[med-svn] [centrifuge] branch master updated (42bbbd8 -> 6b5fa56)

[Andreas Tille]

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

tille pushed a change to branch master
in repository centrifuge.

      from  42bbbd8   Initial packaging
       new  64b022e   New upstream version 1.0.3~beta
       new  2a69c81   Update upstream source from tag 'upstream/1.0.3_beta'
       new  6b5fa56   New upstream version not catched by watch file

The 3 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 ++++---
 debian/changelog                             |   2 +-
 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
 32 files changed, 954 insertions(+), 303 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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