[med-svn] [varscan] branch master updated (07f4528 -> 4b47151)

[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  07f4528   Make sure uscan will choose the proper name automatically
       new  4557f3b   Imported Upstream version 2.3.9+dfsg
       new  ff38814   Merge tag 'upstream/2.3.9+dfsg'
       new  035d2f1   New upstream version; do not patch single files any more but change usage info in d/rules
       new  41a87c3   Upstream has dropped the net subdirectory
       new  c8838c6   cme fix dpkg-control; update changelog; really drop unused quilt patch
       new  4b47151   Revert main class setting in build.xml; fix version mangling in d/watch

The 6 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/build.xml                           |   2 +-
 debian/changelog                           |   9 +
 debian/control                             |  11 +-
 debian/patches/series                      |   1 -
 debian/patches/usage.patch                 | 159 ------
 debian/rules                               |   9 +
 debian/watch                               |   2 +-
 {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 +
 23 files changed, 922 insertions(+), 167 deletions(-)
 delete mode 100644 debian/patches/series
 delete mode 100644 debian/patches/usage.patch
 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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