[med-svn] [sniffles] 02/06: Merge tag 'upstream/1.0.0+ds'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sniffles.

commit 982972cad55734cd6a7ac700d8387ccae958db43
Merge: ef83e42 5b80020
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Oct 14 21:09:17 2016 -0700

    Merge tag 'upstream/1.0.0+ds'
    
    Upstream version 1.0.0+ds

 CMakeLists.txt                                   |  10 +-
 makefile                                         |  62 ++
 objects.mk                                       |   8 +
 sources.mk                                       |  30 +
 src/Alignment.cpp                                | 933 ++++++++++++++++++-----
 src/Alignment.d                                  |  54 ++
 src/Alignment.h                                  |  34 +-
 src/Alignment.o                                  | Bin 0 -> 628428 bytes
 src/BamParser.cpp                                |   5 +-
 src/BamParser.d                                  |  58 ++
 src/BamParser.o                                  | Bin 0 -> 298480 bytes
 src/CMakeLists.txt                               |  18 +-
 src/Genotyper/Genotyper.cpp                      | 246 ++++++
 src/Genotyper/Genotyper.h                        |  40 +
 src/Paramer.h                                    |  27 +-
 src/Parser.cpp                                   |   8 -
 src/Parser.d                                     |  56 ++
 src/Parser.h                                     |   8 +-
 src/Parser.o                                     | Bin 0 -> 8376 bytes
 src/Sniffles.cpp                                 | 125 ++-
 src/Sniffles.d                                   | 148 ++++
 src/Sniffles.o                                   | Bin 0 -> 812932 bytes
 src/cluster/Cluster_SVs.cpp                      | 149 ++++
 src/cluster/Cluster_SVs.h                        |  41 +
 src/phasing/PhaserSV.cpp                         |  13 -
 src/phasing/PhaserSV.h                           |  24 -
 src/plane-sweep/Main.d                           |   1 +
 src/plane-sweep/Main.o                           | Bin 0 -> 1380 bytes
 src/plane-sweep/MyHeap.d                         |  62 ++
 src/plane-sweep/MyHeap.o                         | Bin 0 -> 179100 bytes
 src/plane-sweep/MyList.d                         |  62 ++
 src/plane-sweep/MyList.o                         | Bin 0 -> 91880 bytes
 src/plane-sweep/PlaneSweep.d                     |  67 ++
 src/plane-sweep/PlaneSweep.o                     | Bin 0 -> 125776 bytes
 src/plane-sweep/PlaneSweep_slim.cpp              |  43 ++
 src/plane-sweep/PlaneSweep_slim.h                |  40 +
 src/plane-sweep/subdir.mk                        |  33 +
 src/print/BedePrinter.cpp                        |  59 --
 src/print/{MariaPrinter.cpp => BedpePrinter.cpp} |  20 +-
 src/print/{BedePrinter.h => BedpePrinter.h}      |  12 +-
 src/print/IPrinter.cpp                           |  46 +-
 src/print/IPrinter.h                             |  29 +-
 src/print/MariaPrinter.h                         |  24 -
 src/print/VCFPrinter.cpp                         |  42 +-
 src/sub/Breakpoint.cpp                           | 511 ++++++++-----
 src/sub/Breakpoint.h                             |  35 +-
 src/sub/Detect_Breakpoints.cpp                   | 453 +++++++----
 src/sub/Detect_Breakpoints.h                     |  10 +-
 src/sub/Detect_Breapoints.d                      |  82 ++
 src/sub/Detect_Breapoints.o                      | Bin 0 -> 877496 bytes
 src/sub/subdir.mk                                |  24 +
 src/subdir.mk                                    |  33 +
 src/test                                         |   0
 src/tree/Breakpoint_Tree.cpp                     | 257 +++++++
 src/tree/Breakpoint_Tree.h                       |  50 ++
 src/tree/IntervallTree.cpp                       |  20 +-
 src/tree/IntervallTree.d                         |  67 ++
 src/tree/IntervallTree.h                         |   2 +-
 src/tree/IntervallTree.o                         | Bin 0 -> 297288 bytes
 src/tree/Intervall_bed.cpp                       |   2 +-
 src/tree/Scapegoat.cpp                           |  10 -
 src/tree/Scapegoat.d                             |  66 ++
 src/tree/Scapegoat.h                             | 234 ------
 src/tree/Scapegoat.o                             | Bin 0 -> 8688 bytes
 src/tree/subdir.mk                               |  27 +
 65 files changed, 3472 insertions(+), 1048 deletions(-)

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