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malex-guest pushed a change to branch upstream
in repository bowtie2.
from 7b7c16b New upstream version 2.3.0
new b224a1e New upstream version 2.3.1
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:
MANUAL | 19 ++++
MANUAL.markdown | 40 +++++++
Makefile | 5 +-
NEWS | 28 ++++-
VERSION | 2 +-
bowtie2 | 8 +-
bowtie_main.cpp | 241 +++++++++++++++++++++++++++++++++++++++++--
bt2_idx.h | 6 +-
bt2_search.cpp | 7 +-
doc/manual.html | 24 +++++
doc/website/manual.ssi | 23 ++++-
doc/website/old_news.ssi | 40 +++++++
doc/website/recent_news.ssi | 54 ++--------
doc/website/rhsidebar.ssi | 13 +--
formats.h | 1 +
opts.h | 3 +-
pat.cpp | 145 +++++++++++++++++---------
pat.h | 182 +++++++++++++++++++-------------
pthreadGC2.dll | Bin 60273 -> 0 bytes
read_qseq.cpp | 8 +-
scoring.h | 4 +-
scripts/test/simple_tests.pl | 27 +++--
scripts/test/simple_tests.sh | 3 +-
23 files changed, 676 insertions(+), 207 deletions(-)
delete mode 100644 pthreadGC2.dll
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