[med-svn] [mhap] branch upstream updated (a4d148f -> 564212a)

[Afif Elghraoui]

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

afif pushed a change to branch upstream
in repository mhap.

      from  a4d148f   Imported Upstream version 2.0+dfsg
       new  564212a   Imported Upstream version 2.1+dfsg

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:
 README.md                                          |   6 +-
 docs/source/conf.py                                |   4 +-
 docs/source/installation.rst                       |  22 +-
 docs/source/quickstart.rst                         |  98 +++--
 docs/source/utilities.rst                          |  14 +-
 pom.xml                                            |   6 +-
 .../edu/umd/marbl/mhap/impl/MinHashSearch.java     |  13 +-
 .../edu/umd/marbl/mhap/impl/SequenceSketch.java    |   6 +-
 .../marbl/mhap/impl/SequenceSketchStreamer.java    |  33 +-
 .../java/edu/umd/marbl/mhap/main/EstimateROC.java  |  98 +++--
 .../edu/umd/marbl/mhap/main/GetHistogramStats.java |   2 +-
 .../edu/umd/marbl/mhap/main/KmerStatSimulator.java |   6 +-
 .../java/edu/umd/marbl/mhap/main/MhapMain.java     | 115 ++++--
 .../edu/umd/marbl/mhap/sketch/FrequencyCounts.java | 226 ++++++++--
 .../edu/umd/marbl/mhap/sketch/MinHashSketch.java   |  35 +-
 .../umd/marbl/mhap/sketch/OrderedNGramHashes.java  |   4 +-
 .../marbl/mhap/sketch/OrderedNGramHashesOld.java   | 460 ---------------------
 .../edu/umd/marbl/mhap/utils/ParseOptions.java     |   2 +-
 src/main/java/edu/umd/marbl/mhap/utils/Utils.java  |  59 +--
 19 files changed, 512 insertions(+), 697 deletions(-)
 delete mode 100644 src/main/java/edu/umd/marbl/mhap/sketch/OrderedNGramHashesOld.java

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mhap.git