[med-svn] [centrifuge] 02/03: Update upstream source from tag 'upstream/1.0.3_beta'

[Andreas Tille]

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tille pushed a commit to branch master
in repository centrifuge.

commit 2a69c81580e3fef9756b616f28c1d4de3086a7bb
Merge: 42bbbd8 64b022e
Author: Andreas Tille <tille at debian.org>
Date:   Sat Nov 25 21:58:03 2017 +0100

    Update upstream source from tag 'upstream/1.0.3_beta'
    
    Update to upstream version '1.0.3~beta'
    with Debian dir 20301142b063c526daf59b5a0acc2fc6c2a64699

 MANUAL                                       |  14 +-
 MANUAL.markdown                              |  20 ++-
 Makefile                                     |  35 ++++-
 README.md                                    |   9 +-
 VERSION                                      |   2 +-
 aln_sink.h                                   | 213 ++++++++++++++++----------
 bt2_idx.h                                    |   2 +-
 centrifuge-BuildSharedSequence.pl            |   2 +-
 centrifuge-RemoveEmptySequence.pl            |   2 +-
 centrifuge-RemoveN.pl                        |   2 +-
 centrifuge-compress.pl                       |  22 ++-
 centrifuge-download                          |  88 +++++++----
 centrifuge-kreport                           |  36 +++--
 centrifuge-sort-nt.pl                        | 119 ++++++++++-----
 centrifuge.cpp                               | 136 ++++++++++++++---
 centrifuge.xcodeproj/project.pbxproj         |   8 +-
 classifier.h                                 |  57 ++++---
 doc/index.shtml                              |  13 ++
 doc/manual.inc.html                          |  15 +-
 doc/sidebar.inc.shtml                        |  46 +++---
 doc/strip_markdown.pl                        |   2 +-
 evaluation/centrifuge_evaluate.py            |  18 +--
 evaluation/test/abundance.Rmd                |  53 +++++++
 evaluation/test/centrifuge_evaluate_mason.py | 215 ++++++++++++++++++++++++---
 fast_mutex.h                                 |   0
 indices/Makefile                             |  76 ++++++----
 opts.h                                       |   2 +
 ref_read.cpp                                 |  17 ++-
 taxonomy.h                                   |  31 ++--
 tinythread.cpp                               |   0
 tinythread.h                                 |   0
 31 files changed, 953 insertions(+), 302 deletions(-)

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