[med-svn] [last-align] branch master updated (c5c9c98 -> 448bfc4)

[Andreas Tille]

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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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