[med-svn] [kmc] 09/15: Merge tag 'upstream/2.2'

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
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commit 4f0e84180cae613b837a99d1ddd9b27b813717bb
Merge: 3c56eb5 2169066
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Aug 24 19:23:50 2015 +0000

    Merge tag 'upstream/2.2'
    
    Upstream version 2.2

 API.pdf                             | Bin 0 -> 220319 bytes
 README.md                           |   1 +
 kmc_api/kmc_file.cpp                | 771 ++++++++++++++++++++++++++++--------
 kmc_api/kmc_file.h                  |  23 +-
 kmc_api/kmer_api.cpp                |  29 +-
 kmc_api/kmer_api.h                  | 612 +++++++++++++++-------------
 kmc_api/kmer_defs.h                 |   8 +-
 kmc_api/mmer.cpp                    |   4 +-
 kmc_api/mmer.h                      |   8 +-
 kmc_dump/kmc_dump.cpp               |  45 ++-
 kmc_dump/nc_utils.cpp               |   4 +-
 kmc_dump/nc_utils.h                 |   4 +-
 kmc_dump_sample/kmc_dump_sample.cpp |  33 +-
 kmer_counter.sln                    |   2 +-
 kmer_counter/asmlib_wrapper.h       |   4 +-
 kmer_counter/bkb_merger.h           |   4 +-
 kmer_counter/bkb_reader.cpp         |   4 +-
 kmer_counter/bkb_reader.h           |   4 +-
 kmer_counter/bkb_sorter.h           |   4 +-
 kmer_counter/bkb_subbin.h           |   4 +-
 kmer_counter/bkb_uncompactor.h      |   4 +-
 kmer_counter/bkb_writer.cpp         |   4 +-
 kmer_counter/bkb_writer.h           |   4 +-
 kmer_counter/defs.h                 |   8 +-
 kmer_counter/develop.cpp            | 142 +++++++
 kmer_counter/develop.h              |  16 +
 kmer_counter/fastq_reader.cpp       |   4 +-
 kmer_counter/fastq_reader.h         |   4 +-
 kmer_counter/kb_collector.h         |   4 +-
 kmer_counter/kb_completer.cpp       |   4 +-
 kmer_counter/kb_completer.h         |   4 +-
 kmer_counter/kb_reader.h            |   4 +-
 kmer_counter/kb_sorter.h            |   4 +-
 kmer_counter/kb_storer.cpp          |   4 +-
 kmer_counter/kb_storer.h            |   4 +-
 kmer_counter/kmc.h                  |   4 +-
 kmer_counter/kmer.cpp               |   4 +-
 kmer_counter/kmer.h                 |   4 +-
 kmer_counter/kmer_counter.cpp       |   6 +-
 kmer_counter/kmer_counter.vcxproj   |   2 +
 kmer_counter/kxmer_set.h            |   4 +-
 kmer_counter/mem_disk_file.cpp      |   4 +-
 kmer_counter/mem_disk_file.h        |   4 +-
 kmer_counter/meta_oper.h            |   4 +-
 kmer_counter/mmer.cpp               |   4 +-
 kmer_counter/mmer.h                 |   8 +-
 kmer_counter/params.h               |   4 +-
 kmer_counter/queues.h               |   4 +-
 kmer_counter/radix.cpp              |   4 +-
 kmer_counter/radix.h                |   4 +-
 kmer_counter/rev_byte.cpp           |   4 +-
 kmer_counter/rev_byte.h             |   4 +-
 kmer_counter/s_mapper.h             |   4 +-
 kmer_counter/splitter.h             |   4 +-
 kmer_counter/timer.cpp              |   4 +-
 kmer_counter/timer.h                |   4 +-
 56 files changed, 1287 insertions(+), 583 deletions(-)

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