[med-svn] [centrifuge] branch master updated (42bbbd8 -> 6b5fa56)
Andreas Tille
tille at debian.org
Sat Nov 25 21:00:20 UTC 2017
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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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