[med-svn] [trimmomatic] branch upstream updated (985a058 -> 56676b6)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository trimmomatic.

      from  985a058   Imported Upstream version 0.33+dfsg
       new  56676b6   Imported Upstream version 0.35+dfsg

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
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Summary of changes:
 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(-)
 create mode 100644 src/org/usadellab/trimmomatic/fastq/FastqNamePattern.java
 create mode 100644 src/org/usadellab/trimmomatic/fastq/PairingValidator.java
 create mode 100644 src/org/usadellab/trimmomatic/trim/MaxLenTrimmer.java
 create mode 100644 src/org/usadellab/trimmomatic/util/Logger.java

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