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tille pushed a change to branch master
in repository last-align.
from c5c9c98 Spelling in doc-base + upload to unstable
new 28865eb New upstream version 828
new ac6561a Merge tag 'upstream/828'
new 448bfc4 New upstream version (+ some manpages for new binaries)
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:
ChangeLog.txt | 109 +++++++++-
debian/changelog | 7 +
debian/rules | 7 +
doc/last-split.html | 28 ++-
doc/last-split.txt | 25 ++-
doc/last-tuning.html | 11 +
doc/last-tuning.txt | 13 ++
doc/lastal.html | 5 +
doc/lastal.txt | 7 +
doc/lastdb.html | 42 +++-
doc/lastdb.txt | 41 +++-
makefile | 7 +-
src/Centroid.cc | 438 +++++++++++++++++++++++----------------
src/Centroid.hh | 31 +--
src/DiagonalTable.hh | 9 +-
src/GappedXdropAligner.cc | 21 +-
src/GappedXdropAligner2qual.cc | 21 +-
src/GappedXdropAlignerInl.hh | 7 +
src/GappedXdropAlignerPssm.cc | 21 +-
src/GeneralizedAffineGapCosts.cc | 1 -
src/GeneralizedAffineGapCosts.hh | 7 +-
src/LastalArguments.cc | 2 +-
src/LastalArguments.hh | 20 +-
src/LastdbArguments.cc | 2 +-
src/LastdbArguments.hh | 12 +-
src/MultiSequence.cc | 5 +-
src/MultiSequence.hh | 2 +-
src/SegmentPair.hh | 4 +-
src/SegmentPairPot.cc | 2 +-
src/SegmentPairPot.hh | 2 +-
src/SubsetSuffixArray.cc | 13 +-
src/SubsetSuffixArray.hh | 16 +-
src/SubsetSuffixArraySearch.cc | 18 +-
src/SubsetSuffixArraySort.cc | 9 +-
src/lastal.cc | 34 +--
src/lastdb.cc | 3 +-
src/makefile | 204 ++++++++++--------
src/split/cbrc_split_aligner.cc | 38 ++--
src/split/cbrc_split_aligner.hh | 9 +-
src/split/last-split.cc | 31 +--
src/version.hh | 2 +-
41 files changed, 834 insertions(+), 452 deletions(-)
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