[med-svn] [mhap] 02/04: Merge tag 'upstream/2.1.1+dfsg'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository mhap.

commit 0167fb2786d9d66dd38fc6fb2c104c50a50a6787
Merge: 7ee2279 6f4bf90
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Oct 9 11:20:49 2016 -0700

    Merge tag 'upstream/2.1.1+dfsg'
    
    Upstream version 2.1.1+dfsg

 README.md                                          |  4 +-
 docs/source/installation.rst                       | 18 ++++-----
 docs/source/quickstart.rst                         |  7 +++-
 docs/source/utilities.rst                          |  6 +--
 pom.xml                                            |  2 +-
 .../mhap/impl/MinHashBitSequenceSubSketches.java   |  7 ++--
 .../edu/umd/marbl/mhap/impl/MinHashSearch.java     |  7 +---
 .../edu/umd/marbl/mhap/impl/SequenceSketch.java    | 17 ++++----
 .../marbl/mhap/impl/SequenceSketchStreamer.java    | 45 ++++++++++++++++------
 .../java/edu/umd/marbl/mhap/main/AlignmentTry.java |  3 +-
 .../java/edu/umd/marbl/mhap/main/EstimateROC.java  |  2 +-
 .../edu/umd/marbl/mhap/main/KmerStatSimulator.java | 13 ++++---
 .../java/edu/umd/marbl/mhap/main/MhapMain.java     |  5 +--
 ...edNGramHashes.java => BottomOverlapSketch.java} | 16 ++++----
 .../sketch/{BottomHash.java => BottomSketch.java}  |  8 ++--
 .../edu/umd/marbl/mhap/sketch/FrequencyCounts.java | 34 +++++++++-------
 .../umd/marbl/mhap/sketch/MinHashBitSketch.java    |  2 +-
 .../edu/umd/marbl/mhap/sketch/MinHashSketch.java   | 41 +++++++++++---------
 .../mhap/sketch/ZeroNGramsFoundException.java      | 43 +++++++++++++++++++++
 19 files changed, 177 insertions(+), 103 deletions(-)

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