[med-svn] [trimmomatic] branch master updated (b9c62c7 -> 99e9cd6)

[Andreas Tille]

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tille pushed a change to branch master
in repository trimmomatic.

      from  b9c62c7   Move packaging repository to Git
       new  56676b6   Imported Upstream version 0.35+dfsg
       new  c9d7c30   Merge tag 'upstream/0.35+dfsg'
       new  87506c3   New upstream version
       new  cd99969   Refresh patches
       new  c086579   Delete unused patch
       new  eccfef6   Inject a small wrapper script that simplifies calling Trimmomatic for a heap of sequences
       new  70cfe0e   Do not install batchTrimm in /usr/bin as long as it is not fully tested
       new  49bcc6f   Move batchTrim to examples for the moment
       new  39b7169   Do not compress batchTrim
       new  99e9cd6   Upload to unstable

The 10 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 adapters/TruSeq2-PE.fa                             |   2 +-
 adapters/TruSeq2-SE.fa                             |   2 +-
 build.xml                                          |   2 +-
 debian/bin/batchTrim                               | 295 +++++++++++++++++++++
 debian/changelog                                   |   7 +
 debian/examples                                    |   1 +
 debian/install                                     |   2 +-
 debian/patches/buildxmlJbzip2.patch                |   2 +-
 debian/patches/there_is_no_MANIFEST.MF.patch       |  18 --
 debian/rules                                       |   6 +-
 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 ++++++
 25 files changed, 926 insertions(+), 165 deletions(-)
 create mode 100755 debian/bin/batchTrim
 create mode 100644 debian/examples
 delete mode 100644 debian/patches/there_is_no_MANIFEST.MF.patch
 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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