[med-svn] [centrifuge] branch upstream updated (d9e5f02 -> 64b022e)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository centrifuge.

      from  d9e5f02   New upstream version 1.0.2~beta
       new  64b022e   New upstream version 1.0.3~beta

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:
 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(-)
 mode change 100644 => 100755 centrifuge-RemoveEmptySequence.pl
 mode change 100644 => 100755 centrifuge-RemoveN.pl
 create mode 100644 evaluation/test/abundance.Rmd
 mode change 100755 => 100644 fast_mutex.h
 mode change 100755 => 100644 tinythread.cpp
 mode change 100755 => 100644 tinythread.h

-- 
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