[med-svn] [beagle] 01/05: Update upstream docs
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Tue Feb 14 21:40:37 UTC 2017
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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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