[med-svn] [last-align] branch upstream updated (00a898d -> 899a681)

[Charles Plessy]

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

      from  00a898d   New upstream version 869
       new  899a681   New upstream version 885

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            | 87 +++++++++++++++++++++++++++++++++++++++++++-
 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 +-
 37 files changed, 569 insertions(+), 283 deletions(-)
 create mode 100644 src/mcf_zstream.hh

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