[med-svn] [beagle] 01/02: Update d/upstream.docs/*
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Jun 24 22:17:22 UTC 2017
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 dbd3ecf581dc33414dc7e53008254c41ad83904f
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Fri Jun 23 21:58:48 2017 +0200
Update d/upstream.docs/*
---
debian/beagle-doc.doc-base | 2 +-
debian/beagle-doc.install | 2 +-
debian/source/include-binaries | 2 +-
debian/upstream.docs/README | 6 ++---
debian/upstream.docs/beagle_4.1.pdf | Bin 0 -> 213752 bytes
debian/upstream.docs/beagle_4.1_09Feb16.pdf | Bin 657091 -> 0 bytes
debian/upstream.docs/release_notes | 3 +++
debian/upstream.docs/run.beagle.example | 34 ++++++++++++++--------------
8 files changed, 26 insertions(+), 23 deletions(-)
diff --git a/debian/beagle-doc.doc-base b/debian/beagle-doc.doc-base
index c67f7c2..7474114 100644
--- a/debian/beagle-doc.doc-base
+++ b/debian/beagle-doc.doc-base
@@ -3,7 +3,7 @@ Title: Beagle 4.1
Section: Science/Biology
Format: PDF
-Files: /usr/share/doc/beagle/beagle_4.1_09Feb16.pdf.gz
+Files: /usr/share/doc/beagle/beagle_4.1.pdf.gz
Format: HTML
Index: /usr/share/doc/beagle/api/index.html
diff --git a/debian/beagle-doc.install b/debian/beagle-doc.install
index dbe6834..51a61b6 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.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/upstream.docs/beagle_4.1.pdf /usr/share/doc/beagle/
debian/_jh_build.javadoc/api /usr/share/doc/beagle
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
index 0f26281..5fa962e 100644
--- a/debian/source/include-binaries
+++ b/debian/source/include-binaries
@@ -1,2 +1,2 @@
debian/upstream.docs/beagle_4.1_09Feb16.docx
-debian/upstream.docs/beagle_4.1_09Feb16.pdf
+debian/upstream.docs/beagle_4.1.pdf
diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README
index e4175b0..07ff43d 100644
--- a/debian/upstream.docs/README
+++ b/debian/upstream.docs/README
@@ -4,7 +4,7 @@
# 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.21Jan17.6cc.example -O run.beagle.example
- wget https://faculty.washington.edu/browning/beagle/test.21Jan17.6cc.vcf.gz -O test.vcf.gz && \
+ wget https://faculty.washington.edu/browning/beagle/beagle_4.1_21Jan17.pdf -O beagle_4.1.pdf
+ wget https://faculty.washington.edu/browning/beagle/run.beagle.08Jun17.d8b.example -O run.beagle.example
+ wget https://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz -O test.vcf.gz && \
gunzip test.vcf.gz
diff --git a/debian/upstream.docs/beagle_4.1.pdf b/debian/upstream.docs/beagle_4.1.pdf
new file mode 100644
index 0000000..b35ff3d
Binary files /dev/null and b/debian/upstream.docs/beagle_4.1.pdf differ
diff --git a/debian/upstream.docs/beagle_4.1_09Feb16.pdf b/debian/upstream.docs/beagle_4.1_09Feb16.pdf
deleted file mode 100644
index 28d0b55..0000000
Binary files a/debian/upstream.docs/beagle_4.1_09Feb16.pdf and /dev/null differ
diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes
index 84870f7..5cff96b 100644
--- a/debian/upstream.docs/release_notes
+++ b/debian/upstream.docs/release_notes
@@ -119,4 +119,7 @@ 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.
+Beagle 4.1 (08Jun17.d8b) release notes
+=============================================
+* Fix bug in reading bref files when impute=false
diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example
index 09e72b1..fde7c6f 100644
--- a/debian/upstream.docs/run.beagle.example
+++ b/debian/upstream.docs/run.beagle.example
@@ -1,53 +1,53 @@
#!/bin/bash
-if [ ! -f beagle.21Jan17.6cc.jar ]; then
+if [ ! -f beagle.08Jun17.d8b.jar ]; then
echo
- echo "Downloading beagle.21Jan17.6cc.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.21Jan17.6cc.jar
+ echo "Downloading beagle.08Jun17.d8b.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.08Jun17.d8b.jar
fi
-if [ ! -f bref.21Jan17.6cc.jar ]; then
+if [ ! -f bref.08Jun17.d8b.jar ]; then
echo
- echo "Downloading bref.21Jan17.6cc.jar"
- wget http://faculty.washington.edu/browning/beagle/bref.21Jan17.6cc.jar
+ echo "Downloading bref.08Jun17.d8b.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref.08Jun17.d8b.jar
fi
echo
-if [ ! -f test.21Jan17.6cc.vcf.gz ]; then
+if [ ! -f test.08Jun17.d8b.vcf.gz ]; then
echo
- 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
+ echo "*** Downloading some 1000 Genomes Project data to file: test.08Jun17.d8b.vcf.gz ***"
+ wget http://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz
fi
echo
-echo "*** Creating test files: ref.21Jan17.6cc.vcf.gz target.21Jan17.6cc.vcf.gz ***"
+echo "*** Creating test files: ref.08Jun17.d8b.vcf.gz target.08Jun17.d8b.vcf.gz ***"
echo
-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
+zcat test.08Jun17.d8b.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.08Jun17.d8b.vcf.gz
+zcat test.08Jun17.d8b.vcf.gz | cut -f1-9,191-200 | gzip > target.08Jun17.d8b.vcf.gz
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
-java -jar beagle.21Jan17.6cc.jar gt=test.21Jan17.6cc.vcf.gz out=out.gt
+java -jar beagle.08Jun17.d8b.jar gt=test.08Jun17.d8b.vcf.gz out=out.gt
echo
echo "*** Running test analysis with \"gl=\" argument ***"
echo
-java -jar beagle.21Jan17.6cc.jar gl=test.21Jan17.6cc.vcf.gz out=out.gl
+java -jar beagle.08Jun17.d8b.jar gl=test.08Jun17.d8b.vcf.gz out=out.gl
echo
echo "*** Running test analysis with \"ref=\" argument ***"
echo
-java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.vcf.gz gt=target.21Jan17.6cc.vcf.gz out=out.ref
+java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.vcf.gz gt=target.08Jun17.d8b.vcf.gz out=out.ref
echo
echo "*** Making \"bref\" file ***"
echo
-java -jar bref.21Jan17.6cc.jar ref.21Jan17.6cc.vcf.gz
+java -jar bref.08Jun17.d8b.jar ref.08Jun17.d8b.vcf.gz
echo
echo "*** Running test analysis with \"bref=\" argument ***"
echo
-java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.bref gt=target.21Jan17.6cc.vcf.gz out=out.bref
+java -jar beagle.08Jun17.d8b.jar ref=ref.08Jun17.d8b.bref gt=target.08Jun17.d8b.vcf.gz out=out.bref
--
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