[med-svn] [sniffles] 02/03: Merge tag 'upstream/1.0.1+ds'

[Afif Elghraoui]

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commit f88a3515a7187d7b813d992b2c432f8a56cfd2e3
Merge: 4e5e165 5aa5664
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Oct 24 22:52:46 2016 -0700

    Merge tag 'upstream/1.0.1+ds'
    
    Upstream version 1.0.1+ds

 README.md                          |   6 +-
 cmake/Sniffles                     | Bin 261820 -> 0 bytes
 cmake/makefile                     |  62 ----------------
 cmake/objects.mk                   |   8 --
 cmake/sources.mk                   |  30 --------
 cmake/src/Alignment.d              |  54 --------------
 cmake/src/Alignment.o              | Bin 628428 -> 0 bytes
 cmake/src/BamParser.d              |  58 ---------------
 cmake/src/BamParser.o              | Bin 298480 -> 0 bytes
 cmake/src/Parser.d                 |  56 --------------
 cmake/src/Parser.o                 | Bin 8376 -> 0 bytes
 cmake/src/Sniffles.d               | 148 -------------------------------------
 cmake/src/Sniffles.o               | Bin 812932 -> 0 bytes
 cmake/src/plane-sweep/Main.d       |   1 -
 cmake/src/plane-sweep/Main.o       | Bin 1380 -> 0 bytes
 cmake/src/plane-sweep/MyHeap.d     |  62 ----------------
 cmake/src/plane-sweep/MyHeap.o     | Bin 179100 -> 0 bytes
 cmake/src/plane-sweep/MyList.d     |  62 ----------------
 cmake/src/plane-sweep/MyList.o     | Bin 91880 -> 0 bytes
 cmake/src/plane-sweep/PlaneSweep.d |  67 -----------------
 cmake/src/plane-sweep/PlaneSweep.o | Bin 125776 -> 0 bytes
 cmake/src/plane-sweep/subdir.mk    |  33 ---------
 cmake/src/sub/Detect_Breapoints.d  |  82 --------------------
 cmake/src/sub/Detect_Breapoints.o  | Bin 877496 -> 0 bytes
 cmake/src/sub/subdir.mk            |  24 ------
 cmake/src/subdir.mk                |  33 ---------
 cmake/src/tree/IntervallTree.d     |  67 -----------------
 cmake/src/tree/IntervallTree.o     | Bin 297288 -> 0 bytes
 cmake/src/tree/Scapegoat.d         |  66 -----------------
 cmake/src/tree/Scapegoat.o         | Bin 8688 -> 0 bytes
 cmake/src/tree/subdir.mk           |  27 -------
 makefile                           |  62 ----------------
 objects.mk                         |   8 --
 sources.mk                         |  30 --------
 src/Alignment.cpp                  | 104 ++++++++++++--------------
 src/Alignment.d                    |  54 --------------
 src/Alignment.h                    |   2 +-
 src/Alignment.o                    | Bin 628428 -> 0 bytes
 src/BamParser.d                    |  58 ---------------
 src/BamParser.o                    | Bin 298480 -> 0 bytes
 src/Genotyper/Genotyper.cpp        |  24 +++---
 src/Paramer.h                      |   4 +-
 src/Parser.d                       |  56 --------------
 src/Parser.o                       | Bin 8376 -> 0 bytes
 src/Sniffles.cpp                   |  23 ++++--
 src/Sniffles.d                     | 148 -------------------------------------
 src/Sniffles.o                     | Bin 812932 -> 0 bytes
 src/plane-sweep/Main.d             |   1 -
 src/plane-sweep/Main.o             | Bin 1380 -> 0 bytes
 src/plane-sweep/MyHeap.d           |  62 ----------------
 src/plane-sweep/MyHeap.o           | Bin 179100 -> 0 bytes
 src/plane-sweep/MyList.d           |  62 ----------------
 src/plane-sweep/MyList.o           | Bin 91880 -> 0 bytes
 src/plane-sweep/PlaneSweep.d       |  67 -----------------
 src/plane-sweep/PlaneSweep.o       | Bin 125776 -> 0 bytes
 src/plane-sweep/subdir.mk          |  33 ---------
 src/print/IPrinter.cpp             |   3 +-
 src/print/IPrinter.h               |  20 ++---
 src/print/VCFPrinter.cpp           |  96 ++++++++++++++----------
 src/sub/Breakpoint.cpp             |  90 ++++++++++++----------
 src/sub/Detect_Breakpoints.cpp     | 103 ++++++++++++--------------
 src/sub/Detect_Breapoints.d        |  82 --------------------
 src/sub/Detect_Breapoints.o        | Bin 877496 -> 0 bytes
 src/sub/subdir.mk                  |  24 ------
 src/subdir.mk                      |  33 ---------
 src/tree/IntervallTree.d           |  67 -----------------
 src/tree/IntervallTree.o           | Bin 297288 -> 0 bytes
 src/tree/Scapegoat.d               |  66 -----------------
 src/tree/Scapegoat.o               | Bin 8688 -> 0 bytes
 src/tree/subdir.mk                 |  27 -------
 70 files changed, 251 insertions(+), 2104 deletions(-)

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