[med-svn] [mhap] branch upstream updated (d216c8f -> a4d148f)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository mhap.

      from  d216c8f   Imported Upstream version 1.6+dfsg
       new  a4d148f   Imported Upstream version 2.0+dfsg

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Summary of changes:
 README.md                                          |   25 +-
 build.xml                                          |  377 ---
 docs/source/conf.py                                |    4 +-
 docs/source/contact.rst                            |    2 +-
 docs/source/index.rst                              |    2 +-
 docs/source/installation.rst                       |   32 +-
 docs/source/quickstart.rst                         |   52 +-
 docs/source/utilities.rst                          |   20 +-
 pom.xml                                            |  137 +
 .../marbl/mhap/align/AlignElementDoubleSketch.java |    5 +-
 .../java/edu/umd/marbl/mhap/align/Aligner.java     |   43 +-
 .../java/edu/umd/marbl/mhap/impl/FastaData.java    |   74 +-
 .../java/edu/umd/marbl/mhap/impl/MatchResult.java  |    2 +-
 .../mhap/impl/MinHashBitSequenceSubSketches.java   |  103 +-
 .../edu/umd/marbl/mhap/impl/MinHashSearch.java     |   25 +-
 .../java/edu/umd/marbl/mhap/impl/OverlapInfo.java  |   15 +-
 .../java/edu/umd/marbl/mhap/impl/SequenceId.java   |   14 +-
 .../edu/umd/marbl/mhap/impl/SequenceSketch.java    |   82 +-
 .../marbl/mhap/impl/SequenceSketchStreamer.java    |   10 +-
 .../java/edu/umd/marbl/mhap/main/AlignmentTry.java |    7 +-
 .../java/edu/umd/marbl/mhap/main/EstimateROC.java  |  128 +-
 .../edu/umd/marbl/mhap/main/KmerStatSimulator.java |   10 +
 .../java/edu/umd/marbl/mhap/main/MhapMain.java     |  151 +-
 .../java/edu/umd/marbl/mhap/math/BasicMath.java    |   10 +-
 .../java/edu/umd/marbl/mhap/math/FastMath.java     | 3379 --------------------
 .../umd/marbl/mhap/sketch/AbstractBitSketch.java   |    2 +-
 .../java/edu/umd/marbl/mhap/sketch/BottomHash.java |   72 +
 .../java/edu/umd/marbl/mhap/sketch/CountMin.java   |   20 -
 .../umd/marbl/mhap/sketch/OrderedNGramHashes.java  |  747 +++--
 ...NGramHashes.java => OrderedNGramHashesOld.java} |   12 +-
 .../edu/umd/marbl/mhap/utils/CharacterHash.java    |   51 -
 .../java/edu/umd/marbl/mhap/utils/CyclicHash.java  |   72 -
 .../java/edu/umd/marbl/mhap/utils/PackageInfo.java |   87 -
 .../edu/umd/marbl/mhap/utils/ParseOptions.java     |    2 +-
 34 files changed, 1013 insertions(+), 4761 deletions(-)
 delete mode 100755 build.xml
 create mode 100644 pom.xml
 delete mode 100644 src/main/java/edu/umd/marbl/mhap/math/FastMath.java
 create mode 100644 src/main/java/edu/umd/marbl/mhap/sketch/BottomHash.java
 copy src/main/java/edu/umd/marbl/mhap/sketch/{OrderedNGramHashes.java => OrderedNGramHashesOld.java} (96%)
 delete mode 100644 src/main/java/edu/umd/marbl/mhap/utils/CharacterHash.java
 delete mode 100644 src/main/java/edu/umd/marbl/mhap/utils/CyclicHash.java
 delete mode 100644 src/main/java/edu/umd/marbl/mhap/utils/PackageInfo.java

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