[med-svn] [mhap] branch master updated (b4feb76 -> 25e9b81)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository mhap.

      from  b4feb76   prepare for upload
       new  c353d38   Update email address
       new  26dc88d   Update Standards-Version
       new  16f04e7   Use https for VCS URLs
       new  bb2b65b   Clean up d/control style
       new  bbe9c20   Use readthedocs page as homepage
       new  a4d148f   Imported Upstream version 2.0+dfsg
       new  183349e   Merge tag 'upstream/2.0+dfsg'
       new  ee2b165   Remove obsolete patches
       new  25e9b81   Set up a new revision

The 9 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                                          |   25 +-
 build.xml                                          |  377 ---
 debian/changelog                                   |   10 +
 debian/control                                     |   34 +-
 debian/copyright                                   |    2 +-
 debian/patches/libdir                              |   35 -
 debian/patches/manifestclasspath                   |   20 -
 debian/patches/series                              |    2 -
 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 +-
 40 files changed, 1042 insertions(+), 4835 deletions(-)
 delete mode 100755 build.xml
 delete mode 100644 debian/patches/libdir
 delete mode 100644 debian/patches/manifestclasspath
 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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