Commit afea613d authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

Update upstream files

parent ed1abfd5

debian/upstream.docs/README

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@@ -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

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debian/upstream.docs/release_notes

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@@ -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

+16 −16
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#!/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