[med-svn] [seqan2] branch upstream-develop updated (a58b2c3 -> 8327bef)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jan 13 14:39:35 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream-develop
in repository seqan2.
from a58b2c3 New upstream version 2.3.0~1.20161019~af07bc1+dfsg
new 8327bef New upstream version 2.3.1+dfsg
The 1 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 +-
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 +-
249 files changed, 8514 insertions(+), 1502 deletions(-)
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%)
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