[med-svn] [mhap] branch debian/jessie-backports updated (8b83c0d -> 998a475)

[Andreas Tille]

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tille pushed a change to branch debian/jessie-backports
in repository mhap.

      from  8b83c0d   mhap (1.6+dfsg-1~bpo8+1) jessie-backports; urgency=medium
      adds  c353d38   Update email address
      adds  26dc88d   Update Standards-Version
      adds  16f04e7   Use https for VCS URLs
      adds  bb2b65b   Clean up d/control style
      adds  bbe9c20   Use readthedocs page as homepage
      adds  a4d148f   Imported Upstream version 2.0+dfsg
      adds  183349e   Merge tag 'upstream/2.0+dfsg'
      adds  ee2b165   Remove obsolete patches
      adds  25e9b81   Set up a new revision
      adds  edcff17   Globally use C.UTF-8 locale
      adds  089c860   Don't hardcode upstream version in d/rules
      adds  7e16115   Update jar file version throughout package
      adds  0841450   Update packaging to build with maven
      adds  0912580   Don't hardcode package version or classpath in debian/*
      adds  9320016   Don't force Java 8
      adds  490229a   Replace maven repo copy with a symlink to the jar file in /usr/share/java/
      adds  1d35b09   Remove copyright declaration for now non-existent file
      adds  6dca11e   Update manpage
      adds  740718b   Bump Standards-Version to 3.9.8
      adds  b605727   releasing package mhap version 2.0+dfsg-1
      adds  ccf5b8e   Avoid dependency on graphics libraries by not using java:Depends
      adds  bcd23e5   Imported Upstream version 2.1+dfsg
      adds  f1f7db9   Update package's long description
      adds  7ee2279   releasing package mhap version 2.1+dfsg-1
       new  998a475   Merge tag 'debian/2.1+dfsg-1' into debian/jessie-backports

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                                          |   27 +-
 build.xml                                          |  377 ---
 debian/README.Debian                               |    4 +-
 debian/changelog                                   |   25 +
 debian/control                                     |   57 +-
 debian/copyright                                   |    7 +-
 debian/install                                     |    2 +-
 debian/links.in                                    |    3 +
 debian/manifest                                    |    4 -
 debian/manifest.in                                 |    4 +
 debian/maven.rules                                 |    2 +
 debian/mhap.1                                      |   96 +-
 debian/mhap.poms                                   |   28 +
 debian/patches/libdir                              |   35 -
 debian/patches/manifestclasspath                   |   20 -
 debian/patches/series                              |    2 -
 debian/rules                                       |   30 +-
 docs/source/conf.py                                |    4 +-
 docs/source/contact.rst                            |    2 +-
 docs/source/index.rst                              |    2 +-
 docs/source/installation.rst                       |   32 +-
 docs/source/quickstart.rst                         |  104 +-
 docs/source/utilities.rst                          |   24 +-
 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     |   38 +-
 .../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    |   86 +-
 .../marbl/mhap/impl/SequenceSketchStreamer.java    |   37 +-
 .../java/edu/umd/marbl/mhap/main/AlignmentTry.java |    7 +-
 .../java/edu/umd/marbl/mhap/main/EstimateROC.java  |  184 +-
 .../edu/umd/marbl/mhap/main/GetHistogramStats.java |    2 +-
 .../edu/umd/marbl/mhap/main/KmerStatSimulator.java |   16 +-
 .../java/edu/umd/marbl/mhap/main/MhapMain.java     |  236 +-
 .../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 -
 .../edu/umd/marbl/mhap/sketch/FrequencyCounts.java |  226 +-
 .../edu/umd/marbl/mhap/sketch/MinHashSketch.java   |   35 +-
 .../umd/marbl/mhap/sketch/OrderedNGramHashes.java  |  749 +++--
 .../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     |    4 +-
 src/main/java/edu/umd/marbl/mhap/utils/Utils.java  |   59 +-
 52 files changed, 1576 insertions(+), 5080 deletions(-)
 delete mode 100755 build.xml
 create mode 100644 debian/links.in
 delete mode 100644 debian/manifest
 create mode 100644 debian/manifest.in
 create mode 100644 debian/maven.rules
 create mode 100644 debian/mhap.poms
 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
 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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