[med-svn] [beagle] branch upstream updated (7ef25aa -> ef336ca)

[Dylan Aïssi]

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

      from  7ef25aa   Imported Upstream version 4.1~160222-8ef+dfsg
       new  ef336ca   Imported Upstream version 4.1~160503-862+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:
 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 ++++++++++++++++++-------------------
 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 +++-
 26 files changed, 6399 insertions(+), 6312 deletions(-)

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