[med-svn] [varscan] branch master updated (88ae68a -> 8b6e694)

[Andreas Tille]

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

tille pushed a change to branch master
in repository varscan.

      from  88ae68a   cme fix dpkg-control
       new  061067c   New upstream version 2.4.3
       new  401a0e8   Merge tag 'upstream/2.4.3'
       new  c5843c9   Document issue with unusual way how upstream provides the source.
       new  5fc8e8b   Debhelper 10
       new  9faa215   Upload to unstable
       new  1f63a2a   New upstream version 2.4.3+dfsg
       new  8b6e694   Merge tag 'upstream/2.4.3+dfsg'

The 7 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:
 debian/README.source            |  10 +
 debian/changelog                |   9 +-
 debian/compat                   |   2 +-
 debian/control                  |   2 +-
 debian/copyright                |   6 +-
 sf/varscan/CallMpileup.java     |   8 +-
 sf/varscan/CallPileup.java      |   2 +-
 sf/varscan/Comparison.java      |  10 +-
 sf/varscan/CopyCaller.java      |   5 +-
 sf/varscan/Copynumber.java      | 696 +++++++++++++++++++++-------------------
 sf/varscan/Coverage.java        |   6 +-
 sf/varscan/FilterSomatic.java   |   6 +-
 sf/varscan/FilterVariants.java  |   6 +-
 sf/varscan/FishersExact.java    |   2 +-
 sf/varscan/FpFilter.java        | 305 ++++++++++++++----
 sf/varscan/LimitVariants.java   |   6 +-
 sf/varscan/ProcessSomatic.java  |   6 +-
 sf/varscan/ReadCounts.java      |   6 +-
 sf/varscan/SmartFileReader.java |  37 +++
 sf/varscan/Somatic.java         | 253 ++++++++++++---
 sf/varscan/Trio.java            | 105 ++++--
 sf/varscan/VarScan.java         |  43 +--
 22 files changed, 997 insertions(+), 534 deletions(-)
 create mode 100644 debian/README.source
 create mode 100644 sf/varscan/SmartFileReader.java

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