[med-svn] [last-align] 02/03: Merge tag 'upstream/746'

[Charles Plessy]

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

commit 3d6d038b1ed5a8f16a9cdd1649f8a162eee814b9
Merge: 4e4a8e4 d1b9bf4
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Jul 15 13:31:35 2016 +0900

    Merge tag 'upstream/746'
    
    Upstream version 746
    
    # gpg: Signature made Fri 15 Jul 2016 13:31:30 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 ChangeLog.txt                   |  51 ++++++++++++++++++-
 src/Centroid.cc                 | 110 ++++++++++++++++++++--------------------
 src/Centroid.hh                 |  17 ++++---
 src/GappedXdropAligner.cc       |  29 ++++-------
 src/GappedXdropAligner.hh       |  35 +++++++------
 src/GappedXdropAligner2qual.cc  |   6 +--
 src/GappedXdropAligner3frame.cc |  12 ++---
 src/GappedXdropAlignerPssm.cc   |   6 +--
 src/LastalArguments.cc          |  15 +++---
 src/SubsetSuffixArraySearch.cc  |   3 +-
 src/alp/sls_alp_data.cpp        |  20 +-------
 src/alp/sls_alp_data.hpp        |   4 --
 src/alp/sls_basic.cpp           |  26 +++++++++-
 src/alp/sls_basic.hpp           |   4 +-
 src/alp/sls_fsa1.cpp            |  19 +------
 src/alp/sls_fsa1_utils.cpp      |  18 +------
 src/alp/sls_fsa1_utils.hpp      |   6 ---
 src/lastal.cc                   |   3 ++
 src/version.hh                  |   2 +-
 19 files changed, 202 insertions(+), 184 deletions(-)

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