[med-svn] [mhap] branch upstream updated (564212a -> 6f4bf90)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository mhap.

      from  564212a   Imported Upstream version 2.1+dfsg
       new  6f4bf90   Imported Upstream version 2.1.1+dfsg

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 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(-)
 rename src/main/java/edu/umd/marbl/mhap/sketch/{OrderedNGramHashes.java => BottomOverlapSketch.java} (95%)
 rename src/main/java/edu/umd/marbl/mhap/sketch/{BottomHash.java => BottomSketch.java} (85%)
 create mode 100644 src/main/java/edu/umd/marbl/mhap/sketch/ZeroNGramsFoundException.java

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