[med-svn] [last-align] branch master updated (72682ad -> f1f8b19)

[Charles Plessy]

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

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

      from  72682ad   fix autopkgtest
       new  899a681   New upstream version 885
       new  c2d94c9   Merge tag 'upstream/885'
       new  51e07bd   Re-enable multi-threading.
       new  dc92366   Update comments (s/Subversion/Git/, s/http/https/).
       new  5e39664   Depend on zlib1g-dev.
       new  f1f8b19   last-align (885-1) unstable; urgency=medium

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            | 87 +++++++++++++++++++++++++++++++++++++++++++-
 debian/changelog         |  8 +++++
 debian/control           |  3 +-
 debian/rules             |  5 +--
 doc/last-dotplot.html    | 17 +++++++--
 doc/last-dotplot.txt     | 15 ++++++--
 doc/last-parallel.html   |  4 +--
 doc/last-parallel.txt    |  4 +--
 doc/last-train.html      |  4 +++
 doc/last-train.txt       |  2 ++
 doc/last-tuning.html     |  7 ++--
 doc/last-tuning.txt      |  8 ++---
 doc/last.html            |  4 +--
 doc/last.txt             |  4 +--
 doc/lastal.html          | 13 ++++---
 doc/lastal.txt           |  9 +++--
 doc/lastdb.html          |  5 +--
 doc/lastdb.txt           |  5 +--
 doc/maf-convert.html     | 12 +++----
 doc/maf-convert.txt      | 18 +++++-----
 scripts/fastq-interleave | 10 ++----
 scripts/last-dotplot     | 75 +++++++++++++++++++++++---------------
 scripts/last-postmask    | 23 +++++++-----
 scripts/last-train       | 79 ++++++++++++++++++++++++++--------------
 scripts/maf-convert      | 93 +++++++++++++++++++++++++++++++++++-------------
 src/Alphabet.cc          |  8 -----
 src/Alphabet.hh          |  3 --
 src/LastEvaluer.cc       |  2 +-
 src/LastalArguments.cc   | 33 ++++++++++++-----
 src/MultiSequence.cc     |  7 ----
 src/MultiSequence.hh     | 66 +++++++++++++++++++++++++++++++---
 src/MultiSequenceQual.cc | 22 ++++--------
 src/io.cc                | 11 ++----
 src/io.hh                |  7 ++--
 src/last-pair-probs.cc   |  4 +--
 src/lastal.cc            | 32 ++---------------
 src/lastdb.cc            | 43 ++++++++++------------
 src/makefile             | 32 ++++++++---------
 src/mcf_zstream.hh       | 82 ++++++++++++++++++++++++++++++++++++++++++
 src/version.hh           |  2 +-
 40 files changed, 582 insertions(+), 286 deletions(-)
 create mode 100644 src/mcf_zstream.hh

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