[med-svn] [beagle] 04/04: Initial debian/
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Mar 26 08:07:13 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 653309e7d0b73235c9c9419300deb718073420ef
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Sat Mar 26 08:44:42 2016 +0100
Initial debian/
---
debian/beagle.1 | 186 +++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 24 +
debian/copyright | 118 ++
debian/doc-base | 6 +
debian/examples | 6 +
debian/lintian-overrides | 2 +
debian/rules | 37 +
debian/source/format | 1 +
debian/source/include-binaries | 1 +
debian/tests/control | 2 +
debian/tests/run-sample-analysis | 28 +
debian/upstream.docs/beagle_4.1_09Feb16.pdf | Bin 0 -> 657091 bytes
debian/upstream.docs/release_notes | 82 ++
.../upstream.docs/run.beagle.22Feb16.8ef.example | 53 +
debian/upstream.docs/test.22Feb16.8ef.vcf | 1386 ++++++++++++++++++++
debian/upstream/metadata | 33 +
debian/watch | 2 +
19 files changed, 1973 insertions(+)
diff --git a/debian/beagle.1 b/debian/beagle.1
new file mode 100644
index 0000000..93ec5be
--- /dev/null
+++ b/debian/beagle.1
@@ -0,0 +1,186 @@
+.\"
+.TH Beagle 1 "February 2016" "4.1"
+.SH NAME
+Beagle \- Genotype calling, genotype phasing and imputation of ungenotyped markers
+.SH SYNOPSIS
+.B java -Xmx[GB]g -jar /usr/share/beagle/beagle.jar [\fIoptions\fR]
+.SH DESCRIPTION
+Beagle performs genotype calling, genotype phasing, imputation of ungenotyped
+markers, and identity-by-descent segment detection. Genotypic imputation works
+on phased haplotypes using a Li and Stephens haplotype frequency model.
+Beagle also implements the Refined IBD algorithm for detecting
+homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.
+.SH OPTIONS
+.SS Data input/output parameters
+.TP
+\fBgt\fR=\fIfilename\fR
+Optional
+.br
+Specifies a VCF file containing a GT (genotype) format field for each marker.
+If a genotype contains the phased allele separator, "|", then Beagle will preserve the phase of the genotype during the analysis.
+If you use the gt argument, all genotypes in the output file will be phased and non-missing.
+.TP
+\fBgl\fR=\fIfilename\fR
+Optional
+.br
+Specifies a VCF file containing a GL or PL (genotype likelihood) format field for each marker.
+Any data in the GT format field will be ignored.
+If both GL and PL format fields are present for a marker, the GL format will be used.
+.TP
+\fBgtgl\fR=\fIfilename\fR
+Optional
+.br
+Specifies a VCF file containing a GT, GL or PL format field for each marker.
+If a genotype is non-missing, Beagle will ignore the genotype likelihood.
+If both GL and PL format fields are present for a marker, the GL field will be used.
+.TP
+\fBref\fR=\fIfilename\fR
+Optional
+.br
+Specifies a VCF file containing phased reference genotypes.
+See the impute parameter.
+.TP
+\fBout\fR=\fIprefix\fR
+Required
+.br
+Specifies the output filename prefix.
+The prefix may be an absolute or relative filename, but it cannot be a directory name.
+.TP
+\fBexcludesamples\fR=\fIfilename\fR
+Optional
+.br
+Specifies a file containing non-reference samples (one sample per line) to be excluded from the analysis and output files.
+.TP
+\fBexcludemarkers\fR=\fIfilename\fR
+Optional
+.br
+Specifies a file containing markers (one marker per line) to be excluded from the analysis and the output files.
+An excluded marker identifier can either be an identifier from the VCF record’s ID field or a genomic coordinate in the format: CHROM:POS.
+.TP
+\fBmap\fR=\fIfilename\fR
+Optional
+.br
+Specifies a PLINK format genetic map on the cM scale.
+HapMap GrCh36 and GrCh37 genetic maps in PLINK format are available for download from the Beagle website.
+Use of a genetic map is recommended if you are imputing ungenotyped markers.
+If no genetic map is specified, Beagle will assume a constant recombination rate of 1 cM / Mb.
+.TP
+\fBchrom\fR=\fIchrom:start-end\fR
+Optional
+.br
+Specifies a chromosome or chromosome interval using a chromosome identifier in the VCF file and the starting and ending positions of the interval.
+The entire chromosome, the beginning of the chromosome, and the end of a chromosome can be specified by \fBchrom\fR=[chrom], \fBchrom\fR=[chrom:-end], and \fBchrom\fR=[chrom:start-] respectively.
+.TP
+\fBmaxlr\fR=\fInumber_≥_1\fR
+Default = 5000
+.br
+Specifies the maximum likelihood ratio at a genotype.
+If M is the maximum of the likelihoods of each possible genotype, any likelihood that is less than (M ⁄ maxlr) is set to 0.0 to improve computational efficiency.
+
+.SS General parameters
+.TP
+\fBnthreads\fR=\fIpositive_integer\fR
+Default: machine-dependent
+.br
+Specifies the number of threads of execution.
+If no \fBnthreads\fR parameter is specified, the \fBnthreads\fR parameter will be set equal to the number of CPU cores on the host machine.
+.TP
+\fBlowmem\fR=\fItrue/false\fR
+Default = false
+.br
+Specifies whether a memory efficient algorithm should be used.
+The memory efficient algorithm increases run-time by a factor less than 2.0.
+.TP
+\fBwindow\fR=\fIpositive_integer\fR
+Default = 50000
+.br
+Specifies the number of markers to include in each sliding window.
+The \fBwindow\fR parameter must be at least twice as large as the overlap parameter.
+The \fBwindow\fR parameter controls the amount of memory used in the analysis.
+For human data, it is recommended that the \fBwindow\fR parameter be greater than or equal to the typical number of markers in 5 cM.
+.TP
+\fBoverlap\fR=\fIpositive_integer\fR
+Default = 3000
+.br
+Specifies the number of markers of overlap between sliding windows.
+For human data, it is recommended that the overlap be set to the typical number of markers in 0.5 cM (when \fBibd\fR=false) or 2.0 cM (when \fBibd\fR=true).
+.TP
+\fBseed\fR=\fIinteger\fR
+Default = -99999
+.br
+Specifies the seed for the random number generator.
+
+.SS Phasing and imputation parameters
+.TP
+\fBniterations\fR=\fInon-negative_integer\fR
+Default = 5
+.br
+Specifies the number of phasing iterations.
+The phasing iterations are preceded by 10 burn-in iterations which carry out the Beagle version 4.0 phasing algorithm.
+If you want to phase your data with the Beagle 4.0 phasing algorithm, use \fBniterations\fR=0.
+Accuracy and compute time increase with the number of iterations.
+.TP
+\fBimpute\fR=\fItrue/false\fR
+Default = true
+.br
+Specifies whether markers that are present in the reference panel but absent in your data will be imputed.
+This option has no effect if the \fBref\fR and \fBgt\fR arguments are not used.
+.TP
+\fBgprobs\fR=\fItrue/false\fR
+Default = false
+.br
+Specifies whether a GP (genotype probability) format field will be included in the output VCF file when imputing ungenotyped markers.
+By default, a GP fields is not printed because a DS (alternate allele dose) format field is always printed when imputing ungenotyped markers.
+.TP
+\fBne\fR=\fIinteger\fR
+Default = 1000000
+.br
+Specifies the effective population size when imputing ungenotyped markers.
+The default value is suitable for a large outbred human population.
+Smaller values in the hundreds or thousands for the \fBne\fR parameter are suggested for inbred human and animal populations.
+.TP
+\fBerr\fR=\fInon-negative_number\fR
+Default = 0.0001
+.br
+Specifies the allele miscall rate.
+The default value should give good results for most sequence and SNP array data.
+.TP
+\fBcluster\fR=\fInon-negative_number\fR
+Default = 0.005
+.br
+Specifies the maximum cM distance between individual markers that are combined into an aggregate marker when imputing ungenotyped markers.
+
+.SS IBD parameters
+.TP
+\fBibd\fR=\fItrue/false\fR
+Default = false
+.br
+Specifies whether IBD analysis will be performed when the \fBgt\fR argument is used.
+.TP
+\fBibdlod\fR=\fInon-negative_integer\fR
+Default = 3.0
+.br
+Specifies the minimum LOD score for reported IBD.
+.TP
+\fBibdscale\fR=\fInon-negative_number\fR
+Default: data-dependent
+.br
+Specifies the scale parameter used to build the haplotype frequency model for IBD analysis.
+If no \fBibdscale\fR parameter is specified the scale parameter for the IBD analysis will be set to max{2, sqrt[sample size]/100}, which we have found to work well for outbred populations.
+.TP
+\fBibdtrim\fR=\fInon-negative_integer\fR
+Default = 40
+.br
+Specifies the number of markers trimmed from the end of a shared haplotype when testing for IBD.
+Note: The default \fBibdtrim\fR parameter is designed for European samples genotyped with a 1M SNP array (~ 1 marker per 3 kb).
+For human SNP array data, it is recommended to set the \fBibdtrim\fR parameter to the typical number of markers in a 0.15 cM region.
+Pilot studies of randomly selected genomic regions can be used to fine-tune the values of the \fBibdtrim\fR parameter.
+
+.SH SEE ALSO
+.BR https://faculty.washington.edu/browning/beagle/beagle.html
+.SH AUTHOR
+Beagle was written by Brian L. Browning.
+.PP
+This manual page was written by Dylan Aïssi <bob.dybian at gmail.com>,
+for the Debian project (but may be used by others).
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d1381da
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+beagle (4.1~160222-8ef-1) UNRELEASED; urgency=low
+
+ * Initial Debian Release. (Closes: #????)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 12 Mar 2016 09:11:52 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..46ce506
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: beagle
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+Build-Depends: debhelper (>= 9), javahelper
+Build-Depends-Indep: default-jdk
+Testsuite: autopkgtest
+Standards-Version: 3.9.7
+#Vcs-Browser: https://anonscm.debian.org/git/debian-med/beagle.git
+#Vcs-Git: https://anonscm.debian.org/git/debian-med/beagle.git
+Homepage: https://faculty.washington.edu/browning/beagle/beagle.html
+
+Package: beagle
+Architecture: all
+Depends: ${java:Depends}, ${misc:Depends}
+Recommends: ${java:Recommends}
+Description: Genotype calling, genotype phasing and imputation of ungenotyped markers
+ Beagle performs genotype calling, genotype phasing, imputation of ungenotyped
+ markers, and identity-by-descent segment detection. Genotypic imputation works
+ on phased haplotypes using a Li and Stephens haplotype frequency model.
+ Beagle also implements the Refined IBD algorithm for detecting
+ homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8b9ef0b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,118 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Beagle
+Upstream-Contact: Brian L. Browning <browning at uw.edu>
+Source: https://faculty.washington.edu/browning/beagle/beagle.html
+
+Files: *
+Copyright: 2013-2016 Brian L. Browning
+License: GPL-3+
+
+Files: beagleutil/IntIntervalTree.java
+ beagleutil/BasicIntInterval.java
+ haplotype/GenotypeCorrection.java
+ sample/RecombSingleBaum.java
+ sample/DiploidStates.java
+ sample/RecombSingleBaumLevel.java
+ sample/RestrictedDag.java
+ sample/SamplerData.java
+ vcf/FuzzyGL.java
+Copyright: 2013-2016 Brian L. Browning
+License: Apache-2.0
+
+Files: net/sf/samtools/*
+Copyright: 2009 The Broad Institute (samtools)
+License: Expat
+
+Files: net/sf/samtools/Defaults.java
+Copyright: 2009 Tim Fennell and The Broad Institute (samtools)
+License: Expat
+
+Files: net/sf/samtools/util/HttpUtils.java
+ net/sf/samtools/util/SeekableFileStream.java
+ net/sf/samtools/util/SeekableHTTPStream.java
+Copyright: 2009 jrobinso and The Broad Institute (samtools)
+License: Expat
+
+Files: net/sf/samtools/util/SeekableStream.java
+Copyright: 2007-2009 The Broad Institute and Massachusetts Institute of Technology (samtools)
+License: GPL-2
+
+Files: debian/*
+Copyright: 2016 Dylan Aïssi <bob.dybian at gmail.com>
+License: GPL-3+
+
+Files: debian/upstream.docs/*
+Copyright: 2013-2016 Brian L. Browning
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the full text of the Apache Software License version 2 can
+ be found in the file `/usr/share/common-licenses/Apache-2.0'.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+License: GPL-2
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License in version
+ 2 of the license as published by the Free Software Foundation.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..ecdba36
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,6 @@
+Document: beagle
+Title: Beagle 4.1 - User Guide
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/beagle/beagle_4.1_09Feb16.pdf.gz
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..572d0d3
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,6 @@
+# Upstream samples files
+debian/upstream.docs/run.beagle.22Feb16.8ef.example
+debian/upstream.docs/test.22Feb16.8ef.vcf
+
+# Autopkgtest
+debian/tests/run-sample-analysis
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
new file mode 100644
index 0000000..e91c239
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1,2 @@
+# Beagle really requires Java 8 to run
+beagle: incompatible-java-bytecode-format
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..8933b11
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,37 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# debian/rules file for the Debian/GNU Linux beagle package
+# Copyright 2016 by Dylan Aïssi <bob.dybian at gmail.com>
+
+export JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_jh_build:
+ jh_build --javacopts="-source 1.8" --no-javadoc --main="main.Main" beagle.jar $(CURDIR)
+# jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="main.Main" beagle.jar $(CURDIR)
+
+override_dh_install:
+ dh_install beagle.jar /usr/share/beagle/
+
+override_dh_installman:
+ dh_installman debian/beagle.1
+
+override_dh_installchangelogs:
+ dh_installchangelogs debian/upstream.docs/release_notes
+
+override_dh_installdocs:
+ dh_installdocs debian/upstream.docs/beagle_4.1_09Feb16.pdf
+
+override_dh_link:
+ dh_link /usr/share/beagle/beagle.jar usr/bin/beagle
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compress xz
+ # mv beagle_22Feb16.8ef.orig.tar.xz beagle_4.1~160222-8ef.orig.tar.xz
+ # wget https://faculty.washington.edu/browning/beagle/beagle_4.1_09Feb16.pdf
+ # wget https://faculty.washington.edu/browning/beagle/release_notes
+ # wget https://faculty.washington.edu/browning/beagle/run.beagle.22Feb16.8ef.example
+ # wget http://faculty.washington.edu/browning/beagle/test.22Feb16.8ef.vcf.gz
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..db7abee
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/upstream.docs/beagle_4.1_09Feb16.pdf
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..3403f8a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-sample-analysis
+Depends: @
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
new file mode 100755
index 0000000..73c4e78
--- /dev/null
+++ b/debian/tests/run-sample-analysis
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+# http://dep.debian.net/deps/dep8/
+# Autopkgtest: Test if beagle run analysis correctly
+# Author: Dylan Aïssi <bob.dybian at gmail.com>
+# Last-Update: 2016-03-20
+
+pkg=beagle
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+
+BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar'
+
+# Beagle with gt argument
+$BEAGLE_TEST gt=test.22Feb16.8ef.vcf.gz out=out.gt
+
+# Beagle with gl argument
+$BEAGLE_TEST gl=test.22Feb16.8ef.vcf.gz out=out.gl
+
+# Beagle with ref argument
+zcat test.22Feb16.8ef.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.22Feb16.8ef.vcf.gz
+zcat test.22Feb16.8ef.vcf.gz | cut -f1-9,191-200 | gzip > target.22Feb16.8ef.vcf.gz
+$BEAGLE_TEST ref=ref.22Feb16.8ef.vcf.gz gt=target.22Feb16.8ef.vcf.gz out=out.ref
+
+rm -f $ADTTMP/*
+
diff --git a/debian/upstream.docs/beagle_4.1_09Feb16.pdf b/debian/upstream.docs/beagle_4.1_09Feb16.pdf
new file mode 100644
index 0000000..28d0b55
Binary files /dev/null and b/debian/upstream.docs/beagle_4.1_09Feb16.pdf differ
diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes
new file mode 100644
index 0000000..f198676
--- /dev/null
+++ b/debian/upstream.docs/release_notes
@@ -0,0 +1,82 @@
+Changes in Beagle 4.0
+=========================
+* Added use of a standard file format (VCF) for input/output.
+* Added a more powerful IBD segment detection algorithm: Refined IBD.
+* Added support for multi-threaded computation.
+* Added support for multi-allelic variants.
+* Added a faster imputation algorithm.
+* Eliminated use of temporary files.
+* Added a sliding window to control memory use.
+
+Beagle 4.0, r1274 release notes
+===============================
+* Increased default window parameter from 24000 to 50000.
+* Increased default buildwindow parameter from 500 to 1200.
+* Improved computational efficiency of model-building algorithm.
+* Included reference haplotypes in model when performing IBD detection.
+
+Beagle 4.0, r1389 release notes
+===============================
+* Decreased default singlescale parameter from 1.0 to 0.8.
+* Improved computational efficiency of model-building algorithm.
+* Improved source code architecture.
+
+Beagle 4.0, r1399 release notes (Mar 3, 2015)
+=============================================
+* maintenance release: fixed error in sample identifiers printed to
+ .warnings output file.
+
+Beagle 4.1 (03Oct15.284) release notes
+=============================================
+* Added a new, fast imputation algorithm.
+* Added a new, more accurate phasing algorithm.
+* Added support for bref-compressed reference files.
+* Eliminated the following command-line parameters:
+ 1) usephase
+ 2) nsamples
+ 3) burnin-its
+ 4) phase-its
+ 5) imputation-its
+ 6) singlescale
+ 7) duoscale
+ 8) trioscale
+* Added the following command-line parameters:
+ 1) niterations
+ 2) modelscale (replaces singlescale parameter)
+ 3) ne
+ 4) err
+ 5) cluster
+* Removed option for modeling parent-offspring duos and trios during phasing
+ (the ped parameter has no effect). These options are still available in
+ Beagle 4.0.
+* Require gt command line argument when performing imputation of ungenotyped
+ markers or identity-by-descent segment detection.
+* Change output genotypes to be unphased when gl or gtgl command line
+ argument is used.
+
+Beagle 4.1 (09Nov15.d2a) release notes
+=============================================
+* Major update to the bref program to add support for structural variants.
+ Note: Older versions of bref are not compatible with the current version.
+* Minor update to fix bugs.
+
+Beagle 4.1 (14Jan16.841) release notes
+=============================================
+* Expand effect of nthreads parameter to common ForkJoinPool.
+* Changed default nthreads parameter from 1 to 4.
+
+Beagle 4.1 (27Jan16.aae) release notes
+=============================================
+* Minor update to fix a bug in handling structural variants.
+* Remove DS field from VCF output when there are there are no imputed markers.
+
+Beagle 4.1 (09Feb16.2b7) release notes
+=============================================
+* Improve an error message.
+* Change default number of threads to be number of processors on host.
+
+Beagle 4.1 (22Feb16.8ef) release notes
+=============================================
+* Minor update to the model-building algorithm.
+* Minor update to fix bugs.
+
diff --git a/debian/upstream.docs/run.beagle.22Feb16.8ef.example b/debian/upstream.docs/run.beagle.22Feb16.8ef.example
new file mode 100644
index 0000000..0cf6f02
--- /dev/null
+++ b/debian/upstream.docs/run.beagle.22Feb16.8ef.example
@@ -0,0 +1,53 @@
+#!/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/test.22Feb16.8ef.vcf b/debian/upstream.docs/test.22Feb16.8ef.vcf
new file mode 100644
index 0000000..61c505d
--- /dev/null
+++ b/debian/upstream.docs/test.22Feb16.8ef.vcf
@@ -0,0 +1,1386 @@
+##fileformat=VCFv4.1
+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
+##ALT=<ID=DEL,Description="Deletion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
+##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
+##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
+##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
+##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
+##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
+##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
+##reference=GRCh37
+##reference=GRCh37
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00104 HG00106 HG00108 HG00109 HG00110 HG00111 HG00112 HG00113 HG00114 HG00116 HG00117 HG00118 HG00119 HG00120 HG00121 HG00122 HG00123 HG00124 HG00125 HG00126 HG00127 HG00128 HG00129 HG00130 HG00131 HG00133 HG00134 HG00135 HG00136 HG00137 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00146 HG00148 HG00149 HG00150 HG00151 HG00152 HG00154 HG00155 HG00156 HG00158 HG00159 HG00160 HG0017 [...]
+22 20000086 rs138720731 T C 100 PASS AC=7;RSQ=0.8454;AVGPOST=0.9983;AA=T;AN=2184;LDAF=0.0040;THETA=0.0001;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0003;AF=0.0032;AFR_AF=0.01 GT:DS:GL 0/0:0.000:-0.03,-1.19,-5.00 0/0:0.000:-0.04,-1.05,-5.00 0/0:0.000:-0.07,-0.85,-5.00 0/0:0.000:-0.03,-1.18,-5.00 0/0:0.000:-0.06,-0.87,-5.00 0/0:0.000:-0.03,-1.14,-5.00 0/0:0.000:-0.06,-0.90,-5.00 0/0:0.000:-0.23,-0.45,-1.28 0/0:0.000:-0.03,-1.20,-5.00 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.11,-0.65,-4.40 0/0:0.000: [...]
+22 20000146 rs73387790 G A 100 PASS LDAF=0.0169;RSQ=0.9482;THETA=0.0004;AA=G;AN=2184;AVGPOST=0.9972;VT=SNP;SNPSOURCE=LOWCOV;AC=36;ERATE=0.0003;AF=0.02;AFR_AF=0.07;EUR_AF=0.0013 GT:DS:GL 0/0:0.000:-0.00,-2.68,-5.00 0/0:0.000:-0.07,-0.82,-5.00 0/0:0.000:-0.13,-0.60,-3.05 0/0:0.000:-0.03,-1.24,-5.00 0/0:0.000:-0.18,-0.47,-3.08 0/0:0.000:-0.06,-0.90,-5.00 0/0:0.000:-0.01,-1.48,-5.00 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.16,-0.51,-2.63 0/0:0.000:-0.01,-1.76,-5.00 0/0:0.000:-0.10,-0.67,-5.0 [...]
+22 20000199 rs183293480 A C 100 PASS LDAF=0.0009;THETA=0.0004;AN=2184;AVGPOST=0.9990;VT=SNP;AA=A;RSQ=0.6274;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;AF=0.0005;EUR_AF=0.0013 GT:DS:GL 0/0:0.000:-0.00,-2.04,-5.00 0/0:0.000:-0.07,-0.82,-3.47 0/0:0.000:-0.07,-0.83,-5.00 0/0:0.000:-0.03,-1.12,-5.00 0/0:0.000:-0.11,-0.64,-4.10 0/0:0.000:-0.12,-0.62,-3.85 0/0:0.000:-0.01,-1.47,-5.00 0/0:0.000:-0.01,-1.54,-5.00 0/0:0.000:-0.10,-0.70,-4.70 0/0:0.000:-0.03,-1.18,-5.00 0/0:0.000:-0.16,-0.50,-3.30 0/0:0.00 [...]
+22 20000291 rs185807825 G T 100 PASS ERATE=0.0005;AVGPOST=0.9983;AA=G;AN=2184;LDAF=0.0015;VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5564;AC=2;THETA=0.0003;AF=0.0009;ASN_AF=0.0035 GT:DS:GL 0/0:0.000:-0.00,-2.06,-5.00 0/0:0.000:-0.07,-0.83,-5.00 0/0:0.000:-0.02,-1.27,-5.00 0/0:0.000:-0.01,-1.77,-5.00 0/0:0.000:-0.19,-0.45,-2.14 0/0:0.000:-0.11,-0.66,-5.00 0/0:0.000:-0.03,-1.17,-5.00 0/0:0.000:-0.02,-1.33,-5.00 0/0:0.000:-0.18,-0.48,-2.43 0/0:0.000:-0.05,-0.93,-5.00 0/0:0.000:-0.18,-0.46,-2.76 0/0:0.00 [...]
+22 20000428 rs55902548 G T 100 PASS AC=323;AVGPOST=0.9983;AA=G;AN=2184;VT=SNP;RSQ=0.9949;LDAF=0.1473;SNPSOURCE=LOWCOV;ERATE=0.0003;THETA=0.0003;AF=0.15;ASN_AF=0.0017;AMR_AF=0.15;AFR_AF=0.31;EUR_AF=0.15 GT:DS:GL 1/0:1.000:-5.00,0.00,-5.00 0/0:0.000:-0.35,-0.43,-0.73 0/1:1.000:-1.81,-0.01,-2.95 0/0:0.000:-0.01,-1.79,-5.00 0/0:0.000:-0.06,-0.86,-5.00 1/0:1.000:-0.19,-0.46,-2.18 0/0:0.000:-0.10,-0.68,-5.00 0/1:1.000:-4.40,-0.03,-1.12 0/1:1.000:-5.00,-0.69,-0.10 0/0:0.000:-0.10,-0.69,-4.70 0/ [...]
+22 20000683 rs142720028 A G 100 PASS AVGPOST=0.9985;AN=2184;LDAF=0.0015;VT=SNP;RSQ=0.5718;AA=A;SNPSOURCE=LOWCOV;THETA=0.0007;ERATE=0.0003;AC=2;AF=0.0009;AFR_AF=0.0041 GT:DS:GL 0/0:0.000:-0.10,-0.70,-4.70 0/0:0.000:-0.07,-0.85,-5.00 0/0:0.000:-0.00,-2.28,-5.00 0/0:0.000:-0.02,-1.46,-5.00 0/0:0.000:-0.04,-1.09,-5.00 0/0:0.000:-0.04,-1.06,-5.00 0/0:0.000:-0.00,-2.63,-5.00 0/0:0.000:-0.00,-2.89,-5.00 0/0:0.000:-0.02,-1.46,-5.00 0/0:0.000:-0.05,-0.94,-5.00 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.00 [...]
+22 20000771 rs114690707 A C 100 PASS ERATE=0.0004;AC=28;AN=2184;RSQ=0.9857;VT=SNP;AA=A;LDAF=0.0130;SNPSOURCE=LOWCOV;AVGPOST=0.9995;THETA=0.0003;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 GT:DS:GL 0/0:0.000:-0.03,-1.17,-5.00 0/0:0.000:-0.07,-0.81,-4.70 0/0:0.000:-0.01,-1.79,-5.00 0/0:0.000:-0.02,-1.39,-5.00 0/0:0.000:-0.03,-1.11,-5.00 0/0:0.000:-0.00,-2.12,-5.00 0/0:0.000:-0.00,-2.05,-5.00 0/0:0.000:-0.01,-1.77,-5.00 0/0:0.000:-0.00,-1.99,-5.00 0/0:0.000:-0.00,-2.07,-5.00 0/0:0.000:-0.03,-1.12,-5.00 [...]
+22 20000793 rs189842693 T C 100 PASS ERATE=0.0004;RSQ=0.7411;AA=T;AN=2184;AVGPOST=0.9981;AC=6;VT=SNP;SNPSOURCE=LOWCOV;LDAF=0.0031;THETA=0.0003;AF=0.0027;ASN_AF=0.0035;EUR_AF=0.01 GT:DS:GL 0/0:0.000:-0.05,-0.94,-5.00 0/0:0.000:-0.01,-1.78,-5.00 0/0:0.000:-0.01,-1.53,-5.00 0/0:0.000:-0.03,-1.14,-5.00 0/0:0.000:-0.02,-1.35,-5.00 0/0:0.000:-0.02,-1.35,-5.00 0/0:0.000:-0.00,-2.07,-5.00 0/0:0.000:-0.01,-1.71,-5.00 0/0:0.000:-0.01,-1.66,-5.00 0/0:0.100:-0.03,-1.18,-5.00 0/0:0.000:-0.11,-0.66,-4 [...]
+22 20000810 rs147349046 C T 100 PASS AA=C;AVGPOST=0.9994;AC=28;AN=2184;VT=SNP;RSQ=0.9802;SNPSOURCE=LOWCOV;ERATE=0.0003;LDAF=0.0128;THETA=0.0003;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 GT:DS:GL 0/0:0.000:-0.10,-0.68,-4.70 0/0:0.000:-0.01,-1.78,-5.00 0/0:0.000:-0.04,-1.06,-5.00 0/0:0.000:-0.10,-0.70,-4.70 0/0:0.000:-0.01,-1.62,-5.00 0/0:0.000:-0.04,-1.08,-5.00 0/0:0.000:-0.03,-1.22,-5.00 0/0:0.000:-0.08,-0.77,-4.10 0/0:0.000:-0.01,-1.93,-5.00 0/0:0.000:-0.03,-1.20,-5.00 0/0:0.000:-0.11,-0.66,-4.70 [...]
+22 20000814 rs183154520 T C 100 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0002;AA=T;AN=2184;RSQ=0.4507;VT=SNP;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0012;AF=0.0005;AMR_AF=0.0028 GT:DS:GL 0/0:0.000:-0.05,-0.94,-5.00 0/0:0.000:-0.01,-1.79,-5.00 0/0:0.000:-0.04,-1.01,-5.00 0/0:0.000:-0.10,-0.69,-4.70 0/0:0.000:-0.02,-1.36,-5.00 0/0:0.000:-0.04,-1.07,-5.00 0/0:0.000:-0.03,-1.22,-5.00 0/0:0.000:-0.05,-0.97,-5.00 0/0:0.000:-0.00,-1.96,-5.00 0/0:0.000:-0.05,-0.93,-5.00 0/0:0.000:-0.19,-0.46,-2.42 0/0:0.00 [...]
+22 20000864 rs187930998 G A 100 PASS AC=7;THETA=0.0014;AA=g;AN=2184;LDAF=0.0037;RSQ=0.8089;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9982;AF=0.0032;ASN_AF=0.01 GT:DS:GL 0/0:0.000:-0.05,-0.94,-5.00 0/0:0.000:-0.12,-0.63,-3.25 0/0:0.000:-0.08,-0.79,-3.17 0/0:0.000:-0.11,-0.65,-4.10 0/0:0.000:-0.10,-0.70,-5.00 0/0:0.000:-0.06,-0.86,-5.00 0/0:0.000:-0.05,-0.95,-5.00 0/0:0.000:-0.09,-0.75,-3.25 0/0:0.000:-0.11,-0.65,-3.44 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000: [...]
+22 20000882 rs148068532 C G 100 PASS THETA=0.0004;AN=2184;AC=8;VT=SNP;RSQ=0.9358;AA=c;LDAF=0.0038;SNPSOURCE=LOWCOV;ERATE=0.0003;AVGPOST=0.9995;AF=0.0037;AMR_AF=0.0028;AFR_AF=0.01 GT:DS:GL 0/0:0.000:-0.03,-1.19,-5.00 0/0:0.000:-0.11,-0.63,-3.28 0/0:0.000:-0.13,-0.61,-2.22 0/0:0.000:-0.06,-0.92,-5.00 0/0:0.000:-0.04,-1.10,-5.00 0/0:0.000:-0.18,-0.46,-3.07 0/0:0.000:-0.06,-0.90,-5.00 0/0:0.000:-0.08,-0.77,-4.10 0/0:0.000:-0.18,-0.48,-2.44 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.48,-0.48,-0 [...]
+22 20000950 rs1978233 T G 100 PASS ERATE=0.0005;AA=G;AN=2184;AC=2157;VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.8667;LDAF=0.9857;AVGPOST=0.9950;THETA=0.0003;AF=0.99;ASN_AF=1.00;AMR_AF=0.98;AFR_AF=1.00;EUR_AF=0.97 GT:DS:GL 1/1:2.000:-5.00,-0.69,-0.10 1/1:1.750:-2.26,-0.02,-1.48 1/1:2.000:-5.00,-1.17,-0.03 1/1:1.650:-5.00,-1.30,-0.02 1/1:2.000:-5.00,-1.25,-0.03 1/1:2.000:-5.00,-1.18,-0.03 1/1:2.000:-5.00,-1.19,-0.03 1/1:2.000:-5.00,-2.96,-0.00 1/1:2.000:-5.00,-1.40,-0.02 1/1:2.000:-5.00,-0.67,-0.10 1/1 [...]
+22 20000975 rs141800233 G A 100 PASS ERATE=0.0004;AVGPOST=0.9994;AA=G;AN=2184;THETA=0.0005;VT=SNP;RSQ=0.9593;AC=15;SNPSOURCE=LOWCOV;LDAF=0.0069;AF=0.01;AMR_AF=0.0028;AFR_AF=0.03 GT:DS:GL 0/0:0.000:-0.18,-0.47,-2.79 0/0:0.000:-0.06,-0.86,-5.00 0/0:0.000:-0.01,-1.47,-5.00 0/0:0.000:-0.03,-1.13,-5.00 0/0:0.000:-0.18,-0.47,-3.08 0/0:0.000:-0.04,-1.08,-5.00 0/0:0.000:-0.10,-0.69,-4.70 0/0:0.000:-0.02,-1.39,-5.00 0/0:0.000:-0.18,-0.48,-2.47 0/0:0.000:-0.04,-1.08,-5.00 0/0:0.000:-0.06,-0.89,-5. [...]
+22 20001001 rs192051979 T C 100 PASS LDAF=0.0027;RSQ=0.6246;AA=T;AN=2184;VT=SNP;ERATE=0.0008;AVGPOST=0.9973;SNPSOURCE=LOWCOV;AC=4;THETA=0.0003;AF=0.0018;ASN_AF=0.01;AMR_AF=0.0028 GT:DS:GL 0/0:0.000:-0.19,-0.46,-2.74 0/0:0.000:-0.02,-1.31,-5.00 0/0:0.000:-0.13,-0.60,-2.20 0/0:0.000:-0.06,-0.91,-5.00 0/0:0.000:-0.18,-0.47,-3.07 0/0:0.000:-0.18,-0.47,-3.12 0/0:0.000:-0.18,-0.48,-2.48 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.18,-0.48,-2.46 0/0:0.000:-0.01,-1.48,-5.00 0/0:0.000:-0.19,-0.46,-2 [...]
+22 20001006 rs2079702 G A 100 PASS ERATE=0.0004;RSQ=0.9917;LDAF=0.8452;THETA=0.0004;AN=2184;AVGPOST=0.9972;VT=SNP;AA=A;AC=1847;SNPSOURCE=LOWCOV;AF=0.85;ASN_AF=0.61;AMR_AF=0.83;AFR_AF=0.99;EUR_AF=0.94 GT:DS:GL 1/1:2.000:-3.25,-0.47,-0.18 1/0:1.000:-4.70,-0.19,-0.45 1/1:2.000:-1.89,-0.03,-1.19 0/1:1.100:-5.00,-0.92,-0.06 1/0:1.000:-0.18,-0.47,-3.06 1/1:2.000:-5.00,-0.71,-0.09 1/1:2.000:-3.09,-0.47,-0.18 1/1:2.000:-0.48,-0.48,-0.48 1/1:2.000:-2.89,-0.45,-0.19 1/1:2.000:-5.00,-1.65,-0.01 1/1 [...]
+22 20001016 rs183256914 C T 100 PASS AA=C;AN=2184;LDAF=0.0054;AC=6;VT=SNP;ERATE=0.0011;RSQ=0.5737;SNPSOURCE=LOWCOV;THETA=0.0003;AVGPOST=0.9940;AF=0.0027;AMR_AF=0.01;EUR_AF=0.0013 GT:DS:GL 0/0:0.000:-0.18,-0.46,-2.76 0/0:0.000:-0.12,-0.63,-3.25 0/0:0.000:-0.23,-0.46,-1.22 0/0:0.000:-0.06,-0.91,-5.00 0/0:0.000:-0.18,-0.47,-3.08 0/0:0.000:-0.11,-0.66,-5.00 0/0:0.000:-0.18,-0.46,-2.99 0/0:0.000:-0.48,-0.48,-0.48 0/0:0.000:-0.10,-0.70,-4.70 0/0:0.000:-0.01,-1.62,-5.00 0/0:0.000:-0.11,-0.65,-5 [...]
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+22 20099752 rs73389792 G T 100 PASS ERATE=0.0004;THETA=0.0002;LDAF=0.0790;AA=G;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=170;RSQ=0.9947;AVGPOST=0.9992;AF=0.08;ASN_AF=0.07;AMR_AF=0.01;AFR_AF=0.15;EUR_AF=0.06 GT:DS:GL 0/0:0.000:-0.00,-2.54,-5.00 0/0:0.000:-0.07,-0.83,-5.00 0/0:0.050:-0.12,-0.61,-3.06 0/0:0.000:-0.05,-0.94,-5.00 0/0:0.000:-0.11,-0.64,-4.00 0/0:0.000:-0.18,-0.47,-3.11 0/1:1.000:-4.22,-0.00,-5.00 0/0:0.000:-0.17,-0.50,-2.49 0/0:0.000:-0.04,-1.11,-5.00 0/0:0.000:-0.02,-1.36,-5.00 0/1 [...]
+22 20099891 rs1048659 C G 100 PASS THETA=0.0002;AA=G;AN=2184;RSQ=0.9976;AVGPOST=0.9996;LDAF=0.0787;VT=SNP;SNPSOURCE=LOWCOV;AC=170;ERATE=0.0003;AF=0.08;ASN_AF=0.07;AMR_AF=0.01;AFR_AF=0.15;EUR_AF=0.06 GT:DS:GL 0/0:0.000:-0.00,-2.05,-5.00 0/0:0.000:-0.05,-1.00,-5.00 0/0:0.000:-0.01,-1.52,-5.00 0/0:0.000:-0.00,-2.25,-5.00 0/0:0.000:-0.01,-1.91,-5.00 0/0:0.000:-0.00,-2.57,-5.00 0/1:1.000:-5.00,-0.00,-3.62 0/0:0.000:-0.12,-0.60,-3.17 0/0:0.000:-0.13,-0.61,-2.27 0/0:0.000:0.00,-5.00,-5.00 0/1:1 [...]
+22 20099941 rs113958995 T A 100 PASS THETA=0.0004;AA=T;AN=2184;LDAF=0.0125;VT=SNP;AVGPOST=0.9998;RSQ=0.9922;SNPSOURCE=LOWCOV;AC=27;ERATE=0.0003;AF=0.01;AMR_AF=0.0028;AFR_AF=0.05 GT:DS:GL 0/0:0.000:-0.00,-2.00,-5.00 0/0:0.000:-0.12,-0.62,-2.41 0/0:0.000:-0.05,-0.99,-4.70 0/0:0.000:-0.11,-0.66,-4.70 0/0:0.000:-0.05,-1.00,-5.00 0/0:0.000:-0.00,-2.80,-5.00 0/0:0.000:-0.00,-3.66,-5.00 0/0:0.000:-0.19,-0.45,-2.20 0/0:0.000:-0.05,-0.98,-4.22 0/0:0.000:0.00,-5.00,-5.00 0/0:0.000:0.00,-5.00,-5.00 [...]
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..9128460
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,33 @@
+Contact: Brian L. Browning <browning at uw.edu>
+Name: Beagle
+Reference:
+ - Author: Sharon R. Browning and Brian L. Browning
+ Title: "Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering"
+ Journal: The American Journal of Human Genetics
+ Volume: 81
+ Number: 5
+ Pages: 1084-1097
+ Year: 2007
+ DOI: 10.1086/521987
+ URL: http://www.cell.com/ajhg/abstract/S0002-9297(07)63882-8
+ eprint: http://www.cell.com/ajhg/pdf/S0002-9297(07)63882-8.pdf
+ - Author: Brian L. Browning and Sharon R. Browning
+ Title: "Genotype Imputation with Millions of Reference Samples"
+ Journal: The American Journal of Human Genetics
+ Volume: 98
+ Number: 1
+ Pages: 116-126
+ Year: 2016
+ DOI: 10.1016/j.ajhg.2015.11.020
+ URL: http://www.cell.com/ajhg/abstract/S0002-9297(15)00491-7
+ eprint: http://www.cell.com/ajhg/pdf/S0002-9297(15)00491-7.pdf
+ - Author: Brian L. Browning and Sharon R. Browning
+ Title: "Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data"
+ Journal: Genetics
+ Volume: 194
+ Number: 2
+ Pages: 459-471
+ Year: 2013
+ DOI: 10.1534/genetics.113.150029
+ URL: http://www.genetics.org/content/194/2/459
+ eprint: http://www.genetics.org/content/194/2/459.full-text.pdf+html
\ No newline at end of file
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a5dbf6e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+https://faculty.washington.edu/browning/beagle/beagle.html beagle.(.*).src\.zip
--
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