[med-svn] [seqan2] branch upstream-experimental updated (9f5dc02 -> 817a28f)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Jan 3 13:01:46 UTC 2018
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream-experimental
in repository seqan2.
from 9f5dc02 New upstream version 2.3.2.000platform-issues8-6f85721+dfsg
new 817a28f New upstream version 2.3.2.000platform-issues9-028fd79+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:
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 +-
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 +-
63 files changed, 578 insertions(+), 257 deletions(-)
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