[med-svn] [Git][med-team/beagle][master] Update upstream files

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / beagle


Commits:
afea613d by Dylan Aïssi at 2019-11-21T05:56:49Z
Update upstream files

- - - - -


4 changed files:

- debian/upstream.docs/README
- debian/upstream.docs/beagle_5.1.pdf
- debian/upstream.docs/release_notes
- debian/upstream.docs/run.beagle.example


Changes:

=====================================
debian/upstream.docs/README
=====================================
@@ -4,7 +4,7 @@
 # They should be updated when upstream update them.
 
 	wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
-	wget https://faculty.washington.edu/browning/beagle/beagle_5.1_12Aug19.pdf -O beagle_5.1.pdf
-	wget https://faculty.washington.edu/browning/beagle/run.beagle.21Sep19.ec3.example -O run.beagle.example
-	wget https://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz -O test.vcf.gz && \
+	wget https://faculty.washington.edu/browning/beagle/beagle_5.1_08Nov19.pdf -O beagle_5.1.pdf
+	wget https://faculty.washington.edu/browning/beagle/run.beagle.20Nov19.573.example -O run.beagle.example
+	wget https://faculty.washington.edu/browning/beagle/test.20Nov19.573.vcf.gz -O test.vcf.gz && \
 		gunzip test.vcf.gz


=====================================
debian/upstream.docs/beagle_5.1.pdf
=====================================
Binary files a/debian/upstream.docs/beagle_5.1.pdf and b/debian/upstream.docs/beagle_5.1.pdf differ


=====================================
debian/upstream.docs/release_notes
=====================================
@@ -78,3 +78,10 @@ Beagle 5.1 (21Sep19.ec3) release notes
 ============================================
 * Fixed bugs when phasing or imputing using a reference panel
 
+Beagle 5.1 (08Nov19.3ec) release notes
+============================================
+* Add support for male, haploid chrom X genotypes\
+
+Beagle 5.1 (20Nov19.573) release notes
+============================================
+* Fixed bug when number of marker alleles is >= number of samples


=====================================
debian/upstream.docs/run.beagle.example
=====================================
@@ -1,47 +1,47 @@
 #!/bin/bash
-if [ ! -f beagle.21Sep19.ec3.jar ]; then
+if [ ! -f beagle.20Nov19.573.jar ]; then
   echo
-  echo "Downloading beagle.21Sep19.ec3.jar"
-  wget http://faculty.washington.edu/browning/beagle/beagle.21Sep19.ec3.jar
+  echo "Downloading beagle.20Nov19.573.jar"
+  wget http://faculty.washington.edu/browning/beagle/beagle.20Nov19.573.jar
 fi
 
-if [ ! -f bref3.21Sep19.ec3.jar ]; then
+if [ ! -f bref3.20Nov19.573.jar ]; then
   echo
-  echo "Downloading bref3.21Sep19.ec3.jar"
-  wget http://faculty.washington.edu/browning/beagle/bref3.21Sep19.ec3.jar
+  echo "Downloading bref3.20Nov19.573.jar"
+  wget http://faculty.washington.edu/browning/beagle/bref3.20Nov19.573.jar
 fi
 
 echo
 
-if [ ! -f test.21Sep19.ec3.vcf.gz ]; then
+if [ ! -f test.20Nov19.573.vcf.gz ]; then
     echo
-    echo "*** Downloading some 1000 Genomes Project data to file: test.21Sep19.ec3.vcf.gz ***"
-    wget http://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz
+    echo "*** Downloading some 1000 Genomes Project data to file: test.20Nov19.573.vcf.gz ***"
+    wget http://faculty.washington.edu/browning/beagle/test.20Nov19.573.vcf.gz
 fi
 
 echo
-echo "*** Creating test files: ref.21Sep19.ec3.vcf.gz target.21Sep19.ec3.vcf.gz ***"
+echo "*** Creating test files: ref.20Nov19.573.vcf.gz target.20Nov19.573.vcf.gz ***"
 echo
-zcat test.21Sep19.ec3.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.21Sep19.ec3.vcf.gz
-zcat test.21Sep19.ec3.vcf.gz | cut -f1-9,191-200 | gzip > target.21Sep19.ec3.vcf.gz
+zcat test.20Nov19.573.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.20Nov19.573.vcf.gz
+zcat test.20Nov19.573.vcf.gz | cut -f1-9,191-200 | gzip > target.20Nov19.573.vcf.gz
 
 echo
 echo "*** Running test analysis with \"gt=\" argument ***"
 echo
-java -jar beagle.21Sep19.ec3.jar gt=test.21Sep19.ec3.vcf.gz out=out.gt
+java -jar beagle.20Nov19.573.jar gt=test.20Nov19.573.vcf.gz out=out.gt
 
 echo
 echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
 echo
-java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.vcf.gz gt=target.21Sep19.ec3.vcf.gz out=out.ref
+java -jar beagle.20Nov19.573.jar ref=ref.20Nov19.573.vcf.gz gt=target.20Nov19.573.vcf.gz out=out.ref
 
 echo
 echo "*** Making \"bref3\" file ***"
 echo
-java -jar bref3.21Sep19.ec3.jar ref.21Sep19.ec3.vcf.gz > ref.21Sep19.ec3.bref3
+java -jar bref3.20Nov19.573.jar ref.20Nov19.573.vcf.gz > ref.20Nov19.573.bref3
 
 echo
 echo "*** Running test analysis with \"bref3\" file ***"
 echo
-java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.bref3 gt=target.21Sep19.ec3.vcf.gz out=out.bref3
+java -jar beagle.20Nov19.573.jar ref=ref.20Nov19.573.bref3 gt=target.20Nov19.573.vcf.gz out=out.bref3
 



View it on GitLab: https://salsa.debian.org/med-team/beagle/commit/afea613d160cd45e61ccdca803f98853ff75cfdc

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View it on GitLab: https://salsa.debian.org/med-team/beagle/commit/afea613d160cd45e61ccdca803f98853ff75cfdc
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