[med-svn] [adapterremoval] 02/03: Updated version 2.2.2 from 'upstream/2.2.2'

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository adapterremoval.

commit 869af39de31bc2fcf24f6f6a21d5f559ca825341
Merge: ded3172 663d195
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Tue Jul 18 09:37:40 2017 +1000

    Updated version 2.2.2 from 'upstream/2.2.2'
    
    with Debian dir e483f2a809e45cf1b86f2b52a2c5321520a12ec7

 .travis.yml                                        |   1 +
 CHANGES.md                                         |   7 ++
 Makefile                                           |  47 ++------
 README.md                                          |  11 +-
 include/ar/adapterremoval.h                        |  23 ----
 include/ar/adapterremoval.hpp                      |  23 ++++
 src/{adapterset.cc => adapterset.cpp}              |  47 ++++----
 src/{adapterset.h => adapterset.hpp}               |   4 +-
 src/{alignment.cc => alignment.cpp}                |  28 +++--
 src/{alignment.h => alignment.hpp}                 |   2 +-
 src/{argparse.cc => argparse.cpp}                  |  65 +++++-----
 src/{argparse.h => argparse.hpp}                   |  94 +++++++--------
 src/{commontypes.h => commontypes.hpp}             |  16 +--
 src/{debug.cc => debug.cpp}                        |   2 +-
 src/{debug.h => debug.hpp}                         |   0
 src/{demultiplex.cc => demultiplex.cpp}            |  46 +++----
 src/{demultiplex.h => demultiplex.hpp}             |  19 ++-
 src/{fastq.cc => fastq.cpp}                        |  62 +++++-----
 src/{fastq.h => fastq.hpp}                         |   4 +-
 src/{fastq_enc.cc => fastq_enc.cpp}                |  97 +++++++--------
 src/{fastq_enc.h => fastq_enc.hpp}                 |  29 +++--
 src/{fastq_io.cc => fastq_io.cpp}                  |  73 ++++++------
 src/{fastq_io.h => fastq_io.hpp}                   |  74 +++++-------
 src/{linereader.cc => linereader.cpp}              | 132 ++++++---------------
 src/{linereader.h => linereader.hpp}               |  36 ++----
 ...{linereader_joined.cc => linereader_joined.cpp} |   6 +-
 src/{linereader_joined.h => linereader_joined.hpp} |  14 +--
 src/{main.cc => main.cpp}                          |  43 ++++---
 src/{main.h => main.hpp}                           |   2 +-
 src/{main_adapter_id.cc => main_adapter_id.cpp}    |  37 +++---
 src/{main_adapter_rm.cc => main_adapter_rm.cpp}    | 109 ++++++++---------
 src/{main_demultiplex.cc => main_demultiplex.cpp}  |  26 ++--
 src/{scheduler.cc => scheduler.cpp}                |  23 ++--
 src/{scheduler.h => scheduler.hpp}                 |  21 ++--
 src/{statistics.h => statistics.hpp}               |   6 +-
 src/{strutils.cc => strutils.cpp}                  |  14 +--
 src/{strutils.h => strutils.hpp}                   |   0
 src/{threads.cc => threads.cpp}                    |   2 +-
 src/{threads.h => threads.hpp}                     |  10 +-
 src/{timer.cc => timer.cpp}                        |  10 +-
 src/{timer.h => timer.hpp}                         |   0
 src/{trimmed_reads.cc => trimmed_reads.cpp}        |  16 +--
 src/{trimmed_reads.h => trimmed_reads.hpp}         |  27 +++--
 src/{userconfig.cc => userconfig.cpp}              |  93 +++++++--------
 src/{userconfig.h => userconfig.hpp}               |  35 +++---
 src/{vecutils.h => vecutils.hpp}                   |   0
 tests/{alignment_test.cc => alignment_test.cpp}    |  37 +++---
 tests/{argparse_test.cc => argparse_test.cpp}      |  32 ++---
 tests/{testing.h => fastq_enc_test.cpp}            |  30 +++--
 tests/{fastq_test.cc => fastq_test.cpp}            |  41 ++++++-
 tests/{strutils_test.cc => strutils_test.cpp}      |  23 +++-
 tests/{testing.h => testing.hpp}                   |   2 +-
 validation/run                                     |   8 +-
 53 files changed, 776 insertions(+), 833 deletions(-)

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