[med-svn] [last-align] branch master updated (2f11a49 -> 4548b2e)

[Andreas Tille]

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

      from  2f11a49   Fix OMICS entry
       new  86ec818   New upstream version 921
       new  c5a7ba1   Update upstream source from tag 'upstream/921'
       new  20395c3   New upstream version
       new  234c1da   make build compatible with -Wl, --as-needed
       new  e9f18cd   cme fix dpkg-control
       new  5181ab8   debhelper 11
       new  ea818b3   do not parse changelog
       new  4548b2e   Upload to unstable

The 8 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                       | 177 +++++++-
 debian/changelog                    |  12 +
 debian/compat                       |   2 +-
 debian/control                      |   4 +-
 debian/rules                        |  12 +-
 doc/last-dotplot.html               |  99 +++--
 doc/last-dotplot.txt                |  82 +++-
 doc/last-train.html                 |   3 +
 doc/last-train.txt                  |   2 +
 scripts/last-dotplot                | 829 ++++++++++++++++++++++++------------
 scripts/last-train                  |   3 +
 src/Alignment.cc                    |  36 +-
 src/Alignment.hh                    |  13 +-
 src/AlignmentWrite.cc               |  70 +--
 src/Centroid.cc                     | 290 ++++++-------
 src/Centroid.hh                     |  73 ++--
 src/CyclicSubsetSeed.cc             |   9 +-
 src/LastEvaluer.cc                  |  10 +-
 src/LastEvaluer.hh                  |   3 +-
 src/LastdbArguments.cc              |  13 +-
 src/LastdbArguments.hh              |   1 +
 src/MultiSequence.cc                |  92 +++-
 src/MultiSequence.hh                |  90 ++--
 src/MultiSequenceQual.cc            |  56 +--
 src/ScoreMatrix.cc                  |   7 +-
 src/alp/sls_pvalues.cpp             |   4 +-
 src/io.cc                           |  23 -
 src/io.hh                           |  61 +--
 src/last-pair-probs.cc              |  15 +-
 src/last.hh                         |  55 +++
 src/lastal.cc                       |  76 +---
 src/lastdb.cc                       |  69 ++-
 src/makefile                        |  45 +-
 src/mcf_zstream.hh                  |   4 +-
 src/split/cbrc_split_aligner.cc     |  10 +-
 src/split/cbrc_unsplit_alignment.cc |   3 +-
 src/split/cbrc_unsplit_alignment.hh |   2 +
 src/split/last-split.cc             |   2 +-
 src/version.hh                      |   2 +-
 src/zio.hh                          |  37 ++
 40 files changed, 1483 insertions(+), 913 deletions(-)
 delete mode 100644 src/io.cc
 create mode 100644 src/last.hh
 create mode 100644 src/zio.hh

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