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bob.dybian-guest pushed a commit to branch master
in repository eagle.

commit 22a815ffb92ff1f4e8d8c69e5c414f8ebaf4a33d
Author: Dylan Aïssi <bob.dyb...@gmail.com>
Date:   Sun Sep 18 23:16:04 2016 +0200

    Initial debian/*
---
 debian/README.Debian                 |  28 +++++++++
 debian/README.source                 |   9 +++
 debian/bio-eagle-examples.install    |   2 +
 debian/bio-eagle.1                   | 117 +++++++++++++++++++++++++++++++++++
 debian/bio-eagle.install             |   1 +
 debian/bio-eagle.links               |   2 +
 debian/bio-eagle.manpages            |   1 +
 debian/changelog                     |   5 ++
 debian/compat                        |   1 +
 debian/control                       |  46 ++++++++++++++
 debian/copyright                     |  30 +++++++++
 debian/patches/Clarify_license.patch |  16 +++++
 debian/patches/Fix_FTBFS.patch       |  34 ++++++++++
 debian/patches/Makefile_config.patch |  49 +++++++++++++++
 debian/patches/series                |   3 +
 debian/rules                         |  13 ++++
 debian/source/format                 |   1 +
 debian/tests/control                 |   2 +
 debian/tests/run-sample-analysis     |  52 ++++++++++++++++
 debian/upstream.changelog            |  26 ++++++++
 debian/upstream/metadata             |  16 +++++
 debian/watch                         |   2 +
 22 files changed, 456 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..29e9c3a
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,28 @@
+Name conflict with this eagle from Harvard University for genotype phasing
+  and the eagle from CadSoft for electronics
+=============================================
+
+  Due to a name conflict with /usr/bin/eagle from the eagle from
+  CadSoft for electronics the main executable needs to be renamed.
+  This eagle package provides the binaries:
+  
+    /usr/bin/bio-eagle
+
+  To remain compatible with local user scripts using the name eagle
+  the real executable is provided under the PATH
+  
+    /usr/lib/debian-med/bin/eagle
+
+  So if you want to use bio-eagle with its original name just do the
+  following:  Set the PATH variable like
+
+    export PATH=/usr/lib/debian-med/bin:$PATH
+
+  The PATH can be set very easily by making use of the feature of
+  the med-config package of the Debian Med Blend.  Once med-config
+  is installed for Bash users who create a file ${HOME}/.blends
+  containing the string "debian-med" the PATH is automatically
+  extended and thus users who consider themselves Debian Med users
+  have access to the originally named executables.
+  
+ -- Dylan Aïssi <bob.dyb...@gmail.com>  Sun, 18 Sep 2016 23:08:34 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..390f706
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,9 @@
+Name conflict with this eagle from Harvard University for genotype phasing
+  and the eagle from CadSoft for electronics
+=============================================
+
+  Due to a name conflict with the eagle from CadSoft for electronics,
+  the source package of this eagle from Harvard University for genotype
+  phasing was renamed to bio-eagle according to upstream.
+  
+ -- Dylan Aïssi <bob.dyb...@gmail.com>  Sun, 18 Sep 2016 23:08:34 +0200
diff --git a/debian/bio-eagle-examples.install 
b/debian/bio-eagle-examples.install
new file mode 100644
index 0000000..4e0822b
--- /dev/null
+++ b/debian/bio-eagle-examples.install
@@ -0,0 +1,2 @@
+example/* /usr/share/doc/bio-eagle/examples/
+tables /usr/share/doc/bio-eagle/examples/
diff --git a/debian/bio-eagle.1 b/debian/bio-eagle.1
new file mode 100644
index 0000000..f33a3fb
--- /dev/null
+++ b/debian/bio-eagle.1
@@ -0,0 +1,117 @@
+.\"
+.TH EAGLE 1 "September 2016" "2.3"
+.SH NAME
+eagle \- Haplotype phasing within a genotyped cohort or using a phased 
reference panel
+.SH SYNOPSIS
+.B eagle
+[\fIoptions\fR]
+.SH DESCRIPTION
+Eagle estimates haplotype phase either within a genotyped cohort or using a
+phased reference panel. The basic idea of the Eagle1 algorithm is to harness
+identity-by-descent among distant relatives—which is pervasive at very large
+sample sizes but rare among smaller numbers of samples—to rapidly call phase
+using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a
+full probabilistic model similar to the diploid Li-Stephens model used by
+previous HMM-based methods.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print this help
+.TP
+\fB\-\-geneticMapFile\fR arg
+HapMap genetic map provided with download:
+tables/genetic_map_hg##.txt.gz
+.TP
+\fB\-\-outPrefix\fR arg
+prefix for output files
+.TP
+\fB\-\-numThreads\fR arg (=1)
+number of computational threads
+.SS "Input options for phasing without a reference:"
+.TP
+\fB\-\-bfile\fR arg
+prefix of PLINK .fam, .bim, .bed files
+.TP
+\fB\-\-bfilegz\fR arg
+prefix of PLINK .fam.gz, .bim.gz, .bed.gz files
+.TP
+\fB\-\-fam\fR arg
+PLINK .fam file (note: file names ending in \&.gz are auto\-decompressed)
+.TP
+\fB\-\-bim\fR arg
+PLINK .bim file
+.TP
+\fB\-\-bed\fR arg
+PLINK .bed file
+.TP
+\fB\-\-vcf\fR arg
+[compressed] VCF/BCF file containing input genotypes
+.TP
+\fB\-\-remove\fR arg
+file(s) listing individuals to ignore (no header; FID IID must be first two 
columns)
+.TP
+\fB\-\-exclude\fR arg
+file(s) listing SNPs to ignore (no header; SNP ID must be first column)
+.TP
+\fB\-\-maxMissingPerSnp\fR arg (=0.1)
+QC filter: max missing rate per SNP
+.TP
+\fB\-\-maxMissingPerIndiv\fR arg (=0.1)
+QC filter: max missing rate per person
+.SS "Input/output options for phasing using a reference panel:"
+.TP
+\fB\-\-vcfRef\fR arg
+tabix\-indexed [compressed] VCF/BCF file for reference haplotypes
+.TP
+\fB\-\-vcfTarget\fR arg
+tabix\-indexed [compressed] VCF/BCF file for target genotypes
+.TP
+\fB\-\-vcfOutFormat\fR arg (=z)
+b|u|z|v: compressed BCF (b), uncomp BCF (u), compressed VCF (z), uncomp VCF (v)
+.TP
+\fB\-\-noImpMissing\fR
+disable imputation of missing ./. target genotypes
+.TP
+\fB\-\-allowRefAltSwap\fR
+allow swapping of REF/ALT in target vs. ref VCF
+.SS "Region selection options:"
+.TP
+\fB\-\-chrom\fR arg (=0)
+chromosome to analyze (if input has many)
+.TP
+\fB\-\-bpStart\fR arg (=0)
+minimum base pair position to analyze
+.TP
+\fB\-\-bpEnd\fR arg (=1e9)
+maximum base pair position to analyze
+.TP
+\fB\-\-bpFlanking\fR arg (=0)
+(ref\-mode only) flanking region to use during phasing but discard in output
+.SS "Algorithm options:"
+.TP
+\fB\-\-Kpbwt\fR arg (=10000)
+number of conditioning haplotypes
+.TP
+\fB\-\-pbwtIters\fR arg (=0)
+number of PBWT phasing iterations (0=auto)
+.TP
+\fB\-\-expectIBDcM\fR arg (=2.0)
+expected length of haplotype copying (cM)
+.TP
+\fB\-\-histFactor\fR arg (=0)
+history length multiplier (0=auto)
+.TP
+\fB\-\-genoErrProb\fR arg (=0.003)
+estimated genotype error probability
+.TP
+\fB\-\-pbwtOnly\fR
+in non\-ref mode, use only PBWT iters (automatic for sequence data)
+.TP
+\fB\-\-v1\fR
+use Eagle1 phasing algorithm (instead of default Eagle2 algorithm)
+.PP
+.SH SEE ALSO
+.BR https://data.broadinstitute.org/alkesgroup/Eagle/
+.SH COPYRIGHT
+Copyright \(co 2015\-2016 Harvard University.
+Distributed under the GNU GPLv3+ open source license.
diff --git a/debian/bio-eagle.install b/debian/bio-eagle.install
new file mode 100644
index 0000000..03d1fe1
--- /dev/null
+++ b/debian/bio-eagle.install
@@ -0,0 +1 @@
+src/eagle usr/lib/debian-med/bin/
diff --git a/debian/bio-eagle.links b/debian/bio-eagle.links
new file mode 100644
index 0000000..ca0fb84
--- /dev/null
+++ b/debian/bio-eagle.links
@@ -0,0 +1,2 @@
+usr/lib/debian-med/bin/eagle   usr/bin/bio-eagle
+usr/share/man/man1/bio-eagle.1.gz      
usr/lib/debian-med/share/man/man1/eagle.1.gz
\ No newline at end of file
diff --git a/debian/bio-eagle.manpages b/debian/bio-eagle.manpages
new file mode 100644
index 0000000..ba8fde5
--- /dev/null
+++ b/debian/bio-eagle.manpages
@@ -0,0 +1 @@
+debian/bio-eagle.1
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..58e1279
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bio-eagle (2.3-1) UNRELEASED; urgency=low
+
+  * Initial release. (Closes: #838070)
+
+ -- Dylan Aïssi <bob.dyb...@gmail.com>  Sun, 18 Sep 2016 23:08:34 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f11c82a
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
\ No newline at end of file
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..1534ec4
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,46 @@
+Source: bio-eagle
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dyb...@gmail.com>
+Build-Depends: debhelper (>= 9),
+ libopenblas-dev,
+ libboost-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libhts-dev,
+ zlib1g-dev
+Testsuite: autopkgtest
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/eagle.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/eagle.git
+Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/
+
+Package: bio-eagle
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: med-config (>= 2.1)
+Suggests: bio-eagle-examples
+Description: Haplotype phasing within a genotyped cohort or using a phased 
reference panel
+ Eagle estimates haplotype phase either within a genotyped cohort or using a
+ phased reference panel. The basic idea of the Eagle1 algorithm is to harness
+ identity-by-descent among distant relatives—which is pervasive at very large
+ sample sizes but rare among smaller numbers of samples—to rapidly call phase
+ using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a
+ full probabilistic model similar to the diploid Li-Stephens model used by
+ previous HMM-based methods.
+
+Package: bio-eagle-examples
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: bio-eagle
+Description: Examples for bio-eagle
+ Eagle estimates haplotype phase either within a genotyped cohort or using a
+ phased reference panel. The basic idea of the Eagle1 algorithm is to harness
+ identity-by-descent among distant relatives—which is pervasive at very large
+ sample sizes but rare among smaller numbers of samples—to rapidly call phase
+ using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a
+ full probabilistic model similar to the diploid Li-Stephens model used by
+ previous HMM-based methods.
+ .
+ This package provides some example data for eagle.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7340695
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Eagle
+Upstream-Contact: Po-Ru Loh <loh at hsph.harvard.edu>
+Source: https://data.broadinstitute.org/alkesgroup/Eagle/
+
+Files: *
+Copyright: 2015 Harvard University, Po-Ru Loh
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2016 Dylan Aïssi <bob.dyb...@gmail.com>
+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 complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/patches/Clarify_license.patch 
b/debian/patches/Clarify_license.patch
new file mode 100644
index 0000000..9d1d146
--- /dev/null
+++ b/debian/patches/Clarify_license.patch
@@ -0,0 +1,16 @@
+Author: Dylan Aïssi
+Description: Clarify the license.
+Last-Update: 2016-09-13
+Forwarded: DONE
+
+--- a/src/EagleMain.cpp
++++ b/src/EagleMain.cpp
+@@ -214,7 +214,7 @@
+   cout << endl;
+ 
+   cout << "Copyright (C) 2015-2016 Harvard University." << endl;
+-  cout << "Distributed under the GNU GPLv3 open source license." << endl << 
endl;
++  cout << "Distributed under the GNU GPLv3+ open source license." << endl << 
endl;
+ 
+   //cout << "Boost version: " << BOOST_LIB_VERSION << endl;
+   //cout << endl;
diff --git a/debian/patches/Fix_FTBFS.patch b/debian/patches/Fix_FTBFS.patch
new file mode 100644
index 0000000..7d07b3e
--- /dev/null
+++ b/debian/patches/Fix_FTBFS.patch
@@ -0,0 +1,34 @@
+Author: Po-Ru Loh
+Description: Fix FTBFS with GCC for non_amd64 builds.
+Last-Update: 2016-09-13
+
+--- a/src/EagleImpMiss.cpp
++++ b/src/EagleImpMiss.cpp
+@@ -18,6 +18,7 @@
+ 
+ #include <vector>
+ #include <iostream>
++#include <cmath>
+ 
+ #include "HapHedge.hpp"
+ #include "MemoryUtils.hpp"
+--- a/src/FileUtils.cpp
++++ b/src/FileUtils.cpp
+@@ -151,7 +151,7 @@
+   }
+ 
+   AutoGzIfstream::operator bool() const {
+-    return boost_in;
++    return !boost_in.fail();
+   }
+ 
+   AutoGzIfstream& AutoGzIfstream::read(char *s, std::streamsize n) {
+@@ -209,7 +209,7 @@
+   }
+ 
+   AutoGzOfstream::operator bool() const {
+-    return boost_out;
++    return !boost_out.fail();
+   }
+ 
+ }
diff --git a/debian/patches/Makefile_config.patch 
b/debian/patches/Makefile_config.patch
new file mode 100644
index 0000000..fb6c9a7
--- /dev/null
+++ b/debian/patches/Makefile_config.patch
@@ -0,0 +1,49 @@
+Author: Dylan Aïssi
+Description: Configure the makefile.
+Last-Update: 2016-09-13
+Forwarded: not-needed
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -5,14 +5,14 @@
+ 
+ ### modify these paths to local BLAS, Boost and htslib install directories
+ LBLAS = -lopenblas # alternatively -llapack (just need sgemm_)
+-BLAS_DIR = /opt/openblas/0.2.14/lib
+-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
+-HTSLIB_DIR = /groups/price/poru/external_software/htslib/htslib-1.3
++BLAS_DIR =
++BOOST_INSTALL_DIR =
++HTSLIB_DIR =
+ 
+ 
+ ### these paths are used only for static linking
+-ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
+-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
++ZLIB_STATIC_DIR = # probably unnecessary on most systems
++GLIBC_STATIC_DIR =
+ 
+ 
+ ifeq ($(strip ${linking}),)
+@@ -31,7 +31,7 @@
+       LFLAGS += -pg
+ endif
+ 
+-CFLAGS += -std=c++0x -msse -msse2 -fopenmp -Wall
++CFLAGS += -std=c++0x -fopenmp -Wall
+ LFLAGS += -fopenmp
+ 
+ 
+@@ -93,10 +93,10 @@
+ .PHONY: clean
+ 
+ $T: ${OMAIN}
+-      ${CC} ${LFLAGS} -o $T ${OMAIN} $L
++      ${CC} ${LFLAGS} ${LDFLAGS} -o $T ${OMAIN} $L
+ 
+ %.o: %.cpp
+-      ${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
++      ${CC} ${CFLAGS} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
+ EagleMain.o: Version.hpp
+ Eagle.o: Version.hpp
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..bf8f5c9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+Makefile_config.patch
+Fix_FTBFS.patch
+Clarify_license.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9ed8893
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+       dh $@ --sourcedirectory=src
+
+override_dh_installchangelogs:
+       dh_installchangelogs debian/upstream.changelog
+
+get-orig-source-git-snapshot:
+       wget https://github.com/poruloh/Eagle/archive/master.tar.gz
+       # mv master.tar.gz bio-eagle_2.3+git160722.orig.tar.gz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..46ebe02
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
\ No newline at end of file
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..3403f8a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-sample-analysis
+Depends: @
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
new file mode 100755
index 0000000..21b2d59
--- /dev/null
+++ b/debian/tests/run-sample-analysis
@@ -0,0 +1,52 @@
+#!/bin/sh -e
+# http://dep.debian.net/deps/dep8/
+# Autopkgtest: Test if (bio-)eagle run analysis correctly
+# Author: Dylan Aïssi <bob.dyb...@gmail.com>
+# Last-Update: 2016-09-17
+
+pkg=bio-eagle
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+
+gunzip EUR_test.bed.gz
+gunzip EUR_test.bim.gz
+gunzip EUR_test.fam.gz
+gunzip phased.sample.gz
+gunzip ref.bcf.gz
+
+# From upstream run_example.sh
+bio-eagle \
+    --bfile=EUR_test \
+    --geneticMapFile=USE_BIM \
+    --chrom=21 \
+    --outPrefix=phased \
+    --numThreads=4
+
+bio-eagle \
+    --bfile=EUR_test \
+    --geneticMapFile=USE_BIM \
+    --chrom=21 \
+    --outPrefix=phased \
+    --numThreads=4 \
+    --v1
+
+bio-eagle \
+    --bfile=EUR_test \
+    --geneticMapFile=USE_BIM \
+    --chrom=21 \
+    --outPrefix=phased \
+    --numThreads=4 \
+    --v1fast
+
+# From upstream run_example_ref.sh
+bio-eagle \
+    --vcfRef=ref.bcf \
+    --vcfTarget=target.vcf.gz \
+    --geneticMapFile=tables/genetic_map_hg19_example.txt.gz \
+    --outPrefix=target.phased
+
+rm -rf $ADTTMP/*
+
diff --git a/debian/upstream.changelog b/debian/upstream.changelog
new file mode 100644
index 0000000..8399e7a
--- /dev/null
+++ b/debian/upstream.changelog
@@ -0,0 +1,26 @@
+# Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/
+
+Version 2.3 (July 22, 2016):
+    Added support for phasing chrX (and added chrX genetic map).
+    Optimized performance when phasing sequence data without a reference.
+    Disallowed REF/ALT swaps for indels even with --allowRefAltSwap.
+    Improved error-checking.
+Version 2.2 (July 15, 2016):
+    Added support for VCF/BCF input in non-reference mode.
+    Reduced RAM when phasing sequence data in non-ref mode.
+    Fixed bug causing crashes on samples with no hets.
+    Fixed bug causing crashes on target hets monomorphic in the reference.
+    Fixed other minor bugs. (Thanks to Stephan Ripke, Giulio Genovese, 
Christian Fuchsberger, and Sebastian Schoenherr for reporting bugs and 
assisting with debugging.)
+Version 2.1 (July 6, 2016):
+    Replaced in-sample imputation algorithm; new algorithm fills in missing 
genotypes during phasing (improving overall efficiency on sequence data).
+    Added experimental --usePS parameter for specifying FORMAT:PS phase set 
constraints (--usePS=1 for soft constraint; --usePS=2 for harder constraint).
+    Fixed minor error in recombination probability formula.
+    Fixed minor bug (incorrect memset call) in first step of 
non-reference-based phasing algorithm.
+    Fixed bug in input-checking (incorrect exit upon finding ”.” genotypes in 
target VCF).
+Version 2.0.5 (May 26, 2016): Fixed bug in genetic map interpolation when 
using the --chrom flag.
+Version 2.0.4 (May 24, 2016): Added error check for 0 Mb / 0 cM region span; 
added error check for memory allocation failures.
+Version 2.0.3 (May 19, 2016): Added error check for 0 or 1 SNPs in 
intersection of target and ref.
+Version 2.0.2 (May 19, 2016): Added --allowRefAltSwap flag to allow swapping 
of REF/ALT in target vs. ref VCF.
+Version 2.0.1 (May 9, 2016): Fixed bug in region handling (thanks to Petr 
Danecek); added command line to VCF header.
+Version 2.0 (May 3, 2016): Initial release of Eagle2.
+Version 1.0 (September 23, 2015): Initial release of Eagle1.
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..ad266b2
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,16 @@
+Contact: Po-Ru Loh <loh at hsph.harvard.edu>
+Name: eagle
+Reference:
+  - Author: Po-Ru Loh and Pier Francesco Palamara and Alkes L Price
+    Title: "Fast and accurate long-range phasing in a UK Biobank cohort"
+    Journal: Nature Genetics
+    Year: 2016
+    DOI: 10.1038/ng.3571
+    URL: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3571.html
+  - Author: Po-Ru Loh and Petr Danecek and Pier Francesco Palamara and 
Christian Fuchsberger and Yakir A Reshef and Hilary K Finucane and Sebastian 
Schoenherr and Lukas Forer and Shane McCarthy and Goncalo R Abecasis and 
Richard Durbin and Alkes L Price
+    Title: "Reference-based phasing using the Haplotype Reference Consortium 
panel"
+    Journal: BioRxiv
+    Year: 2016
+    DOI: 10.1101/052308
+    URL: http://biorxiv.org/content/early/2016/05/10/052308
+    eprint: http://biorxiv.org/content/early/2016/05/10/052308.full.pdf
\ No newline at end of file
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b122855
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+ https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ 
Eagle_v(\d\S*)\.tar\.gz

-- 
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