[med-svn] [last-align] branch upstream updated (fe2831f -> 28865eb)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository last-align.

      from  fe2831f   New upstream version 809
       new  28865eb   New upstream version 828

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:
 ChangeLog.txt                    | 109 +++++++++-
 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 +-
 39 files changed, 820 insertions(+), 452 deletions(-)

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