[med-svn] [mhap] 01/02: Merge tag 'debian/2.1.1+dfsg-1' into debian/jessie-backports

[Afif Elghraoui]

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

commit 1b8dec85e5948de239f1cdc244d001c5caefcf32
Merge: 34b0e64 ca8a777
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Oct 16 14:25:41 2016 -0700

    Merge tag 'debian/2.1.1+dfsg-1' into debian/jessie-backports
    
    tagging package mhap version debian/2.1.1+dfsg-1

 README.md                                          |  4 +-
 debian/changelog                                   |  7 ++++
 debian/control                                     |  2 +-
 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 +++++++++++++++++++++
 21 files changed, 185 insertions(+), 104 deletions(-)

diff --cc debian/changelog
index f71c975,a4d8b8a..29d89b5
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,13 -1,10 +1,20 @@@
+ mhap (2.1.1+dfsg-1) unstable; urgency=medium
+ 
+   * Imported Upstream version 2.1.1+dfsg
+   * Remove duplicate word from package description
+ 
+  -- Afif Elghraoui <afif at debian.org>  Sun, 09 Oct 2016 11:39:51 -0700
+ 
 +mhap (2.1+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports
 +  * Force Java 8
 +  * Bump minimum required libguava-java
 +  * Add build-dependency on libmaven-shade-plugin-java
 +  * Workaround lack of maven artifacts for fastutil
 +
 + -- Afif Elghraoui <afif at debian.org>  Wed, 12 Oct 2016 18:58:50 -0700
 +
  mhap (2.1+dfsg-1) unstable; urgency=medium
  
    * Avoid dependency on graphics libraries by not using java:Depends

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