[med-svn] [last-align] branch upstream updated (857fbc1 -> 00a898d)

[Sascha Steinbiss]

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

      from  857fbc1   New upstream version 830
       new  00a898d   New upstream version 869

The 1 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                          | 198 +++++++++++++-
 doc/last-dotplot.html                  | 126 ++++++++-
 doc/last-dotplot.txt                   |  99 +++++--
 doc/last-papers.html                   |   5 +
 doc/last-papers.txt                    |   8 +
 doc/last-train.html                    |  24 +-
 doc/last-train.txt                     |  21 +-
 doc/last-tutorial.html                 |  28 +-
 doc/last-tutorial.txt                  |  27 +-
 doc/lastal.html                        |  12 +-
 doc/lastal.txt                         |  12 +-
 doc/lastdb.html                        |   2 +-
 doc/lastdb.txt                         |   2 +-
 scripts/last-dotplot                   | 463 ++++++++++++++++++++++++---------
 scripts/last-postmask                  |   8 +-
 scripts/last-train                     | 129 ++++++---
 scripts/maf-convert                    |  52 ++--
 src/Alignment.cc                       |  25 +-
 src/AlignmentWrite.cc                  |   5 +-
 src/Centroid.cc                        |  52 ++--
 src/Centroid.hh                        |  13 +-
 src/LastEvaluer.cc                     |  17 +-
 src/LastalArguments.cc                 |  25 +-
 src/LastalArguments.hh                 |   1 +
 src/LastdbArguments.cc                 |  18 +-
 src/alp/sls_alignment_evaluer.cpp      |  14 +-
 src/alp/sls_alignment_evaluer.hpp      |   4 +-
 src/alp/sls_alp_data.cpp               |   9 +-
 src/alp/sls_alp_data.hpp               |   4 +
 src/alp/sls_basic.hpp                  |   8 +-
 src/alp/sls_falp_alignment_evaluer.cpp |  10 -
 src/alp/sls_fsa1_pvalues.cpp           |  54 +---
 src/alp/sls_fsa1_pvalues.hpp           |  21 --
 src/alp/sls_pvalues.cpp                |  54 +---
 src/alp/sls_pvalues.hpp                |  20 --
 src/getoptUtil.hh                      |  17 ++
 src/lastal.cc                          |  13 +-
 src/makefile                           |   4 +-
 src/split/cbrc_split_aligner.hh        |   2 +-
 src/split/last-split.cc                |  15 +-
 src/version.hh                         |   2 +-
 41 files changed, 1113 insertions(+), 510 deletions(-)
 create mode 100644 src/getoptUtil.hh

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