[med-svn] [seqan2] branch debian-experimental updated (275acf8 -> 91b2729)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Oct 11 19:22:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch debian-experimental
in repository seqan2.
from 275acf8 Try patch from upstream to fix kfreebsd/hurd builds
new d45d8d2 bump version
new a7057cf switch to upstream's patch
new 52afd09 Restrict archs for now.
adds 6f07e3e New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
new 922aa9c Merge tag 'upstream/2.3.0_0.20161011_73a5aaf+dfsg' into debian-experimental
new 91b2729 test upstream's develop branch
The 5 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:
CONTRIBUTING.rst | 2 +-
apps/bs_tools/tests/run_tests.py | 6 +-
apps/fiona/index_qgram_parallel.h | 44 ++---
apps/razers3/razers_match_filter.h | 8 +-
debian/changelog | 6 +-
debian/patches/pthread-linking | 14 --
debian/patches/series | 1 -
include/seqan/align.h | 2 +-
include/seqan/align/align_interface_wrapper.h | 2 +-
include/seqan/align/dp_align_simd_helper.h | 2 +-
.../align/global_alignment_myers_hirschberg_impl.h | 1 -
include/seqan/arg_parse.h | 4 +
include/seqan/arg_parse/arg_parse_doc.h | 56 +++++-
include/seqan/basic/basic_allocator.h | 1 -
include/seqan/basic/basic_simd_vector.h | 48 +++--
include/seqan/file/file_page.h | 42 ++---
include/seqan/file/string_external.h | 200 ++++++++++-----------
include/seqan/graph_algorithms.h | 2 +
.../seqan/graph_algorithms/depth_first_search.h | 101 +++++++----
.../strongly_connected_compnents.h | 29 +++
include/seqan/graph_msa/graph_align_tcoffee_io.h | 2 +-
.../seqan/graph_msa/graph_align_tcoffee_library.h | 71 ++++----
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 +-
include/seqan/modifier/modifier_padding.h | 12 ++
include/seqan/parallel/parallel_lock.h | 4 +-
include/seqan/score.h | 2 +-
include/seqan/stream/file_stream.h | 24 +--
include/seqan/stream/formatted_file.h | 20 +++
include/seqan/stream/stream_base.h | 9 +-
include/seqan/tabix_io/tabix_index_tbi.h | 3 +
include/seqan/version.h | 2 +-
.../Infrastructure/Use/CustomBuildSystem.rst | 4 +
manual/source/Infrastructure/Use/Install.rst | 44 ++---
manual/source/index.rst | 2 +-
tests/bam_io/test_bam_file.h | 42 +++++
tests/bam_io/test_bam_io.cpp | 4 +
tests/basic/test_basic_simd_vector.cpp | 6 +-
tests/basic/test_basic_simd_vector.h | 7 +-
tests/bed_io/test_bed_io.cpp | 42 +++++
tests/gff_io/test_gff_io.cpp | 4 +
tests/gff_io/test_gff_io.h | 38 ++++
tests/graph_msa/test_graph_tcoffee.h | 2 +-
tests/index/test_index_bifm.cpp | 58 +++---
tests/roi_io/test_roi_io.cpp | 42 +++++
tests/seq_io/test_seq_io.cpp | 4 +
tests/seq_io/test_sequence_file.h | 42 +++++
tests/vcf_io/test_vcf_io.cpp | 3 +
tests/vcf_io/test_vcf_io.h | 38 ++++
util/cmake/FindSeqAn.cmake | 22 ++-
52 files changed, 924 insertions(+), 400 deletions(-)
delete mode 100644 debian/patches/pthread-linking
--
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