[med-svn] [beagle] branch upstream updated (3db72fd -> 6f5d56f)

[Dylan Aïssi]

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

      from  3db72fd   Imported Upstream version 4.1~160616-7e4+dfsg
       new  6f5d56f   Imported Upstream version 4.1~160727.86a+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:
 blbutil/Utilities.java     |   4 +-
 dag/MergeableDagLevel.java |   8 +--
 main/Main.java             |   6 +--
 sample/LSHapBaum.java      | 126 ++++++++++++++++++---------------------------
 vcf/VcfRecBuilder.java     | 118 ++++++++++++++++++++----------------------
 vcf/VcfWriter.java         |   2 +-
 6 files changed, 117 insertions(+), 147 deletions(-)

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