[med-svn] [last-align] 02/03: Merge tag 'upstream/828'

[Andreas Tille]

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tille pushed a commit to branch master
in repository last-align.

commit ac6561a02c5b505825513a3ae770fed41369b199
Merge: c5c9c98 28865eb
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 9 14:16:09 2017 +0100

    Merge tag 'upstream/828'
    
    Upstream version 828

 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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