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commit 282a7752354470032569947aaab0082366065388 Author: Dylan Aïssi <[email protected]> Date: Tue Feb 14 22:25:04 2017 +0100 Update upstream docs --- debian/changelog | 6 ++++++ debian/upstream.docs/README | 4 ++-- debian/upstream.docs/release_notes | 7 +++++++ debian/upstream.docs/run.beagle.example | 34 ++++++++++++++++----------------- 4 files changed, 32 insertions(+), 19 deletions(-) diff --git a/debian/changelog b/debian/changelog index 85f19e8..670f44a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +beagle (4.1~170121-6cc+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + + -- Dylan Aïssi <[email protected]> Tue, 07 Feb 2017 23:12:39 +0100 + beagle (4.1~160727-86a+dfsg-1) unstable; urgency=medium * New upstream release. diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README index 8b1534e..e4175b0 100644 --- a/debian/upstream.docs/README +++ b/debian/upstream.docs/README @@ -5,6 +5,6 @@ wget https://faculty.washington.edu/browning/beagle/release_notes wget https://faculty.washington.edu/browning/beagle/beagle_4.1_03May16.pdf - wget https://faculty.washington.edu/browning/beagle/run.beagle.16Jun16.7e4.example -O run.beagle.example - wget https://faculty.washington.edu/browning/beagle/test.16Jun16.7e4.vcf.gz -O test.vcf.gz && \ + wget https://faculty.washington.edu/browning/beagle/run.beagle.21Jan17.6cc.example -O run.beagle.example + wget https://faculty.washington.edu/browning/beagle/test.21Jan17.6cc.vcf.gz -O test.vcf.gz && \ gunzip test.vcf.gz diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes index f82ffa0..84870f7 100644 --- a/debian/upstream.docs/release_notes +++ b/debian/upstream.docs/release_notes @@ -113,3 +113,10 @@ Beagle 4.1 (23Jul16.fb0) release notes Beagle 4.1 (27Jul16.86a) release notes ============================================= * Improve computational efficiency of genotype imputation. + +Beagle 4.1 (21Jan17.6cc) release notes +============================================= +* add gzip compression to IBD and HBD output files. +* add ibdcm parameter to apply length threshold to output IBD/HBD segments. + + diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example index b27c9b2..09e72b1 100644 --- a/debian/upstream.docs/run.beagle.example +++ b/debian/upstream.docs/run.beagle.example @@ -1,53 +1,53 @@ #!/bin/bash -if [ ! -f beagle.27Jul16.86a.jar ]; then +if [ ! -f beagle.21Jan17.6cc.jar ]; then echo - echo "Downloading beagle.27Jul16.86a.jar" - wget http://faculty.washington.edu/browning/beagle/beagle.27Jul16.86a.jar + echo "Downloading beagle.21Jan17.6cc.jar" + wget http://faculty.washington.edu/browning/beagle/beagle.21Jan17.6cc.jar fi -if [ ! -f bref.27Jul16.86a.jar ]; then +if [ ! -f bref.21Jan17.6cc.jar ]; then echo - echo "Downloading bref.27Jul16.86a.jar" - wget http://faculty.washington.edu/browning/beagle/bref.27Jul16.86a.jar + echo "Downloading bref.21Jan17.6cc.jar" + wget http://faculty.washington.edu/browning/beagle/bref.21Jan17.6cc.jar fi echo -if [ ! -f test.27Jul16.86a.vcf.gz ]; then +if [ ! -f test.21Jan17.6cc.vcf.gz ]; then echo - echo "*** Downloading some 1000 Genomes Project data to file: test.27Jul16.86a.vcf.gz ***" - wget http://faculty.washington.edu/browning/beagle/test.27Jul16.86a.vcf.gz + echo "*** Downloading some 1000 Genomes Project data to file: test.21Jan17.6cc.vcf.gz ***" + wget http://faculty.washington.edu/browning/beagle/test.21Jan17.6cc.vcf.gz fi echo -echo "*** Creating test files: ref.27Jul16.86a.vcf.gz target.27Jul16.86a.vcf.gz ***" +echo "*** Creating test files: ref.21Jan17.6cc.vcf.gz target.21Jan17.6cc.vcf.gz ***" echo -zcat test.27Jul16.86a.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.27Jul16.86a.vcf.gz -zcat test.27Jul16.86a.vcf.gz | cut -f1-9,191-200 | gzip > target.27Jul16.86a.vcf.gz +zcat test.21Jan17.6cc.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.21Jan17.6cc.vcf.gz +zcat test.21Jan17.6cc.vcf.gz | cut -f1-9,191-200 | gzip > target.21Jan17.6cc.vcf.gz echo echo "*** Running test analysis with \"gt=\" argument ***" echo -java -jar beagle.27Jul16.86a.jar gt=test.27Jul16.86a.vcf.gz out=out.gt +java -jar beagle.21Jan17.6cc.jar gt=test.21Jan17.6cc.vcf.gz out=out.gt echo echo "*** Running test analysis with \"gl=\" argument ***" echo -java -jar beagle.27Jul16.86a.jar gl=test.27Jul16.86a.vcf.gz out=out.gl +java -jar beagle.21Jan17.6cc.jar gl=test.21Jan17.6cc.vcf.gz out=out.gl echo echo "*** Running test analysis with \"ref=\" argument ***" echo -java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.vcf.gz gt=target.27Jul16.86a.vcf.gz out=out.ref +java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.vcf.gz gt=target.21Jan17.6cc.vcf.gz out=out.ref echo echo "*** Making \"bref\" file ***" echo -java -jar bref.27Jul16.86a.jar ref.27Jul16.86a.vcf.gz +java -jar bref.21Jan17.6cc.jar ref.21Jan17.6cc.vcf.gz echo echo "*** Running test analysis with \"bref=\" argument ***" echo -java -jar beagle.27Jul16.86a.jar ref=ref.27Jul16.86a.bref gt=target.27Jul16.86a.vcf.gz out=out.bref +java -jar beagle.21Jan17.6cc.jar ref=ref.21Jan17.6cc.bref gt=target.21Jan17.6cc.vcf.gz out=out.bref -- 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
