[med-svn] [last-align] branch master updated (4e4a8e4 -> 35d1253)

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

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

      from  4e4a8e4   Better hardening and upload to unstable
       new  d1b9bf4   Imported Upstream version 746
       new  3d6d038   Merge tag 'upstream/746'
       new  35d1253   New upstream release; no new copyright nor license notice.

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                   |  51 ++++++++++++++++++-
 debian/changelog                |   8 ++-
 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 +-
 20 files changed, 209 insertions(+), 185 deletions(-)

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