[med-svn] [last-align] 02/06: Merge tag 'upstream/885'

[Charles Plessy]

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

commit c2d94c99456d4f9e97d0c90cae937b584964cd29
Merge: 72682ad 899a681
Author: Charles Plessy <plessy at debian.org>
Date:   Sun Oct 15 22:05:41 2017 +0900

    Merge tag 'upstream/885'
    
    Upstream version 885
    
    # gpg: Signature faite le dim. 15 oct. 2017 22:05:38 JST
    # gpg:                avec la clef RSA 73471499CC60ED9EEE805946C5BD6C8F2295D502
    # gpg: Bonne signature de « Charles Plessy <plessy at debian.org> » [totale]
    # Empreinte de clef principale : 7347 1499 CC60 ED9E EE80  5946 C5BD 6C8F 2295 D502

 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(-)

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