[med-svn] [beagle] branch upstream updated (ef336ca -> 3db72fd)
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Jun 25 13:05:45 UTC 2016
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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
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