[med-svn] [beagle] 06/06: Build the tool bref.jar
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Jun 25 13:05:44 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 5b41984f78d73fc89a7cc13bbfb5898855a7bd0d
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Sat Jun 25 13:03:57 2016 +0200
Build the tool bref.jar
---
debian/beagle.1 | 2 +-
debian/beagle.install | 2 ++
debian/beagle.links | 2 ++
debian/beagle.manpages | 2 ++
debian/bref.1 | 44 ++++++++++++++++++++++++++++++++++++++++
debian/changelog | 1 +
debian/rules | 16 ++-------------
debian/tests/run-sample-analysis | 5 ++++-
8 files changed, 58 insertions(+), 16 deletions(-)
diff --git a/debian/beagle.1 b/debian/beagle.1
index 93ec5be..8cfa37e 100644
--- a/debian/beagle.1
+++ b/debian/beagle.1
@@ -3,7 +3,7 @@
.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]
+\fBjava -Xmx[GB]g -jar /usr/share/beagle/beagle.jar\fR [\fIoptions\fR]
.SH DESCRIPTION
Beagle performs genotype calling, genotype phasing, imputation of ungenotyped
markers, and identity-by-descent segment detection. Genotypic imputation works
diff --git a/debian/beagle.install b/debian/beagle.install
new file mode 100644
index 0000000..2a092ae
--- /dev/null
+++ b/debian/beagle.install
@@ -0,0 +1,2 @@
+beagle.jar /usr/share/beagle/
+bref.jar /usr/share/beagle/
\ No newline at end of file
diff --git a/debian/beagle.links b/debian/beagle.links
new file mode 100644
index 0000000..6388f3a
--- /dev/null
+++ b/debian/beagle.links
@@ -0,0 +1,2 @@
+/usr/share/beagle/beagle.jar usr/bin/beagle
+/usr/share/beagle/bref.jar usr/bin/bref
\ No newline at end of file
diff --git a/debian/beagle.manpages b/debian/beagle.manpages
new file mode 100644
index 0000000..8189d4d
--- /dev/null
+++ b/debian/beagle.manpages
@@ -0,0 +1,2 @@
+debian/beagle.1
+debian/bref.1
diff --git a/debian/bref.1 b/debian/bref.1
new file mode 100644
index 0000000..893ca3d
--- /dev/null
+++ b/debian/bref.1
@@ -0,0 +1,44 @@
+.\"
+.TH Bref 1 "June 2016" "4.1"
+.SH NAME
+Bref \- Tool for compressing diploid reference VCF files for the Beagle program.
+
+.SH SYNOPSIS
+\fBjava -jar /usr/share/beagle/bref.jar\fR [\fIvcf\fR]
+.br
+or
+.br
+\fBjava -jar /usr/share/beagle/bref.jar\fR [\fIbref\fR]
+
+.SH DESCRIPTION
+Bref is a tool for compressing diploid reference VCF files.
+.br
+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
+.TP
+\fBvcf\fR=\fIfilename\fR
+Creates a .bref file.
+.br
+Specifies a VCF file with phase, non-missing genotype data.
+If the VCF file is a text file, its filename should end in ".vcf".
+If the VCF file is GZIP-compressed, its filename should end in ".vcf.gz".
+.TP
+\fBbref\fR=\fIfilename\fR
+Prints a .vcf file to standard out.
+.br
+Specifies a binary reference file.
+The filename should end in ".bref".
+
+.SH SEE ALSO
+.BR https://faculty.washington.edu/browning/beagle/beagle.html
+.SH AUTHOR
+Beagle and Bref were 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
index e916963..eeb9f2a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ beagle (4.1~160616-7e4+dfsg-1) UNRELEASED; urgency=low
* Rework autopkgtest to simply update.
* Remove unnecessary Depends and Recommends for beagle-doc.
* Update uscan options.
+ * Build the tool bref.jar.
-- Dylan Aïssi <bob.dybian at gmail.com> Sat, 25 Jun 2016 00:31:32 +0200
diff --git a/debian/rules b/debian/rules
index 579969e..106a2a1 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,24 +10,12 @@ override_jh_build:
# This ugly thing below because jh_build search .java files in .pc folder so FTBFS...
rm -rf $(CURDIR)/.pc/
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
+ jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="vcf.Bref" bref.jar $(CURDIR)
override_dh_installchangelogs:
dh_installchangelogs debian/upstream.docs/release_notes
-override_dh_link:
- dh_link /usr/share/beagle/beagle.jar usr/bin/beagle
-
get-orig-source:
uscan --verbose --force-download
- # mv beagle_22Feb16.8ef+dfsg.orig.tar.xz beagle_4.1~160222-8ef+dfsg.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
+ # mv beagle_16Jun16.7e4+dfsg.orig.tar.xz beagle_4.1~160616-7e4+dfsg.orig.tar.xz
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
index dadde77..7b7d938 100755
--- a/debian/tests/run-sample-analysis
+++ b/debian/tests/run-sample-analysis
@@ -16,6 +16,7 @@ BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar'
# Generate necessary files
zcat test.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.vcf.gz
zcat test.vcf.gz | cut -f1-9,191-200 | gzip > target.vcf.gz
+java -jar /usr/share/beagle/bref.jar ref.vcf.gz
# Beagle with gt argument
$BEAGLE_TEST gt=test.vcf.gz out=out.gt
@@ -26,5 +27,7 @@ $BEAGLE_TEST gl=test.vcf.gz out=out.gl
# Beagle with ref argument
$BEAGLE_TEST ref=ref.vcf.gz gt=target.vcf.gz out=out.ref
-rm -f $ADTTMP/*
+# Beagle with bref argument
+$BEAGLE_TEST ref=ref.bref gt=target.vcf.gz out=out.bref
+rm -f $ADTTMP/*
--
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