[med-svn] [varscan] branch upstream updated (f0352e7 -> 4557f3b)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository varscan.

      from  f0352e7   Imported Upstream version 2.3.7+dfsg
       new  4557f3b   Imported Upstream version 2.3.9+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
been added to this reference.


Summary of changes:
 {net/sf => sf}/varscan/CallMpileup.java    |   0
 {net/sf => sf}/varscan/CallPileup.java     |   0
 {net/sf => sf}/varscan/Comparison.java     |   0
 {net/sf => sf}/varscan/CopyCaller.java     |   0
 {net/sf => sf}/varscan/Copynumber.java     |   0
 {net/sf => sf}/varscan/Coverage.java       |   0
 {net/sf => sf}/varscan/FilterSomatic.java  |   0
 {net/sf => sf}/varscan/FilterVariants.java |   0
 {net/sf => sf}/varscan/FishersExact.java   |   0
 sf/varscan/FpFilter.java                   | 874 +++++++++++++++++++++++++++++
 {net/sf => sf}/varscan/LimitVariants.java  |   0
 {net/sf => sf}/varscan/ProcessSomatic.java |   0
 {net/sf => sf}/varscan/ReadCounts.java     |   0
 {net/sf => sf}/varscan/Somatic.java        |   0
 {net/sf => sf}/varscan/Trio.java           |   0
 {net/sf => sf}/varscan/VarScan.java        |  22 +
 16 files changed, 896 insertions(+)
 rename {net/sf => sf}/varscan/CallMpileup.java (100%)
 rename {net/sf => sf}/varscan/CallPileup.java (100%)
 rename {net/sf => sf}/varscan/Comparison.java (100%)
 rename {net/sf => sf}/varscan/CopyCaller.java (100%)
 rename {net/sf => sf}/varscan/Copynumber.java (100%)
 rename {net/sf => sf}/varscan/Coverage.java (100%)
 rename {net/sf => sf}/varscan/FilterSomatic.java (100%)
 rename {net/sf => sf}/varscan/FilterVariants.java (100%)
 rename {net/sf => sf}/varscan/FishersExact.java (100%)
 create mode 100644 sf/varscan/FpFilter.java
 rename {net/sf => sf}/varscan/LimitVariants.java (100%)
 rename {net/sf => sf}/varscan/ProcessSomatic.java (100%)
 rename {net/sf => sf}/varscan/ReadCounts.java (100%)
 rename {net/sf => sf}/varscan/Somatic.java (100%)
 rename {net/sf => sf}/varscan/Trio.java (100%)
 rename {net/sf => sf}/varscan/VarScan.java (98%)

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