[med-svn] [varscan] 01/07: Merge tag 'upstream/2.4.3'

[Andreas Tille]

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tille pushed a commit to branch master
in repository varscan.

commit 401a0e8069ee69595e9a15906cab41a9b222df00
Merge: 88ae68a 061067c
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 4 08:26:08 2016 +0100

    Merge tag 'upstream/2.4.3'
    
    Upstream version 2.4.3

 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(-)

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