[med-svn] [sniffles] branch master updated (a2fed05 -> 1a9aef9)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository sniffles.

      from  a2fed05   releasing package sniffles version 1.0.1+ds-1
       new  b4da08b   New upstream version 1.0.2+ds
       new  58a8876   Merge tag 'upstream/1.0.2+ds'
       new  2276001   New upstream version
       new  504cf4d   refresh patches
       new  fa435c2   Apply changes of `cme fix dpkg-control` manually to not conflict with Uploaders formating preferences
       new  a76b1f3   debhelper 10 (making --parallel redundant)
       new  1a9aef9   hardening=+all, upload to unstable

The 7 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:
 CMakeLists.txt                       |   4 +-
 README.md                            |  90 ++------
 debian/changelog                     |  11 +
 debian/compat                        |   2 +-
 debian/control                       |  12 +-
 debian/patches/external-libs.patch   |  12 +-
 debian/patches/no-extra-binary.patch |  12 +-
 debian/rules                         |   4 +-
 src/Alignment.cpp                    | 367 ++++++++++++++++++++++-----------
 src/Alignment.h                      |   9 +-
 src/BamParser.cpp                    |   1 +
 src/CMakeLists.txt                   |   2 +
 src/Genotyper/Genotyper.cpp          |  50 +++--
 src/Genotyper/Genotyper.h            |   2 +-
 src/Paramer.h                        |   8 +-
 src/Sniffles.cpp                     | 240 +++++++++++++++-------
 src/Version.h                        |   6 +-
 src/cluster/Cluster_SVs.cpp          |  53 ++---
 src/cluster/Cluster_SVs.h            |   8 +-
 src/print/BedpePrinter.cpp           |   2 +-
 src/print/IPrinter.cpp               | 151 +++++++++++++-
 src/print/IPrinter.h                 |  15 +-
 src/print/VCFPrinter.cpp             | 171 ++++++++++------
 src/sub/Breakpoint.cpp               | 381 +++++++++++++++++++++-------------
 src/sub/Breakpoint.h                 |  22 +-
 src/sub/Detect_Breakpoints.cpp       | 384 ++++++++++++++++++++++++-----------
 src/sub/Detect_Breakpoints.h         |  14 +-
 src/test                             |   0
 src/tree/IntervallContainer.h        |  27 +++
 src/tree/IntervallList.cpp           |  43 ++++
 src/tree/IntervallList.h             |  32 +++
 src/tree/IntervallTree.cpp           |  66 ++++--
 src/tree/IntervallTree.h             |  10 +-
 src/tree/TNode.h                     |   9 -
 34 files changed, 1517 insertions(+), 703 deletions(-)
 delete mode 100644 src/test
 create mode 100644 src/tree/IntervallContainer.h
 create mode 100644 src/tree/IntervallList.cpp
 create mode 100644 src/tree/IntervallList.h

-- 
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