[med-svn] [beagle] 03/03: Update d/*

[Dylan Aïssi]

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

commit 8cc60e6ea03048b517f0114db44ebe462cc70a16
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat Oct 1 00:16:36 2016 +0200

    Update d/*
---
 debian/changelog                        |  8 +++++++-
 debian/upstream.docs/release_notes      | 19 ++++++++++++++++--
 debian/upstream.docs/run.beagle.example | 34 ++++++++++++++++-----------------
 3 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 67e0315..782a160 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,13 @@
+beagle (4.1~160727-86a+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Fri, 30 Sep 2016 23:53:12 +0200
+
 beagle (4.1~160616-7e4+dfsg-1) unstable; urgency=medium
 
   * New upstream release.
-  * Rework autopkgtest to simply update.
+  * Rework autopkgtest to simplify update.
   * Remove unnecessary Depends and Recommends for beagle-doc.
   * Update uscan options.
   * Build the tool bref.jar.
diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes
index a68216e..f82ffa0 100644
--- a/debian/upstream.docs/release_notes
+++ b/debian/upstream.docs/release_notes
@@ -94,7 +94,22 @@ Beagle 4.1 (14Jun16.dd3) release notes
 =============================================
 * Improve accuracy and computational efficiency of genotype imputation.
 
-Beagle 4.1 (16Jun16.7e4) release notes
+Beagle 4.1 (16Jun.7e4) release notes
 =============================================
-* Simplify code for writing BGZIP files
+* Simplify code for writing BGZIP files.
 
+Beagle 4.1 (27Jun16.b16) release notes
+=============================================
+* Correct an output VCF file meta-information line.
+
+Beagle 4.1 (05Jul16.587) release notes
+=============================================
+* Minor update to fix a bug.
+
+Beagle 4.1 (23Jul16.fb0) release notes
+=============================================
+* Minor update to fix a bug.
+
+Beagle 4.1 (27Jul16.86a) release notes
+=============================================
+* Improve computational efficiency of genotype imputation.
diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example
index 44a39c1..b27c9b2 100644
--- a/debian/upstream.docs/run.beagle.example
+++ b/debian/upstream.docs/run.beagle.example
@@ -1,53 +1,53 @@
 #!/bin/bash
-if [ ! -f beagle.16Jun16.7e4.jar ]; then
+if [ ! -f beagle.27Jul16.86a.jar ]; then
   echo
-  echo "Downloading beagle.16Jun16.7e4.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.16Jun16.7e4.jar
+  echo "Downloading beagle.27Jul16.86a.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.27Jul16.86a.jar
 fi
 
-if [ ! -f bref.16Jun16.7e4.jar ]; then
+if [ ! -f bref.27Jul16.86a.jar ]; then
   echo
-  echo "Downloading bref.16Jun16.7e4.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref.16Jun16.7e4.jar
+  echo "Downloading bref.27Jul16.86a.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref.27Jul16.86a.jar
 fi
 
 echo
 
-if [ ! -f test.16Jun16.7e4.vcf.gz ]; then
+if [ ! -f test.27Jul16.86a.vcf.gz ]; then
     echo
-    echo "*** Downloading some 1000 Genomes Project data to file: test.16Jun16.7e4.vcf.gz ***"
-    wget http://faculty.washington.edu/browning/beagle/test.16Jun16.7e4.vcf.gz
+    echo "*** Downloading some 1000 Genomes Project data to file: test.27Jul16.86a.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.27Jul16.86a.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.16Jun16.7e4.vcf.gz target.16Jun16.7e4.vcf.gz ***"
+echo "*** Creating test files: ref.27Jul16.86a.vcf.gz target.27Jul16.86a.vcf.gz ***"
 echo
-zcat test.16Jun16.7e4.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.16Jun16.7e4.vcf.gz
-zcat test.16Jun16.7e4.vcf.gz | cut -f1-9,191-200 | gzip > target.16Jun16.7e4.vcf.gz
+zcat test.27Jul16.86a.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.27Jul16.86a.vcf.gz
+zcat test.27Jul16.86a.vcf.gz | cut -f1-9,191-200 | gzip > target.27Jul16.86a.vcf.gz
 
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.16Jun16.7e4.jar gt=test.16Jun16.7e4.vcf.gz out=out.gt
+java -jar beagle.27Jul16.86a.jar gt=test.27Jul16.86a.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"gl=\" argument ***"
 echo
-java -jar beagle.16Jun16.7e4.jar gl=test.16Jun16.7e4.vcf.gz out=out.gl
+java -jar beagle.27Jul16.86a.jar gl=test.27Jul16.86a.vcf.gz out=out.gl
 
 echo
 echo "*** Running test analysis with \"ref=\" argument ***"
 echo
-java -jar beagle.16Jun16.7e4.jar ref=ref.16Jun16.7e4.vcf.gz gt=target.16Jun16.7e4.vcf.gz out=out.ref
+java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.vcf.gz gt=target.27Jul16.86a.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref\" file ***"
 echo
-java -jar bref.16Jun16.7e4.jar ref.16Jun16.7e4.vcf.gz
+java -jar bref.27Jul16.86a.jar ref.27Jul16.86a.vcf.gz
 
 echo
 echo "*** Running test analysis with \"bref=\" argument ***"
 echo
-java -jar beagle.16Jun16.7e4.jar ref=ref.16Jun16.7e4.bref gt=target.16Jun16.7e4.vcf.gz out=out.bref
+java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.bref gt=target.27Jul16.86a.vcf.gz out=out.bref
 

-- 
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