[med-svn] [trimmomatic] 02/10: Merge tag 'upstream/0.35+dfsg'

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository trimmomatic.

commit c9d7c301b29db937889d7d9e85555d18bd84df38
Merge: b9c62c7 56676b6
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 26 09:58:43 2015 +0100

    Merge tag 'upstream/0.35+dfsg'
    
    Upstream version 0.35+dfsg

 adapters/TruSeq2-PE.fa                             |   2 +-
 adapters/TruSeq2-SE.fa                             |   2 +-
 build.xml                                          |   2 +-
 src/org/usadellab/trimmomatic/Trimmomatic.java     |  41 ++++-
 src/org/usadellab/trimmomatic/TrimmomaticPE.java   | 169 ++++++++++++---------
 src/org/usadellab/trimmomatic/TrimmomaticSE.java   |  94 +++++++-----
 .../trimmomatic/fastq/FastqNamePattern.java        |  82 ++++++++++
 .../usadellab/trimmomatic/fastq/FastqParser.java   |  10 +-
 .../usadellab/trimmomatic/fastq/FastqRecord.java   |   2 +-
 .../trimmomatic/fastq/PairingValidator.java        | 131 ++++++++++++++++
 .../trimmomatic/threading/BlockOfRecords.java      |   1 +
 .../trimmomatic/threading/BlockOfWork.java         |  12 +-
 .../usadellab/trimmomatic/trim/CropTrimmer.java    |  21 +++
 .../trimmomatic/trim/IlluminaClippingTrimmer.java  |  33 ++--
 .../usadellab/trimmomatic/trim/MaxLenTrimmer.java  |  29 ++++
 .../usadellab/trimmomatic/trim/TrimmerFactory.java |  13 +-
 .../trimmomatic/util/ConcatGZIPInputStream.java    |  38 ++++-
 src/org/usadellab/trimmomatic/util/Logger.java     |  78 ++++++++++
 18 files changed, 619 insertions(+), 141 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trimmomatic.git