[med-svn] [last-align] branch upstream updated (899a681 -> 86ec818)

[Andreas Tille]

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

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

      from  899a681   New upstream version 885
       new  86ec818   New upstream version 921

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                       | 177 +++++++-
 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 ++
 36 files changed, 1462 insertions(+), 904 deletions(-)
 delete mode 100644 src/io.cc
 create mode 100644 src/last.hh
 create mode 100644 src/zio.hh

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