[med-svn] [kmc] 02/15: Merge tag 'upstream/2.1.1'

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
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commit 7844cc54595ce62c1eaaedea56e5eaa5535ee1f6
Merge: 941c4f5 2f7cba5
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sun Aug 23 15:37:05 2015 +0000

    Merge tag 'upstream/2.1.1'
    
    Upstream version 2.1.1

 .gitattributes                              |   22 +
 .gitignore                                  |   43 +
 LICENSE                                     |  674 -------
 README.md                                   |   80 +-
 kmc_api/kmc_file.cpp                        | 1333 +++++++------
 kmc_api/kmc_file.h                          |  244 +--
 kmc_api/kmer_api.cpp                        |   46 +-
 kmc_api/kmer_api.h                          | 1079 +++++------
 kmc_api/kmer_defs.h                         |  101 +-
 kmc_api/mmer.cpp                            |   98 +-
 kmc_api/mmer.h                              |  362 ++--
 kmc_api/stdafx.h                            |    0
 kmc_dump/ReadMe.txt                         |   40 -
 kmc_dump/kmc_dump.cpp                       |  292 +--
 kmc_dump/kmc_dump.vcxproj                   |  336 ++--
 kmc_dump/nc_utils.cpp                       |   38 +-
 kmc_dump/nc_utils.h                         |  274 +--
 kmc_dump/stdafx.cpp                         |   16 +-
 kmc_dump/stdafx.h                           |   37 +-
 kmc_dump/targetver.h                        |   16 +-
 kmc_dump_sample/ReadMe.txt                  |   40 -
 kmc_dump_sample/kmc_dump_sample.cpp         |  266 +--
 kmc_dump_sample/kmc_dump_sample.vcxproj     |  332 ++--
 kmc_dump_sample/stdafx.cpp                  |   16 +-
 kmc_dump_sample/stdafx.h                    |   37 +-
 kmc_dump_sample/targetver.h                 |   16 +-
 kmer_counter.sln                            |  124 +-
 kmer_counter/ReadMe.txt                     |   40 -
 kmer_counter/{kmer.cpp => asmlib_wrapper.h} |   40 +-
 kmer_counter/bkb_merger.h                   |  280 +++
 kmer_counter/bkb_reader.cpp                 |  100 +
 kmer_counter/bkb_reader.h                   |   51 +
 kmer_counter/bkb_sorter.h                   |  577 ++++++
 kmer_counter/bkb_subbin.h                   |  151 ++
 kmer_counter/bkb_uncompactor.h              |  688 +++++++
 kmer_counter/bkb_writer.cpp                 |  142 ++
 kmer_counter/bkb_writer.h                   |   52 +
 kmer_counter/defs.h                         |  265 +--
 kmer_counter/fastq_reader.cpp               |  949 +++++-----
 kmer_counter/fastq_reader.h                 |  246 +--
 kmer_counter/kb_collector.h                 |  454 ++---
 kmer_counter/kb_completer.cpp               |  586 +++---
 kmer_counter/kb_completer.h                 |  160 +-
 kmer_counter/kb_reader.h                    |  471 ++---
 kmer_counter/kb_sorter.h                    | 2717 +++++++++++++--------------
 kmer_counter/kb_storer.cpp                  |  536 +++---
 kmer_counter/kb_storer.h                    |  183 +-
 kmer_counter/kmc.h                          | 1763 +++++++++--------
 kmer_counter/kmer.cpp                       |   36 +-
 kmer_counter/kmer.h                         | 2098 ++++++++++-----------
 kmer_counter/kmer_counter.cpp               |  854 +++++----
 kmer_counter/kmer_counter.vcxproj           |  463 ++---
 kmer_counter/kxmer_set.h                    |  234 +--
 kmer_counter/mem_disk_file.cpp              |  226 +--
 kmer_counter/mem_disk_file.h                |   85 +-
 kmer_counter/meta_oper.h                    |   90 +-
 kmer_counter/mmer.cpp                       |   98 +-
 kmer_counter/mmer.h                         |  362 ++--
 kmer_counter/params.h                       |  357 ++--
 kmer_counter/queues.h                       | 2336 ++++++++++++++---------
 kmer_counter/radix.cpp                      |  584 +++---
 kmer_counter/radix.h                        |   87 +-
 kmer_counter/rev_byte.cpp                   |   28 +-
 kmer_counter/rev_byte.h                     |   56 +-
 kmer_counter/s_mapper.h                     |  324 ++--
 kmer_counter/splitter.h                     | 1882 +++++++++----------
 kmer_counter/stdafx.cpp                     |   16 +-
 kmer_counter/stdafx.h                       |   43 +-
 kmer_counter/targetver.h                    |   16 +-
 kmer_counter/timer.cpp                      |  122 +-
 kmer_counter/timer.h                        |  116 +-
 kmer_counter/x64/Release/kmer.obj           |  Bin 0 -> 680826 bytes
 makefile                                    |   54 +-
 makefile_mac                                |   64 +
 readme.txt                                  |   60 +
 75 files changed, 14772 insertions(+), 12332 deletions(-)

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