[med-svn] [beagle] branch upstream updated (ef336ca -> 3db72fd)

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

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

      from  ef336ca   Imported Upstream version 4.1~160503-862+dfsg
       new  3db72fd   Imported Upstream version 4.1~160616-7e4+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/BGZIPOutputStream.java | 237 ++++++++++++++++++++++++
 blbutil/FileUtil.java          | 161 +++++++++-------
 blbutil/InputIt.java           |  11 +-
 main/CurrentData.java          | 100 +++++-----
 main/Main.java                 |  60 ++++--
 main/MainHelper.java           |   4 +-
 main/WindowWriter.java         | 227 ++++++++++++++++-------
 sample/HaplotypeCoder.java     |  15 +-
 sample/ImputationData.java     |  99 +++++-----
 sample/LSHapBaum.java          |  54 +++---
 sample/RefHapSegs.java         | 108 ++++-------
 vcf/AllData.java               |   4 +-
 vcf/Data.java                  |  18 +-
 vcf/R2Estimator.java           | 153 ++++++++++++++++
 vcf/VcfRecBuilder.java         | 406 +++++++++++++++++++++++++++++++++++++++++
 vcf/VcfWindow.java             | 107 ++---------
 vcf/VcfWriter.java             | 319 ++++++++++----------------------
 17 files changed, 1402 insertions(+), 681 deletions(-)
 create mode 100644 blbutil/BGZIPOutputStream.java
 create mode 100644 vcf/R2Estimator.java
 create mode 100644 vcf/VcfRecBuilder.java

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beagle.git