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misterc-guest pushed a change to branch experimental
in repository seqan2.
from b19650a cleanup build flags
adds 4955144 New upstream version
2.3.2.001platform-issues10-6f85721+dfsg
adds 9b11d08 Update upstream source from tag
'upstream/2.3.2.001platform-issues10-6f85721+dfsg'
adds 3792038 hopefully final update from upstream before 2.4
new 06b4aa4 enable asyncio everywhere & disable parallel building on
powerpcspe
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:
apps/alf/CMakeLists.txt | 2 +-
apps/alf/alf.cpp | 2 +-
apps/bs_tools/CMakeLists.txt | 2 +-
apps/dfi/CMakeLists.txt | 2 +-
apps/fiona/CMakeLists.txt | 2 +-
apps/fiona/compute_gain.cpp | 6 +-
apps/fx_tools/CMakeLists.txt | 2 +-
apps/gustaf/CMakeLists.txt | 2 +-
apps/insegt/CMakeLists.txt | 2 +-
apps/mason2/CMakeLists.txt | 2 +-
apps/mason2/mason_genome.cpp | 2 +-
apps/mason2/mason_variator.cpp | 10 +-
apps/micro_razers/CMakeLists.txt | 2 +-
apps/ngs_roi/CMakeLists.txt | 4 +-
apps/pair_align/CMakeLists.txt | 2 +-
apps/param_chooser/CMakeLists.txt | 2 +-
apps/rabema/CMakeLists.txt | 4 +-
apps/rabema/rabema_build_gold_standard.cpp | 2 +-
apps/rabema/rabema_evaluate.cpp | 4 +-
apps/razers/CMakeLists.txt | 2 +-
apps/razers3/CMakeLists.txt | 2 +-
apps/rep_sep/CMakeLists.txt | 2 +-
apps/sak/CMakeLists.txt | 4 +-
apps/sam2matrix/CMakeLists.txt | 2 +-
apps/samcat/CMakeLists.txt | 2 +-
apps/searchjoin/CMakeLists.txt | 2 +-
apps/searchjoin/db.h | 8 +-
apps/seqan_tcoffee/CMakeLists.txt | 2 +-
apps/seqcons2/CMakeLists.txt | 2 +-
apps/sgip/CMakeLists.txt | 2 +-
apps/snp_store/CMakeLists.txt | 2 +-
apps/splazers/CMakeLists.txt | 2 +-
apps/stellar/CMakeLists.txt | 2 +-
apps/stellar/stellar.cpp | 2 +-
apps/tree_recon/CMakeLists.txt | 2 +-
apps/yara/CMakeLists.txt | 2 +-
debian/changelog | 13 ++
debian/rules | 12 +-
dox/CMakeLists.txt | 2 +-
.../align/local_alignment_waterman_eggert_impl.h | 39 ++---
include/seqan/arg_parse/arg_parse_argument.h | 36 +----
include/seqan/arg_parse/tool_doc.h | 7 -
include/seqan/bam_io/bam_alignment_record_util.h | 2 +-
include/seqan/index/index_base.h | 2 +-
include/seqan/index/index_fm_compressed_sa.h | 6 +-
include/seqan/index/index_fm_lf_table.h | 2 +-
.../seqan/index/index_fm_rank_dictionary_base.h | 2 +-
.../seqan/index/index_fm_rank_dictionary_levels.h | 6 +-
.../seqan/index/index_fm_rank_dictionary_naive.h | 2 +-
include/seqan/index/index_qgram.h | 2 +-
include/seqan/modifier/modifier_padding.h | 51 +-----
include/seqan/platform.h | 4 +-
include/seqan/seeds/seeds_global_chaining.h | 162 ++++++++-----------
include/seqan/stream/iter_stream.h | 178 +++++++++------------
manual/source/Infrastructure/Use/Install.rst | 42 ++---
tests/align/test_alignment_algorithms_local.h | 47 ------
.../align/test_alignment_algorithms_local_banded.h | 32 ----
tests/arg_parse/test_arg_parse.cpp | 1 -
tests/arg_parse/test_arg_parse_argument.h | 28 ----
tests/modifier/test_modifier.cpp | 3 +-
tests/modifier/test_modifier_string_padding.h | 24 ---
tests/seeds/test_seeds_global_chaining.cpp | 26 ---
util/cmake/SeqAnBuildSystem.cmake | 25 +--
util/pkgconfig/seqan.pc.in | 4 +-
util/skel/app_template/CMakeLists.txt | 2 +-
65 files changed, 276 insertions(+), 584 deletions(-)
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