[med-svn] [mhap] 01/01: Merge tag 'debian/2.1+dfsg-1' into debian/jessie-backports

[Andreas Tille]

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

commit 998a475770ab5a76cf5fae7a9deccd4d8abbfa9c
Merge: 8b83c0d 7ee2279
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 7 14:19:14 2016 +0200

    Merge tag 'debian/2.1+dfsg-1' into debian/jessie-backports
    
    mhap (2.1+dfsg-1) unstable; urgency=medium
    
      * Avoid dependency on graphics libraries by not using java:Depends
      * Imported Upstream version 2.1+dfsg
      * Update package's long description

 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(-)

diff --cc debian/changelog
index 09057c7,dbd493c..f9e09df
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,28 +1,34 @@@
+ mhap (2.1+dfsg-1) unstable; urgency=medium
+ 
+   * Avoid dependency on graphics libraries by not using java:Depends
+   * Imported Upstream version 2.1+dfsg
+   * Update package's long description
+ 
+  -- Afif Elghraoui <afif at debian.org>  Wed, 13 Jul 2016 22:38:44 -0700
+ 
+ mhap (2.0+dfsg-1) unstable; urgency=medium
+ 
+   * Update Standards-Version
+   * Use https for VCS URLs
+   * Adjust project homepage
+   * Imported Upstream version 2.0+dfsg
+     - Remove obsolete patches
+     - Update packaging to build with maven.
+       (Thanks to Tony Mancill for patches and advice)
+     - Update manpage
+     - Remove copyright declaration for now non-existent file
+   * Globally use C.UTF-8 locale
+   * Don't hardcode package version or classpath in debian/*
+   * Don't force Java 8
+ 
+  -- Afif Elghraoui <afif at debian.org>  Wed, 13 Jul 2016 01:04:35 -0700
+ 
 +mhap (1.6+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Thu, 17 Dec 2015 00:29:31 -0800
 +
  mhap (1.6+dfsg-1) unstable; urgency=low
  
    * Initial release (Closes: #796640)

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