[med-svn] [beagle] branch master updated (b32dc8b -> 5b41984)

[Dylan Aïssi]

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

      from  b32dc8b   Merge tag 'upstream/4.1_160503-862+dfsg'
       new  5e95ccc   Imported Upstream version 4.1~160616-7e4+dfsg
       new  0559ec6   Update upstream docs
       new  4975d54   Rework autopkgtest to simply update
       new  19fb339   Update d/changelog
       new  82d3764   Refresh patch
       new  5b41984   Build the tool bref.jar

The 6 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 +-
 debian/beagle-doc.install                          |   4 +-
 debian/beagle.1                                    |   2 +-
 debian/beagle.install                              |   2 +
 debian/beagle.links                                |   2 +
 debian/beagle.manpages                             |   2 +
 debian/bref.1                                      |  44 +++
 debian/changelog                                   |  10 +
 debian/patches/01_Update_htsjtk.patch              |  27 +-
 debian/rules                                       |  16 +-
 debian/tests/run-sample-analysis                   |  19 +-
 debian/upstream.docs/README                        |  10 +
 debian/upstream.docs/release_notes                 |  18 +
 .../upstream.docs/run.beagle.22Feb16.8ef.example   |  53 ---
 debian/upstream.docs/run.beagle.example            |  53 +++
 .../{test.22Feb16.8ef.vcf => test.vcf}             |   0
 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 +++++-----------
 32 files changed, 1568 insertions(+), 777 deletions(-)
 create mode 100644 blbutil/BGZIPOutputStream.java
 create mode 100644 debian/beagle.install
 create mode 100644 debian/beagle.links
 create mode 100644 debian/beagle.manpages
 create mode 100644 debian/bref.1
 create mode 100644 debian/upstream.docs/README
 delete mode 100644 debian/upstream.docs/run.beagle.22Feb16.8ef.example
 create mode 100644 debian/upstream.docs/run.beagle.example
 rename debian/upstream.docs/{test.22Feb16.8ef.vcf => test.vcf} (100%)
 create mode 100644 vcf/R2Estimator.java
 create mode 100644 vcf/VcfRecBuilder.java

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