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commit 5b41984f78d73fc89a7cc13bbfb5898855a7bd0d Author: Dylan Aïssi <[email protected]> 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 <[email protected]>, +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 <[email protected]> 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/* -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beagle.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
