[med-svn] [last-align] branch master updated (53dd487 -> 43e919c)

[Andreas Tille]

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

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

      from  53dd487   New upstream version
       new  9dfdbad   New upstream version 755
       new  2be4b68   Merge tag 'upstream/755'
       new  a7b0338   New upstream version
       new  efc6116   New upstream version 759
       new  bb1b7f8   Merge tag 'upstream/759'
       new  43e919c   New upstream version

The 6 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 +++++++++++++-
 debian/changelog                  |  12 ++++
 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 +-
 33 files changed, 683 insertions(+), 455 deletions(-)

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