[med-svn] [sniffles] branch upstream updated (5b80020 -> 5aa5664)

[Afif Elghraoui]

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

afif pushed a change to branch upstream
in repository sniffles.

      from  5b80020   Imported Upstream version 1.0.0+ds
       new  5aa5664   Imported Upstream version 1.0.1+ds

The 1 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                          |   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(-)
 delete mode 100755 cmake/Sniffles
 delete mode 100644 cmake/makefile
 delete mode 100644 cmake/objects.mk
 delete mode 100644 cmake/sources.mk
 delete mode 100644 cmake/src/Alignment.d
 delete mode 100644 cmake/src/Alignment.o
 delete mode 100644 cmake/src/BamParser.d
 delete mode 100644 cmake/src/BamParser.o
 delete mode 100644 cmake/src/Parser.d
 delete mode 100644 cmake/src/Parser.o
 delete mode 100644 cmake/src/Sniffles.d
 delete mode 100644 cmake/src/Sniffles.o
 delete mode 100644 cmake/src/plane-sweep/Main.d
 delete mode 100644 cmake/src/plane-sweep/Main.o
 delete mode 100644 cmake/src/plane-sweep/MyHeap.d
 delete mode 100644 cmake/src/plane-sweep/MyHeap.o
 delete mode 100644 cmake/src/plane-sweep/MyList.d
 delete mode 100644 cmake/src/plane-sweep/MyList.o
 delete mode 100644 cmake/src/plane-sweep/PlaneSweep.d
 delete mode 100644 cmake/src/plane-sweep/PlaneSweep.o
 delete mode 100644 cmake/src/plane-sweep/subdir.mk
 delete mode 100644 cmake/src/sub/Detect_Breapoints.d
 delete mode 100644 cmake/src/sub/Detect_Breapoints.o
 delete mode 100644 cmake/src/sub/subdir.mk
 delete mode 100644 cmake/src/subdir.mk
 delete mode 100644 cmake/src/tree/IntervallTree.d
 delete mode 100644 cmake/src/tree/IntervallTree.o
 delete mode 100644 cmake/src/tree/Scapegoat.d
 delete mode 100644 cmake/src/tree/Scapegoat.o
 delete mode 100644 cmake/src/tree/subdir.mk
 delete mode 100644 makefile
 delete mode 100644 objects.mk
 delete mode 100644 sources.mk
 delete mode 100644 src/Alignment.d
 delete mode 100644 src/Alignment.o
 delete mode 100644 src/BamParser.d
 delete mode 100644 src/BamParser.o
 delete mode 100644 src/Parser.d
 delete mode 100644 src/Parser.o
 delete mode 100644 src/Sniffles.d
 delete mode 100644 src/Sniffles.o
 delete mode 100644 src/plane-sweep/Main.d
 delete mode 100644 src/plane-sweep/Main.o
 delete mode 100644 src/plane-sweep/MyHeap.d
 delete mode 100644 src/plane-sweep/MyHeap.o
 delete mode 100644 src/plane-sweep/MyList.d
 delete mode 100644 src/plane-sweep/MyList.o
 delete mode 100644 src/plane-sweep/PlaneSweep.d
 delete mode 100644 src/plane-sweep/PlaneSweep.o
 delete mode 100644 src/plane-sweep/subdir.mk
 delete mode 100644 src/sub/Detect_Breapoints.d
 delete mode 100644 src/sub/Detect_Breapoints.o
 delete mode 100644 src/sub/subdir.mk
 delete mode 100644 src/subdir.mk
 delete mode 100644 src/tree/IntervallTree.d
 delete mode 100644 src/tree/IntervallTree.o
 delete mode 100644 src/tree/Scapegoat.d
 delete mode 100644 src/tree/Scapegoat.o
 delete mode 100644 src/tree/subdir.mk

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sniffles.git