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tille pushed a change to branch master
in repository tophat.
from d332277 d/changelog: upload to unstable d/patches: applied cme
fix dpkg, s/Descriptions/Description/
new 900b07c Add repacksuffix to debian/watch
new edb0104 Imported Upstream version 2.1.0+dfsg
new d11a467 Merge tag 'upstream/2.1.0+dfsg'
new 7f84939 New upstream version
The 4 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:
Makefile.in | 3 +-
README | 7 +-
config.guess | 544 ++++++++++--------
config.sub | 390 ++++++++++---
configure | 24 +-
configure.ac | 2 +-
debian/changelog | 6 +
debian/patches/bashism_in_shell_script.patch | 4 +-
debian/patches/fix_build_w_seqan1.4.patch | 6 +-
debian/patches/fix_includes_path.patch | 28 +-
debian/patches/hardening4samtools.patch | 6 +-
debian/watch | 2 +-
depcomp | 409 ++++++++++---
install-sh | 538 +++++++++++------
missing | 234 ++++----
src/GBase.cpp | 87 ++-
src/GBase.h | 19 +-
src/GHash.hh | 6 +-
src/GList.hh | 7 +-
src/GVec.hh | 21 +-
src/align_status.cpp | 0
src/align_status.h | 0
src/common.cpp | 2 +-
src/common.h | 1 +
src/deletions.cpp | 0
src/deletions.h | 0
src/fusions.cpp | 2 +-
src/fusions.h | 0
src/gff.cpp | 824 ++++++++++++++-------------
src/gff.h | 144 +++--
src/insertions.cpp | 0
src/insertions.h | 0
src/tophat-fusion-post | 347 +++++++++--
src/tophat.py | 8 +-
src/tophat_reports.cpp | 5 +-
35 files changed, 2408 insertions(+), 1268 deletions(-)
mode change 100755 => 100644 src/align_status.cpp
mode change 100755 => 100644 src/align_status.h
mode change 100755 => 100644 src/deletions.cpp
mode change 100755 => 100644 src/deletions.h
mode change 100755 => 100644 src/fusions.cpp
mode change 100755 => 100644 src/fusions.h
mode change 100755 => 100644 src/insertions.cpp
mode change 100755 => 100644 src/insertions.h
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