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vcfanno_0.3.2+ds-1_amd64.changes (click to toggle)
Format:1.8
Date:Sat, 18 Jul 2020 13:49:49 +0200
Source:vcfanno
Binary:vcfanno vcfanno-examples
Architecture:source all amd64
Version:0.3.2+ds-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Andreas Tille <tille@debian.org>
Description:
vcfanno    - annotate a VCF with other VCFs/BEDs/tabixed files
vcfanno-examples - examples for vcfanno: annotate a VCF with other VCFs/BEDs/tabixed
Closes:965252
Changes:
vcfanno (0.3.2+ds-1) unstable; urgency=medium

  * Initial release (Closes: #965252)
Files:
bfe01f3554f89cc09dd9bb187dc7a99e 2434 science optional vcfanno_0.3.2+ds-1.dsc
c886d003515e7d5faf320340663f2e39 501276 science optional vcfanno_0.3.2+ds.orig.tar.xz
ad2fbfacfc2e902a167233e23ccd05ae 2268300 science optional vcfanno_0.3.2+ds-1.debian.tar.xz
9d063e5fcf01c5b7931c994ed69ea5a1 5752140 science optional vcfanno-examples_0.3.2+ds-1_all.deb
48c2608f56dce61edfcbe267698b5c9a 7973 science optional vcfanno_0.3.2+ds-1_amd64.buildinfo
464ce700137bf29e2feda1453972ac20 2394072 science optional vcfanno_0.3.2+ds-1_amd64.deb
vcfanno_0.3.2+ds-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:vcfanno
Binary:vcfanno, vcfanno-examples
Architecture:any all
Version:0.3.2+ds-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>, Nilesh Patra <npatra974@gmail.com>
Homepage:https://github.com/brentp/vcfanno
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/vcfanno
Vcs-Git:https://salsa.debian.org/med-team/vcfanno.git
Testsuite:autopkgtest
Build-Depends:debhelper-compat (=13), dh-golang, golang-any, golang-github-biogo-hts-dev, golang-gopkg-check.v1-dev, golang-toml-dev, golang-github-brentp-irelate-dev, golang-github-brentp-vcfgo-dev, golang-github-brentp-bix-dev, golang-github-shenwei356-xopen-dev, golang-github-pkg-errors-dev, golang-github-brentp-goluaez-dev, samtools, tabix
Package-List:vcfanno deb science optional arch=any vcfanno-examples deb science optional arch=all
Files:
c886d003515e7d5faf320340663f2e39 501276 vcfanno_0.3.2+ds.orig.tar.xz
ad2fbfacfc2e902a167233e23ccd05ae 2268300 vcfanno_0.3.2+ds-1.debian.tar.xz
Go-Import-Path:github.com/brentp/vcfanno
lintian 2.79.0~bpo10+1 check for vcfanno_0.3.2+ds-1.dsc (click to toggle)
README.source for vcfanno_0.3.2+ds-1.dsc (click to toggle)
Upstream provides binary files without sources for:

* example/ex.bam 
* example/ex.bam.bai

These have been converted to corresponding text (.sam) files with the commands:
* samtools view -h -o ex.sam example/ex.bam 

And the corresponding *.sam files are added to: debian/missing-sources

They can be generated back with the following commands:
* cat debian/missing-sources/ex.sam| samtools view -Sb - > example/ex.bam
* samtools index data/ex.bam data/ex.bam.bai

These commands are also being run in debian/rules since these binaries are needed for testing.

 -- Nilesh Patra <npatra974@gmail.com>  Sat, 18 Jul 2020 04:33:13 +0530

control file for vcfanno_0.3.2+ds-1_amd64.deb (click to toggle)
Package:vcfanno
Version:0.3.2+ds-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:7411
Depends:libc6 (>=2.4)
Built-Using:golang-1.14 (= 1.14.4-2), golang-github-biogo-hts (= 1.1.0+dfsg1-1), golang-github-brentp-bix (= 0.0~git20190718.00aa7a7+ds-2), golang-github-brentp-goluaez (= 0.0~git20160116.dd35d08-2), golang-github-brentp-irelate (= 0.0.1+ds-1), golang-github-brentp-vcfgo (= 0.0~git20190824.654ed2e-2), golang-github-klauspost-compress (= 1.9.5-2), golang-github-klauspost-pgzip (= 1.2.1-1), golang-github-pkg-errors (= 0.9.1-1), golang-github-shenwei356-xopen (= 0.0~git20181203.f4f16dd-1), golang-github-yuin-gluare (= 0.0~git20170607.d7c94f1-2), golang-github-yuin-gopher-lua (= 0.0~git20170915.0.eb1c729-4), golang-toml (= 0.3.1-1)
Section:science
Priority:optional
Homepage:https://github.com/brentp/vcfanno
Description:
annotate a VCF with other VCFs/BEDs/tabixed files
 Vcfanno allows you to quickly annotate your VCF with any number of INFO
 fields from any number of VCFs or BED files. It uses a simple conf file
 to allow the user to specify the source annotation files and fields and
 how they will be added to the info of the query VCF.
 .
   * For VCF, values are pulled by name from the INFO field with special
     cases of ID and FILTER to pull from those VCF columns.
   * For BED, values are pulled from (1-based) column number.
   * For BAM, depth (count), "mapq" and "seq" are currently supported.
 .
 Vcfanno is written in go and it supports custom user-scripts written in
 Lua. It can annotate more than 8000 variants per second with 34
 annotations from 9 files on a modest laptop and over 30K variants per
 second using 12 processes on a server.
lintian 2.79.0~bpo10+1 check for vcfanno_0.3.2+ds-1_amd64.deb (click to toggle)
W: vcfanno: hardening-no-pie usr/bin/vcfanno
W: vcfanno: hardening-no-relro usr/bin/vcfanno
contents of vcfanno_0.3.2+ds-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-07-18 11:49 ./
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/bin/
-rwxr-xr-x root/root   7570968 2020-07-18 11:49 ./usr/bin/vcfanno
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno/
-rw-r--r-- root/root       157 2020-07-18 11:49 ./usr/share/doc/vcfanno/changelog.Debian.gz
-rw-r--r-- root/root      3305 2019-07-19 02:07 ./usr/share/doc/vcfanno/changelog.gz
-rw-r--r-- root/root      1511 2020-07-18 11:49 ./usr/share/doc/vcfanno/copyright
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/man/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/man/man1/
-rw-r--r-- root/root       610 2020-07-18 11:49 ./usr/share/man/man1/vcfanno.1.gz
control file for vcfanno-examples_0.3.2+ds-1_all.deb (click to toggle)
Package:vcfanno-examples
Source:vcfanno
Version:0.3.2+ds-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:5706
Section:science
Priority:optional
Homepage:https://github.com/brentp/vcfanno
Description:
examples for vcfanno: annotate a VCF with other VCFs/BEDs/tabixed files
 Vcfanno allows you to quickly annotate your VCF with any number of INFO
 fields from any number of VCFs or BED files. It uses a simple conf file
 to allow the user to specify the source annotation files and fields and
 how they will be added to the info of the query VCF.
 .
   * For VCF, values are pulled by name from the INFO field with special
     cases of ID and FILTER to pull from those VCF columns.
   * For BED, values are pulled from (1-based) column number.
   * For BAM, depth (count), "mapq" and "seq" are currently supported.
 .
 This package contains a test data set as well as sample scripts
 running some test suite provided by Debian also as autopkgtest.
lintian 2.79.0~bpo10+1 check for vcfanno-examples_0.3.2+ds-1_all.deb (click to toggle)
contents of vcfanno-examples_0.3.2+ds-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-07-18 11:49 ./
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/
-rw-r--r-- root/root       157 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/changelog.Debian.gz
-rw-r--r-- root/root      3305 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/changelog.gz
-rw-r--r-- root/root      1511 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/copyright
-rw-r--r-- root/root   2653879 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/ex.sam.gz
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/example/
-rw-r--r-- root/root      1531 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/conf.toml
-rw-r--r-- root/root      3503 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/custom.lua
-rw-r--r-- root/root      1080 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/example/ex.bam.bai
-rw-r--r-- root/root   2931725 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/example/ex.bam.gz
-rw-r--r-- root/root     46414 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/exac.vcf.gz
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-rw-r--r-- root/root      2721 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/gnomad.conf
-rw-r--r-- root/root     20979 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/query.vcf.gz
-rw-r--r-- root/root      2963 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/rare-disease.conf
-rw-r--r-- root/root      1820 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/example/rare-disease.lua
-rw-r--r-- root/root       602 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/run-unit-test
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/tests/
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/tests/astar/
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drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/tests/by_alt_float/
-rw-r--r-- root/root       237 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/tests/by_alt_float/annotation.tsv.gz
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-rw-r--r-- root/root       306 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/tests/by_alt_float/q.vcf
drwxr-xr-x root/root         0 2020-07-18 11:49 ./usr/share/doc/vcfanno-examples/tests/citest/
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-rw-r--r-- root/root       342 2019-07-19 02:07 ./usr/share/doc/vcfanno-examples/tests/ref-alt-test/tmp_annotations.toml
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Timestamp: 18.07.2020 / 13:01:17 (UTC)