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

      from  f587ced   Imported Upstream version 752
       new  9dfdbad   New upstream version 755
       new  efc6116   New upstream version 759

The 2 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                     |  46 +++++++++++++-
 doc/last-map-probs.html           |   6 +-
 doc/last-map-probs.txt            |   6 +-
 doc/last-pair-probs.html          |  16 ++---
 doc/last-pair-probs.txt           |  16 ++---
 doc/last-parallel.html            |   4 +-
 doc/last-parallel.txt             |   4 +-
 doc/last-split.html               |  28 ++++----
 doc/last-split.txt                |  29 +++++----
 doc/last-tuning.html              |  37 ++++++-----
 doc/last-tuning.txt               |  43 ++++++-------
 doc/last-tutorial.html            | 129 ++++++++++++++++++-------------------
 doc/last-tutorial.txt             | 130 +++++++++++++++++---------------------
 doc/lastal.html                   | 107 +++++++++++++++----------------
 doc/lastal.txt                    |  92 ++++++++++++++-------------
 doc/lastdb.html                   |  63 +++++++++---------
 doc/lastdb.txt                    |  63 +++++++++---------
 examples/last-bisulfite-paired.sh |   8 +--
 examples/last-bisulfite.sh        |   4 +-
 scripts/last-dotplot              |   2 +-
 src/LastalArguments.cc            |  48 +++++++-------
 src/LastdbArguments.cc            |  12 ++--
 src/gaplessPssmXdrop.cc           |  39 ++++++++++++
 src/gaplessPssmXdrop.hh           |   7 ++
 src/gaplessTwoQualityXdrop.cc     |  46 ++++++++++++++
 src/gaplessTwoQualityXdrop.hh     |  11 ++++
 src/gaplessXdrop.cc               |  40 ++++++++++++
 src/gaplessXdrop.hh               |  15 +++++
 src/lastal.cc                     |  69 +++++++++++++-------
 src/split/last-split-main.cc      |   2 +-
 src/split/last-split.cc           |   2 +-
 src/version.hh                    |   2 +-
 32 files changed, 671 insertions(+), 455 deletions(-)

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