[med-svn] [minia] 01/02: Merge branch 'minia2'

[Andreas Tille]

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tille pushed a commit to branch master
in repository minia.

commit 2dc0368ed1e114d179048dc81141e1ee0ba9cb12
Merge: 6d8f7b6 3df5410
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 1 10:04:49 2017 +0100

    Merge branch 'minia2'

 .gitignore                     |     1 +
 .gitmodules                    |     3 +
 Bank.cpp                       |  1087 -----
 Bank.h                         |   200 -
 Bloom.cpp                      |   474 --
 Bloom.h                        |   248 -
 CMakeLists.txt                 |   119 +
 Debloom.cpp                    |   466 --
 Debloom.h                      |    45 -
 GraphOutput.cpp                |   380 --
 GraphOutput.h                  |   204 -
 Hash16.cpp                     |   404 --
 Hash16.h                       |    95 -
 Hashing.cpp                    |    42 -
 Hashing.h                      |    31 -
 INSTALL                        |    20 +
 Kmer.cpp                       |   373 --
 Kmer.h                         |    84 -
 LICENSE                        |  1175 +++--
 LargeInt.cpp                   |   277 --
 LargeInt.h                     |    48 -
 LinearCounter.cpp              |    47 -
 LinearCounter.h                |    29 -
 Minia.cpp                      |   351 --
 MultiConsumer.cpp              |   144 -
 MultiConsumer.h                |    86 -
 OAHash.cpp                     |   212 -
 OAHash.h                       |    77 -
 Pool.cpp                       |   156 -
 Pool.h                         |    92 -
 README                         |    18 -
 README.md                      |    38 +
 Set.cpp                        |   305 --
 Set.h                          |   158 -
 SortingCount.cpp               |   847 ----
 SortingCount.h                 |    27 -
 Terminator.cpp                 |   410 --
 Terminator.h                   |    79 -
 Traversal.cpp                  |   955 ----
 Traversal.h                    |   168 -
 Utils.cpp                      |   647 ---
 Utils.h                        |   103 -
 debian/changelog               |     9 +
 debian/control                 |     4 +-
 debian/patches/add_hardening   |    34 -
 debian/patches/series          |     1 -
 doc/CMakeLists.txt             |    13 +
 doc/manual.tex                 |   142 +
 lut.h                          |   272 --
 makefile                       |    76 -
 manual/manual.pdf              |   Bin 1155669 -> 0 bytes
 manual/manual.tex              |   124 -
 rvalues.h                      |   131 -
 simple_test.sh                 |    20 -
 src/Minia.cpp                  |   296 ++
 src/Minia.hpp                  |    61 +
 src/NodeSelector.cpp           |   244 +
 src/NodeSelector.hpp           |   125 +
 src/main.cpp                   |    50 +
 test/read50x_ref10K_e001.fasta | 10000 ---------------------------------------
 test/result10K.fasta           |     2 -
 ttmath/ttmath.h                |  2849 -----------
 ttmath/ttmathbig.h             |  6061 ------------------------
 ttmath/ttmathint.h             |  1924 --------
 ttmath/ttmathmisc.h            |   250 -
 ttmath/ttmathobjects.h         |   809 ----
 ttmath/ttmathparser.h          |  2765 -----------
 ttmath/ttmaththreads.h         |   250 -
 ttmath/ttmathtypes.h           |   667 ---
 ttmath/ttmathuint.h            |  4062 ----------------
 ttmath/ttmathuint_noasm.h      |  1017 ----
 ttmath/ttmathuint_x86.h        |  1602 -------
 ttmath/ttmathuint_x86_64.h     |  1146 -----
 73 files changed, 1785 insertions(+), 43946 deletions(-)

diff --cc debian/control
index 6675062,c191ae2..6dae2cb
--- a/debian/control
+++ b/debian/control
@@@ -4,9 -5,10 +5,10 @@@ Uploaders: Olivier Sallou <osallou at debi
  Section: science
  Priority: optional
  Build-Depends: debhelper (>= 10),
+                cmake,
                 bc,
                 zlib1g-dev
 -Standards-Version: 4.0.0
 +Standards-Version: 4.1.1
  Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/minia.git
  Vcs-Git: https://anonscm.debian.org/git/debian-med/minia.git
  Homepage: http://minia.genouest.org/

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