test_index_bifm.cpp
create mode 100644 tests/modifier/test_modifier_string_padding.h
rename tests/{cuda => platform}/CMakeLists.txt (52%)
rename tests/{cuda/test_cuda_common.h => platform/test_platform.cpp} (74%)
rename include/seqan/system/system_critical_section.h => tests/platform/test_platform_range_based_for_loops.h (56%)
delete mode 100755 util/bin/release_page.py
delete mode 100755 util/colornvcc
create mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-treeview/css/bootstrap-treeview.css
create mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-treeview/js/bootstrap-treeview.js
delete mode 100644 util/py_lib/seqan/one_package.html
delete mode 100644 util/py_lib/seqan/release_page.html
delete mode 100644 util/py_lib/seqan/release_page.py
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