Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits: 1189b855 by Dylan Aïssi at 2019-10-14T19:33:06Z Update d/changelog - - - - - 8205bf03 by Dylan Aïssi at 2019-10-14T19:39:52Z Update upstream docs - - - - - 21a6e931 by Dylan Aïssi at 2019-10-14T19:47:43Z Standards-Version: 4.4.1 (no changes needed) - - - - - 6 changed files: - debian/README.source - debian/changelog - debian/control - debian/upstream.docs/README - debian/upstream.docs/release_notes - debian/upstream.docs/run.beagle.example Changes: ===================================== debian/README.source ===================================== @@ -2,7 +2,7 @@ How to rename the upstream sources ============================================= uscan -mv beagle_180703+dfsg.orig.tar.xz \ - beagle_5.0-180703+dfsg.orig.tar.xz +mv beagle_190921+dfsg.orig.tar.xz \ + beagle_5.1-190921+dfsg.orig.tar.xz -- Dylan Aïssi <[email protected]> Tue, 30 Jan 2018 23:28:16 +0100 ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +beagle (5.1-190921+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + * Standards-Version: 4.4.1 (no changes needed). + + -- Dylan Aïssi <[email protected]> Mon, 14 Oct 2019 21:31:05 +0200 + beagle (5.1-190824+dfsg-2) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12), javahelper Build-Depends-Indep: default-jdk, libhtsjdk-java -Standards-Version: 4.4.0 +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/beagle Vcs-Git: https://salsa.debian.org/med-team/beagle.git Homepage: https://faculty.washington.edu/browning/beagle/beagle.html ===================================== debian/upstream.docs/README ===================================== @@ -5,6 +5,6 @@ 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.24Aug19.3e8.example -O run.beagle.example - wget https://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz -O test.vcf.gz && \ + 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 && \ gunzip test.vcf.gz ===================================== debian/upstream.docs/release_notes ===================================== @@ -73,3 +73,8 @@ Beagle 5.1 (13Aug19.a31) release notes Beagle 5.1 (24Aug19.3e8) release notes ============================================ * Fixed a bug that can arise when phasing inbred samples + +Beagle 5.1 (21Sep19.ec3) release notes +============================================ +* Fixed bugs when phasing or imputing using a reference panel + ===================================== debian/upstream.docs/run.beagle.example ===================================== @@ -1,47 +1,47 @@ #!/bin/bash -if [ ! -f beagle.24Aug19.3e8.jar ]; then +if [ ! -f beagle.21Sep19.ec3.jar ]; then echo - echo "Downloading beagle.24Aug19.3e8.jar" - wget http://faculty.washington.edu/browning/beagle/beagle.24Aug19.3e8.jar + echo "Downloading beagle.21Sep19.ec3.jar" + wget http://faculty.washington.edu/browning/beagle/beagle.21Sep19.ec3.jar fi -if [ ! -f bref3.24Aug19.3e8.jar ]; then +if [ ! -f bref3.21Sep19.ec3.jar ]; then echo - echo "Downloading bref3.24Aug19.3e8.jar" - wget http://faculty.washington.edu/browning/beagle/bref3.24Aug19.3e8.jar + echo "Downloading bref3.21Sep19.ec3.jar" + wget http://faculty.washington.edu/browning/beagle/bref3.21Sep19.ec3.jar fi echo -if [ ! -f test.24Aug19.3e8.vcf.gz ]; then +if [ ! -f test.21Sep19.ec3.vcf.gz ]; then echo - echo "*** Downloading some 1000 Genomes Project data to file: test.24Aug19.3e8.vcf.gz ***" - wget http://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz + 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 fi echo -echo "*** Creating test files: ref.24Aug19.3e8.vcf.gz target.24Aug19.3e8.vcf.gz ***" +echo "*** Creating test files: ref.21Sep19.ec3.vcf.gz target.21Sep19.ec3.vcf.gz ***" echo -zcat test.24Aug19.3e8.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.24Aug19.3e8.vcf.gz -zcat test.24Aug19.3e8.vcf.gz | cut -f1-9,191-200 | gzip > target.24Aug19.3e8.vcf.gz +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 echo echo "*** Running test analysis with \"gt=\" argument ***" echo -java -jar beagle.24Aug19.3e8.jar gt=test.24Aug19.3e8.vcf.gz out=out.gt +java -jar beagle.21Sep19.ec3.jar gt=test.21Sep19.ec3.vcf.gz out=out.gt echo echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***" echo -java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.vcf.gz gt=target.24Aug19.3e8.vcf.gz out=out.ref +java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.vcf.gz gt=target.21Sep19.ec3.vcf.gz out=out.ref echo echo "*** Making \"bref3\" file ***" echo -java -jar bref3.24Aug19.3e8.jar ref.24Aug19.3e8.vcf.gz > ref.24Aug19.3e8.bref3 +java -jar bref3.21Sep19.ec3.jar ref.21Sep19.ec3.vcf.gz > ref.21Sep19.ec3.bref3 echo echo "*** Running test analysis with \"bref3\" file ***" echo -java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.bref3 gt=target.24Aug19.3e8.vcf.gz out=out.bref3 +java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.bref3 gt=target.21Sep19.ec3.vcf.gz out=out.bref3 View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/d8d6175f10bd2bfb2e409bec23680bc3318cb64e...21a6e93102e4a423dc99a92158b3fd452b1d3428 -- View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/d8d6175f10bd2bfb2e409bec23680bc3318cb64e...21a6e93102e4a423dc99a92158b3fd452b1d3428 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
