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commit 0559ec6c2dd10c812dd5aca1f33d39651b3b2238 Author: Dylan Aïssi <[email protected]> Date: Sat Jun 25 00:29:11 2016 +0200 Update upstream docs --- debian/beagle-doc.install | 4 +- debian/upstream.docs/README | 10 ++++ debian/upstream.docs/release_notes | 18 ++++++++ .../upstream.docs/run.beagle.22Feb16.8ef.example | 53 ---------------------- debian/upstream.docs/run.beagle.example | 53 ++++++++++++++++++++++ .../{test.22Feb16.8ef.vcf => test.vcf} | 0 6 files changed, 83 insertions(+), 55 deletions(-) diff --git a/debian/beagle-doc.install b/debian/beagle-doc.install index 3175374..dbe6834 100644 --- a/debian/beagle-doc.install +++ b/debian/beagle-doc.install @@ -1,5 +1,5 @@ debian/tests/run-sample-analysis /usr/share/doc/beagle/examples/ -debian/upstream.docs/run.beagle.22Feb16.8ef.example /usr/share/doc/beagle/examples/ -debian/upstream.docs/test.22Feb16.8ef.vcf /usr/share/doc/beagle/examples/ +debian/upstream.docs/run.beagle.example /usr/share/doc/beagle/examples/ +debian/upstream.docs/test.vcf /usr/share/doc/beagle/examples/ debian/upstream.docs/beagle_4.1_09Feb16.pdf /usr/share/doc/beagle/ debian/_jh_build.javadoc/api /usr/share/doc/beagle diff --git a/debian/upstream.docs/README b/debian/upstream.docs/README new file mode 100644 index 0000000..8b1534e --- /dev/null +++ b/debian/upstream.docs/README @@ -0,0 +1,10 @@ +# Author: Dylan A�ssi <[email protected]> +# Last-Update: 2016-06-17 +# These files were downloaded from https://faculty.washington.edu/browning/beagle/ +# They should be updated when upstream update them. + + 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 && \ + gunzip test.vcf.gz diff --git a/debian/upstream.docs/release_notes b/debian/upstream.docs/release_notes index f198676..a68216e 100644 --- a/debian/upstream.docs/release_notes +++ b/debian/upstream.docs/release_notes @@ -80,3 +80,21 @@ Beagle 4.1 (22Feb16.8ef) release notes * Minor update to the model-building algorithm. * Minor update to fix bugs. +Beagle 4.1 (15Apr16.63e) release notes +Beagle 4.1 (22Apr16.1cf) release notes +============================================= +* Minor updates to fix a bug in the genotype calling algorithm. + +Beagle 4.1 (03May16.862) release notes +============================================= +* Improve INFO field accuracy for low-MAF markers. +* Add "IMP" INFO field to mark imputed markers. + +Beagle 4.1 (14Jun16.dd3) release notes +============================================= +* Improve accuracy and computational efficiency of genotype imputation. + +Beagle 4.1 (16Jun16.7e4) release notes +============================================= +* Simplify code for writing BGZIP files + diff --git a/debian/upstream.docs/run.beagle.22Feb16.8ef.example b/debian/upstream.docs/run.beagle.22Feb16.8ef.example deleted file mode 100644 index 0cf6f02..0000000 --- a/debian/upstream.docs/run.beagle.22Feb16.8ef.example +++ /dev/null @@ -1,53 +0,0 @@ -#!/bin/bash -if [ ! -f beagle.22Feb16.8ef.jar ]; then - echo - echo "Downloading beagle.22Feb16.8ef.jar" - wget http://faculty.washington.edu/browning/beagle/beagle.22Feb16.8ef.jar -fi - -if [ ! -f bref.22Feb16.8ef.jar ]; then - echo - echo "Downloading bref.22Feb16.8ef.jar" - wget http://faculty.washington.edu/browning/beagle/bref.22Feb16.8ef.jar -fi - -echo - -if [ ! -f test.22Feb16.8ef.vcf.gz ]; then - echo - echo "*** Downloading some 1000 Genomes Project data to file: test.22Feb16.8ef.vcf.gz ***" - wget http://faculty.washington.edu/browning/beagle/test.22Feb16.8ef.vcf.gz -fi - -echo -echo "*** Creating test files: ref.22Feb16.8ef.vcf.gz target.22Feb16.8ef.vcf.gz ***" -echo -zcat test.22Feb16.8ef.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.22Feb16.8ef.vcf.gz -zcat test.22Feb16.8ef.vcf.gz | cut -f1-9,191-200 | gzip > target.22Feb16.8ef.vcf.gz - - -echo -echo "*** Running test analysis with \"gt=\" argument ***" -echo -java -jar beagle.22Feb16.8ef.jar gt=test.22Feb16.8ef.vcf.gz out=out.gt - -echo -echo "*** Running test analysis with \"gl=\" argument ***" -echo -java -jar beagle.22Feb16.8ef.jar gl=test.22Feb16.8ef.vcf.gz out=out.gl - -echo -echo "*** Running test analysis with \"ref=\" argument ***" -echo -java -jar beagle.22Feb16.8ef.jar ref=ref.22Feb16.8ef.vcf.gz gt=target.22Feb16.8ef.vcf.gz out=out.ref - -echo -echo "*** Making \"bref\" file ***" -echo -java -jar bref.22Feb16.8ef.jar ref.22Feb16.8ef.vcf.gz - -echo -echo "*** Running test analysis with \"bref=\" argument ***" -echo -java -jar beagle.22Feb16.8ef.jar ref=ref.22Feb16.8ef.bref gt=target.22Feb16.8ef.vcf.gz out=out.bref - diff --git a/debian/upstream.docs/run.beagle.example b/debian/upstream.docs/run.beagle.example new file mode 100644 index 0000000..44a39c1 --- /dev/null +++ b/debian/upstream.docs/run.beagle.example @@ -0,0 +1,53 @@ +#!/bin/bash +if [ ! -f beagle.16Jun16.7e4.jar ]; then + echo + echo "Downloading beagle.16Jun16.7e4.jar" + wget http://faculty.washington.edu/browning/beagle/beagle.16Jun16.7e4.jar +fi + +if [ ! -f bref.16Jun16.7e4.jar ]; then + echo + echo "Downloading bref.16Jun16.7e4.jar" + wget http://faculty.washington.edu/browning/beagle/bref.16Jun16.7e4.jar +fi + +echo + +if [ ! -f test.16Jun16.7e4.vcf.gz ]; then + echo + echo "*** Downloading some 1000 Genomes Project data to file: test.16Jun16.7e4.vcf.gz ***" + wget http://faculty.washington.edu/browning/beagle/test.16Jun16.7e4.vcf.gz +fi + +echo +echo "*** Creating test files: ref.16Jun16.7e4.vcf.gz target.16Jun16.7e4.vcf.gz ***" +echo +zcat test.16Jun16.7e4.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.16Jun16.7e4.vcf.gz +zcat test.16Jun16.7e4.vcf.gz | cut -f1-9,191-200 | gzip > target.16Jun16.7e4.vcf.gz + + +echo +echo "*** Running test analysis with \"gt=\" argument ***" +echo +java -jar beagle.16Jun16.7e4.jar gt=test.16Jun16.7e4.vcf.gz out=out.gt + +echo +echo "*** Running test analysis with \"gl=\" argument ***" +echo +java -jar beagle.16Jun16.7e4.jar gl=test.16Jun16.7e4.vcf.gz out=out.gl + +echo +echo "*** Running test analysis with \"ref=\" argument ***" +echo +java -jar beagle.16Jun16.7e4.jar ref=ref.16Jun16.7e4.vcf.gz gt=target.16Jun16.7e4.vcf.gz out=out.ref + +echo +echo "*** Making \"bref\" file ***" +echo +java -jar bref.16Jun16.7e4.jar ref.16Jun16.7e4.vcf.gz + +echo +echo "*** Running test analysis with \"bref=\" argument ***" +echo +java -jar beagle.16Jun16.7e4.jar ref=ref.16Jun16.7e4.bref gt=target.16Jun16.7e4.vcf.gz out=out.bref + diff --git a/debian/upstream.docs/test.22Feb16.8ef.vcf b/debian/upstream.docs/test.vcf similarity index 100% rename from debian/upstream.docs/test.22Feb16.8ef.vcf rename to debian/upstream.docs/test.vcf -- 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
