[med-svn] [adapterremoval] branch upstream updated (39c5a9d -> 663d195)

[Kevin Murray]

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daube-guest pushed a change to branch upstream
in repository adapterremoval.

      from  39c5a9d   New upstream version 2.2.1a
       new  663d195   New upstream version 2.2.2

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:
 .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(-)
 delete mode 100644 include/ar/adapterremoval.h
 create mode 100644 include/ar/adapterremoval.hpp
 rename src/{adapterset.cc => adapterset.cpp} (92%)
 rename src/{adapterset.h => adapterset.hpp} (98%)
 rename src/{alignment.cc => alignment.cpp} (95%)
 rename src/{alignment.h => alignment.hpp} (99%)
 rename src/{argparse.cc => argparse.cpp} (89%)
 rename src/{argparse.h => argparse.hpp} (87%)
 rename src/{commontypes.h => commontypes.hpp} (96%)
 rename src/{debug.cc => debug.cpp} (99%)
 rename src/{debug.h => debug.hpp} (100%)
 rename src/{demultiplex.cc => demultiplex.cpp} (92%)
 rename src/{demultiplex.h => demultiplex.hpp} (94%)
 rename src/{fastq.cc => fastq.cpp} (89%)
 rename src/{fastq.h => fastq.hpp} (99%)
 rename src/{fastq_enc.cc => fastq_enc.cpp} (77%)
 rename src/{fastq_enc.h => fastq_enc.hpp} (86%)
 rename src/{fastq_io.cc => fastq_io.cpp} (92%)
 rename src/{fastq_io.h => fastq_io.hpp} (91%)
 rename src/{linereader.cc => linereader.cpp} (88%)
 rename src/{linereader.h => linereader.hpp} (91%)
 rename src/{linereader_joined.cc => linereader_joined.cpp} (97%)
 rename src/{linereader_joined.h => linereader_joined.hpp} (91%)
 rename src/{main.cc => main.cpp} (81%)
 rename src/{main.h => main.hpp} (98%)
 rename src/{main_adapter_id.cc => main_adapter_id.cpp} (95%)
 rename src/{main_adapter_rm.cc => main_adapter_rm.cpp} (90%)
 rename src/{main_demultiplex.cc => main_demultiplex.cpp} (96%)
 rename src/{scheduler.cc => scheduler.cpp} (95%)
 rename src/{scheduler.h => scheduler.hpp} (95%)
 rename src/{statistics.h => statistics.hpp} (98%)
 rename src/{strutils.cc => strutils.cpp} (96%)
 rename src/{strutils.h => strutils.hpp} (100%)
 rename src/{threads.cc => threads.cpp} (99%)
 rename src/{threads.h => threads.hpp} (95%)
 rename src/{timer.cc => timer.cpp} (95%)
 rename src/{timer.h => timer.hpp} (100%)
 rename src/{trimmed_reads.cc => trimmed_reads.cpp} (91%)
 rename src/{trimmed_reads.h => trimmed_reads.hpp} (91%)
 rename src/{userconfig.cc => userconfig.cpp} (94%)
 rename src/{userconfig.h => userconfig.hpp} (94%)
 rename src/{vecutils.h => vecutils.hpp} (100%)
 rename tests/{alignment_test.cc => alignment_test.cpp} (98%)
 rename tests/{argparse_test.cc => argparse_test.cpp} (96%)
 copy tests/{testing.h => fastq_enc_test.cpp} (77%)
 rename tests/{fastq_test.cc => fastq_test.cpp} (97%)
 rename tests/{strutils_test.cc => strutils_test.cpp} (95%)
 rename tests/{testing.h => testing.hpp} (98%)

-- 
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