[med-svn] [beagle] 01/05: Update upstream docs

[Dylan Aïssi]

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

commit 282a7752354470032569947aaab0082366065388
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Tue Feb 14 22:25:04 2017 +0100

    Update upstream docs
---
 debian/changelog                        |  6 ++++++
 debian/upstream.docs/README             |  4 ++--
 debian/upstream.docs/release_notes      |  7 +++++++
 debian/upstream.docs/run.beagle.example | 34 ++++++++++++++++-----------------
 4 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 85f19e8..670f44a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+beagle (4.1~170121-6cc+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Tue, 07 Feb 2017 23:12:39 +0100
+
 beagle (4.1~160727-86a+dfsg-1) unstable; urgency=medium
 
   * New upstream release.
diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README
index 8b1534e..e4175b0 100644
--- a/debian/upstream.docs/README
+++ b/debian/upstream.docs/README
@@ -5,6 +5,6 @@
 
 	wget https://faculty.washington.edu/browning/beagle/release_notes
 	wget https://faculty.washington.edu/browning/beagle/beagle_4.1_03May16.pdf
-	wget https://faculty.washington.edu/browning/beagle/run.beagle.16Jun16.7e4.example -O run.beagle.example
-	wget https://faculty.washington.edu/browning/beagle/test.16Jun16.7e4.vcf.gz -O test.vcf.gz && \
+	wget https://faculty.washington.edu/browning/beagle/run.beagle.21Jan17.6cc.example -O run.beagle.example
+	wget https://faculty.washington.edu/browning/beagle/test.21Jan17.6cc.vcf.gz -O test.vcf.gz && \
 		gunzip test.vcf.gz
diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes
index f82ffa0..84870f7 100644
--- a/debian/upstream.docs/release_notes
+++ b/debian/upstream.docs/release_notes
@@ -113,3 +113,10 @@ Beagle 4.1 (23Jul16.fb0) release notes
 Beagle 4.1 (27Jul16.86a) release notes
 =============================================
 * Improve computational efficiency of genotype imputation.
+
+Beagle 4.1 (21Jan17.6cc) release notes
+=============================================
+* add gzip compression to IBD and HBD output files.
+* add ibdcm parameter to apply length threshold to output IBD/HBD segments.
+
+
diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example
index b27c9b2..09e72b1 100644
--- a/debian/upstream.docs/run.beagle.example
+++ b/debian/upstream.docs/run.beagle.example
@@ -1,53 +1,53 @@
 #!/bin/bash
-if [ ! -f beagle.27Jul16.86a.jar ]; then
+if [ ! -f beagle.21Jan17.6cc.jar ]; then
   echo
-  echo "Downloading beagle.27Jul16.86a.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.27Jul16.86a.jar
+  echo "Downloading beagle.21Jan17.6cc.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.21Jan17.6cc.jar
 fi
 
-if [ ! -f bref.27Jul16.86a.jar ]; then
+if [ ! -f bref.21Jan17.6cc.jar ]; then
   echo
-  echo "Downloading bref.27Jul16.86a.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref.27Jul16.86a.jar
+  echo "Downloading bref.21Jan17.6cc.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref.21Jan17.6cc.jar
 fi
 
 echo
 
-if [ ! -f test.27Jul16.86a.vcf.gz ]; then
+if [ ! -f test.21Jan17.6cc.vcf.gz ]; then
     echo
-    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
+    echo "*** Downloading some 1000 Genomes Project data to file: test.21Jan17.6cc.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.21Jan17.6cc.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.27Jul16.86a.vcf.gz target.27Jul16.86a.vcf.gz ***"
+echo "*** Creating test files: ref.21Jan17.6cc.vcf.gz target.21Jan17.6cc.vcf.gz ***"
 echo
-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
+zcat test.21Jan17.6cc.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.21Jan17.6cc.vcf.gz
+zcat test.21Jan17.6cc.vcf.gz | cut -f1-9,191-200 | gzip > target.21Jan17.6cc.vcf.gz
 
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.27Jul16.86a.jar gt=test.27Jul16.86a.vcf.gz out=out.gt
+java -jar beagle.21Jan17.6cc.jar gt=test.21Jan17.6cc.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"gl=\" argument ***"
 echo
-java -jar beagle.27Jul16.86a.jar gl=test.27Jul16.86a.vcf.gz out=out.gl
+java -jar beagle.21Jan17.6cc.jar gl=test.21Jan17.6cc.vcf.gz out=out.gl
 
 echo
 echo "*** Running test analysis with \"ref=\" argument ***"
 echo
-java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.vcf.gz gt=target.27Jul16.86a.vcf.gz out=out.ref
+java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.vcf.gz gt=target.21Jan17.6cc.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref\" file ***"
 echo
-java -jar bref.27Jul16.86a.jar ref.27Jul16.86a.vcf.gz
+java -jar bref.21Jan17.6cc.jar ref.21Jan17.6cc.vcf.gz
 
 echo
 echo "*** Running test analysis with \"bref=\" argument ***"
 echo
-java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.bref gt=target.27Jul16.86a.vcf.gz out=out.bref
+java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.bref gt=target.21Jan17.6cc.vcf.gz out=out.bref
 

-- 
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