[med-svn] [beagle] branch master updated (95e19b6 -> b32dc8b)

[Dylan Aïssi]

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bob.dybian-guest pushed a change to branch master
in repository beagle.

      from  95e19b6   Upload to new
       new  b90c085   Remove unnecessary Depends and Recommends for beagle-doc
       new  f1f1bdd   Update uscan options
       new  ef336ca   Imported Upstream version 4.1~160503-862+dfsg
       new  b32dc8b   Merge tag 'upstream/4.1_160503-862+dfsg'

The 4 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
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Summary of changes:
 beagleutil/BasicIntInterval.java  |  296 ++++----
 blbutil/Const.java                |  186 ++---
 blbutil/IndexMap.java             |  390 +++++-----
 blbutil/IndexSet.java             |  304 ++++----
 blbutil/InputIt.java              |  640 ++++++++--------
 blbutil/StringUtil.java           |  562 +++++++-------
 blbutil/Utilities.java            |  416 +++++------
 dag/MergeableDagLevel.java        | 1460 ++++++++++++++++++-------------------
 debian/control                    |    3 +-
 debian/rules                      |    2 +-
 debian/watch                      |    2 +-
 gpl_license                       | 1348 +++++++++++++++++-----------------
 haplotype/RefHapPairs.java        |  378 +++++-----
 ibd/HaploidIbd.java               |  528 +++++++-------
 main/ConstrainedAlleleProbs.java  |   37 +-
 main/Main.java                    |   16 +-
 main/WindowWriter.java            |   24 +-
 sample/DuoBaumLevel.java          | 1282 ++++++++++++++++----------------
 sample/DuoNodes.java              |  676 ++++++++---------
 sample/HapNodes.java              |  466 ++++++------
 sample/RecombSingleBaumLevel.java |    8 +-
 sample/RecombSingleNodes.java     |  722 +++++++++---------
 sample/SingleBaumLevel.java       |    8 +-
 sample/SingleNodes.java           |  588 +++++++--------
 vcf/AllData.java                  |  710 +++++++++---------
 vcf/GprobsStatistics.java         |  106 +--
 vcf/Markers.java                  |  778 ++++++++++----------
 vcf/VcfWindow.java                |  642 ++++++++--------
 vcf/VcfWriter.java                |  140 +++-
 29 files changed, 6402 insertions(+), 6316 deletions(-)

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