[med-svn] [beagle] 02/06: Update upstream docs
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Jun 25 13:05:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository beagle.
commit 0559ec6c2dd10c812dd5aca1f33d39651b3b2238
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Sat Jun 25 00:29:11 2016 +0200
Update upstream docs
---
debian/beagle-doc.install | 4 +-
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
6 files changed, 83 insertions(+), 55 deletions(-)
diff --git a/debian/beagle-doc.install b/debian/beagle-doc.install
index 3175374..dbe6834 100644
--- a/debian/beagle-doc.install
+++ b/debian/beagle-doc.install
@@ -1,5 +1,5 @@
debian/tests/run-sample-analysis /usr/share/doc/beagle/examples/
-debian/upstream.docs/run.beagle.22Feb16.8ef.example /usr/share/doc/beagle/examples/
-debian/upstream.docs/test.22Feb16.8ef.vcf /usr/share/doc/beagle/examples/
+debian/upstream.docs/run.beagle.example /usr/share/doc/beagle/examples/
+debian/upstream.docs/test.vcf /usr/share/doc/beagle/examples/
debian/upstream.docs/beagle_4.1_09Feb16.pdf /usr/share/doc/beagle/
debian/_jh_build.javadoc/api /usr/share/doc/beagle
diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README
new file mode 100644
index 0000000..8b1534e
--- /dev/null
+++ b/debian/upstream.docs/README
@@ -0,0 +1,10 @@
+# Author: Dylan A�ssi <bob.dybian at gmail.com>
+# Last-Update: 2016-06-17
+# These files were downloaded from https://faculty.washington.edu/browning/beagle/
+# They should be updated when upstream update them.
+
+ 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 && \
+ gunzip test.vcf.gz
diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes
index f198676..a68216e 100644
--- a/debian/upstream.docs/release_notes
+++ b/debian/upstream.docs/release_notes
@@ -80,3 +80,21 @@ Beagle 4.1 (22Feb16.8ef) release notes
* Minor update to the model-building algorithm.
* Minor update to fix bugs.
+Beagle 4.1 (15Apr16.63e) release notes
+Beagle 4.1 (22Apr16.1cf) release notes
+=============================================
+* Minor updates to fix a bug in the genotype calling algorithm.
+
+Beagle 4.1 (03May16.862) release notes
+=============================================
+* Improve INFO field accuracy for low-MAF markers.
+* Add "IMP" INFO field to mark imputed markers.
+
+Beagle 4.1 (14Jun16.dd3) release notes
+=============================================
+* Improve accuracy and computational efficiency of genotype imputation.
+
+Beagle 4.1 (16Jun16.7e4) release notes
+=============================================
+* Simplify code for writing BGZIP files
+
diff --git a/debian/upstream.docs/run.beagle.22Feb16.8ef.example b/debian/upstream.docs/run.beagle.22Feb16.8ef.example
deleted file mode 100644
index 0cf6f02..0000000
--- a/debian/upstream.docs/run.beagle.22Feb16.8ef.example
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/bin/bash
-if [ ! -f beagle.22Feb16.8ef.jar ]; then
- echo
- echo "Downloading beagle.22Feb16.8ef.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.22Feb16.8ef.jar
-fi
-
-if [ ! -f bref.22Feb16.8ef.jar ]; then
- echo
- echo "Downloading bref.22Feb16.8ef.jar"
- wget http://faculty.washington.edu/browning/beagle/bref.22Feb16.8ef.jar
-fi
-
-echo
-
-if [ ! -f test.22Feb16.8ef.vcf.gz ]; then
- echo
- echo "*** Downloading some 1000 Genomes Project data to file: test.22Feb16.8ef.vcf.gz ***"
- wget http://faculty.washington.edu/browning/beagle/test.22Feb16.8ef.vcf.gz
-fi
-
-echo
-echo "*** Creating test files: ref.22Feb16.8ef.vcf.gz target.22Feb16.8ef.vcf.gz ***"
-echo
-zcat test.22Feb16.8ef.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.22Feb16.8ef.vcf.gz
-zcat test.22Feb16.8ef.vcf.gz | cut -f1-9,191-200 | gzip > target.22Feb16.8ef.vcf.gz
-
-
-echo
-echo "*** Running test analysis with \"gt=\" argument ***"
-echo
-java -jar beagle.22Feb16.8ef.jar gt=test.22Feb16.8ef.vcf.gz out=out.gt
-
-echo
-echo "*** Running test analysis with \"gl=\" argument ***"
-echo
-java -jar beagle.22Feb16.8ef.jar gl=test.22Feb16.8ef.vcf.gz out=out.gl
-
-echo
-echo "*** Running test analysis with \"ref=\" argument ***"
-echo
-java -jar beagle.22Feb16.8ef.jar ref=ref.22Feb16.8ef.vcf.gz gt=target.22Feb16.8ef.vcf.gz out=out.ref
-
-echo
-echo "*** Making \"bref\" file ***"
-echo
-java -jar bref.22Feb16.8ef.jar ref.22Feb16.8ef.vcf.gz
-
-echo
-echo "*** Running test analysis with \"bref=\" argument ***"
-echo
-java -jar beagle.22Feb16.8ef.jar ref=ref.22Feb16.8ef.bref gt=target.22Feb16.8ef.vcf.gz out=out.bref
-
diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example
new file mode 100644
index 0000000..44a39c1
--- /dev/null
+++ b/debian/upstream.docs/run.beagle.example
@@ -0,0 +1,53 @@
+#!/bin/bash
+if [ ! -f beagle.16Jun16.7e4.jar ]; then
+ echo
+ echo "Downloading beagle.16Jun16.7e4.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.16Jun16.7e4.jar
+fi
+
+if [ ! -f bref.16Jun16.7e4.jar ]; then
+ echo
+ echo "Downloading bref.16Jun16.7e4.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref.16Jun16.7e4.jar
+fi
+
+echo
+
+if [ ! -f test.16Jun16.7e4.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
+fi
+
+echo
+echo "*** Creating test files: ref.16Jun16.7e4.vcf.gz target.16Jun16.7e4.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
+
+
+echo
+echo "*** Running test analysis with \"gt=\" argument ***"
+echo
+java -jar beagle.16Jun16.7e4.jar gt=test.16Jun16.7e4.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
+
+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
+
+echo
+echo "*** Making \"bref\" file ***"
+echo
+java -jar bref.16Jun16.7e4.jar ref.16Jun16.7e4.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
+
diff --git a/debian/upstream.docs/test.22Feb16.8ef.vcf b/debian/upstream.docs/test.vcf
similarity index 100%
rename from debian/upstream.docs/test.22Feb16.8ef.vcf
rename to debian/upstream.docs/test.vcf
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