[med-svn] [beagle] 04/04: Merge tag 'upstream/4.1_160503-862+dfsg'

[Dylan Aïssi]

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

commit b32dc8bb71a4eb0296f45ba535eb899e79b26d52
Merge: f1f1bdd ef336ca
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri May 6 10:51:45 2016 +0200

    Merge tag 'upstream/4.1_160503-862+dfsg'
    
    Upstream version 4.1~160503-862+dfsg

 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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