[med-svn] [last-align] branch master updated (34b894a -> 72682ad)

[Sascha Steinbiss]

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

      from  34b894a   Added references to RRID, OMICtools, bio.tools
       new  00a898d   New upstream version 869
       new  0e7bcc0   Merge tag 'upstream/869'
       new  116d814   new upstream release, bug fix
       new  72682ad   fix autopkgtest

The 4 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 +++++++++++++-
 debian/changelog                       |  13 +-
 debian/control                         |   4 +-
 debian/tests/control                   |   2 +-
 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 +-
 44 files changed, 1127 insertions(+), 515 deletions(-)
 create mode 100644 src/getoptUtil.hh

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