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tille pushed a change to branch master
in repository hilive.
from 7a67501 New upstream version
new 9eef8b7 New upstream version 1.0
new 0a552c2 Updated version 1.0 from 'upstream/1.0'
new 6061b61 Adapt patches
The 3 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:
CMakeLists.txt | 67 +--
CONTRIBUTORS | 12 +-
LICENSE | 2 +-
README.md | 80 ++--
debian/patches/do_not_set_rpath.patch | 2 +-
debian/patches/use_FindSeQan.patch | 25 +-
lib/alignmentSettings.h | 773 ++++++++++++++++++++++++++++++
lib/alnread.cpp | 874 +++++++++++++++++++++++++---------
lib/alnread.h | 91 +++-
lib/alnstream.cpp | 675 +++++++++++++++-----------
lib/alnstream.h | 39 +-
lib/argument_parser.cpp | 778 ++++++++++++++++++++++--------
lib/argument_parser.h | 481 ++++++++++++++++++-
lib/config.h.in | 7 -
lib/definitions.h | 378 ++++++++++-----
lib/global_variables.h | 7 +
lib/headers.h | 9 +-
lib/kindex.cpp | 263 +++++-----
lib/kindex.h | 36 +-
lib/parallel.cpp | 183 +++----
lib/parallel.h | 80 +++-
lib/tools.cpp | 296 +++++-------
lib/tools.h | 161 +++++--
lib/tools_static.cpp | 181 +++++++
lib/tools_static.h | 171 +++++++
tools/build_index.cpp | 147 ++----
tools/hilive.cpp | 265 +++++++----
tools/hilive_out.cpp | 66 +++
28 files changed, 4531 insertions(+), 1618 deletions(-)
create mode 100644 lib/alignmentSettings.h
delete mode 100644 lib/config.h.in
create mode 100644 lib/global_variables.h
create mode 100644 lib/tools_static.cpp
create mode 100644 lib/tools_static.h
create mode 100644 tools/hilive_out.cpp
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