[med-svn] [varscan] branch upstream updated (4557f3b -> 1f63a2a)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository varscan.

      from  4557f3b   Imported Upstream version 2.3.9+dfsg
       new  061067c   New upstream version 2.4.3
       new  1f63a2a   New upstream version 2.4.3+dfsg

The 2 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:
 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 +--
 17 files changed, 979 insertions(+), 523 deletions(-)
 create mode 100644 sf/varscan/SmartFileReader.java

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