[med-svn] [last-align] 02/08: Update upstream source from tag 'upstream/921'

[Andreas Tille]

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

commit c5a7ba18630b3e9240e7493194f8f2b7fcc3fa7d
Merge: 2f11a49 86ec818
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 5 10:29:17 2018 +0100

    Update upstream source from tag 'upstream/921'
    
    Update to upstream version '921'
    with Debian dir 86534f173cb02fd42fc26365ffc1be3d45e3b63c

 ChangeLog.txt                       | 177 +++++++-
 doc/last-dotplot.html               |  99 +++--
 doc/last-dotplot.txt                |  82 +++-
 doc/last-train.html                 |   3 +
 doc/last-train.txt                  |   2 +
 scripts/last-dotplot                | 829 ++++++++++++++++++++++++------------
 scripts/last-train                  |   3 +
 src/Alignment.cc                    |  36 +-
 src/Alignment.hh                    |  13 +-
 src/AlignmentWrite.cc               |  70 +--
 src/Centroid.cc                     | 290 ++++++-------
 src/Centroid.hh                     |  73 ++--
 src/CyclicSubsetSeed.cc             |   9 +-
 src/LastEvaluer.cc                  |  10 +-
 src/LastEvaluer.hh                  |   3 +-
 src/LastdbArguments.cc              |  13 +-
 src/LastdbArguments.hh              |   1 +
 src/MultiSequence.cc                |  92 +++-
 src/MultiSequence.hh                |  90 ++--
 src/MultiSequenceQual.cc            |  56 +--
 src/ScoreMatrix.cc                  |   7 +-
 src/alp/sls_pvalues.cpp             |   4 +-
 src/io.cc                           |  23 -
 src/io.hh                           |  61 +--
 src/last-pair-probs.cc              |  15 +-
 src/last.hh                         |  55 +++
 src/lastal.cc                       |  76 +---
 src/lastdb.cc                       |  69 ++-
 src/makefile                        |  45 +-
 src/mcf_zstream.hh                  |   4 +-
 src/split/cbrc_split_aligner.cc     |  10 +-
 src/split/cbrc_unsplit_alignment.cc |   3 +-
 src/split/cbrc_unsplit_alignment.hh |   2 +
 src/split/last-split.cc             |   2 +-
 src/version.hh                      |   2 +-
 src/zio.hh                          |  37 ++
 36 files changed, 1462 insertions(+), 904 deletions(-)

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