[med-svn] [mhap] branch master updated (7ee2279 -> ca8a777)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 9 19:02:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository mhap.
from 7ee2279 releasing package mhap version 2.1+dfsg-1
adds 564212a Imported Upstream version 2.1+dfsg
new 6f4bf90 Imported Upstream version 2.1.1+dfsg
new 0167fb2 Merge tag 'upstream/2.1.1+dfsg'
new 46da486 Remove duplicate word from package description
new ca8a777 releasing package mhap version 2.1.1+dfsg-1
The 4 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 | 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(-)
rename src/main/java/edu/umd/marbl/mhap/sketch/{OrderedNGramHashes.java => BottomOverlapSketch.java} (95%)
rename src/main/java/edu/umd/marbl/mhap/sketch/{BottomHash.java => BottomSketch.java} (85%)
create mode 100644 src/main/java/edu/umd/marbl/mhap/sketch/ZeroNGramsFoundException.java
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