[med-svn] [Git][med-team/vcfanno][master] 5 commits: New upstream version 0.3.5+ds
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat Dec 31 11:51:36 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / vcfanno
Commits:
291e023a by Nilesh Patra at 2022-12-31T17:14:40+05:30
New upstream version 0.3.5+ds
- - - - -
e66e1928 by Nilesh Patra at 2022-12-31T17:14:40+05:30
Update upstream source from tag 'upstream/0.3.5+ds'
Update to upstream version '0.3.5+ds'
with Debian dir b6cf1f960d3021e3e2ca14e2859c1e981f67340f
- - - - -
1c2d04b6 by Nilesh Patra at 2022-12-31T17:14:47+05:30
Bump Standards-Version to 4.6.2 (no changes needed)
- - - - -
bd90310b by Nilesh Patra at 2022-12-31T17:15:42+05:30
Update patch
- - - - -
947d868b by Nilesh Patra at 2022-12-31T17:15:43+05:30
Upload to unstable
- - - - -
8 changed files:
- − .github/ISSUE_TEMPLATE.md
- − .travis.yml
- debian/changelog
- debian/control
- debian/patches/use-archive-xopen.patch
- go.mod
- tests/functional-test.sh
- vcfanno.go
Changes:
=====================================
.github/ISSUE_TEMPLATE.md deleted
=====================================
@@ -1,9 +0,0 @@
-If you have encountered an error, please include:
-
-- [ ] minimal conf and lua files that you are using.
-- [ ] urls or actual files for annotations in conf file.
-- [ ] minimal query file.
-- [ ] the command you used to invoke vcfanno
-- [ ] the **full** error message
-
-
=====================================
.travis.yml deleted
=====================================
@@ -1,18 +0,0 @@
-language: go
-
-os:
- - linux
- - osx
-
-go:
- - 1.16.x
- - 1.17.x
-
-before_install:
- - make
- - go get github.com/axw/gocov/gocov
- - go get github.com/mattn/goveralls
- - go get golang.org/x/tools/cmd/cover
-script:
- - ./tests/functional-test.sh
-
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+vcfanno (0.3.5+ds-1) unstable; urgency=medium
+
+ * New upstream version 0.3.5+ds
+ * Bump Standards-Version to 4.6.2 (no changes needed)
+
+ -- Nilesh Patra <nilesh at debian.org> Sat, 31 Dec 2022 17:14:51 +0530
+
vcfanno (0.3.4+ds-1) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -17,7 +17,7 @@ Build-Depends: debhelper-compat (= 13),
golang-github-brentp-goluaez-dev,
samtools,
tabix
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/vcfanno
Vcs-Git: https://salsa.debian.org/med-team/vcfanno.git
Homepage: https://github.com/brentp/vcfanno
=====================================
debian/patches/use-archive-xopen.patch
=====================================
@@ -3,7 +3,7 @@ Description: Instead of github.com/brentp/xopen, its fork github.com/shenwei356/
Last Changed: Mon July 13, 2020
--- a/bench_test.go
+++ b/bench_test.go
-@@ -13,7 +13,7 @@ import (
+@@ -13,7 +13,7 @@
"github.com/brentp/irelate/parsers"
"github.com/brentp/vcfanno/api"
"github.com/brentp/vcfanno/shared"
@@ -14,7 +14,7 @@ Last Changed: Mon July 13, 2020
func benchmarkAnno(b *testing.B) {
--- a/shared/shared.go
+++ b/shared/shared.go
-@@ -7,7 +7,7 @@ import (
+@@ -7,7 +7,7 @@
"strings"
. "github.com/brentp/vcfanno/api"
@@ -25,7 +25,7 @@ Last Changed: Mon July 13, 2020
type Config struct {
--- a/vcfanno.go
+++ b/vcfanno.go
-@@ -23,7 +23,7 @@ import (
+@@ -23,7 +23,7 @@
. "github.com/brentp/vcfanno/api"
. "github.com/brentp/vcfanno/shared"
"github.com/brentp/vcfgo"
@@ -33,4 +33,4 @@ Last Changed: Mon July 13, 2020
+ "github.com/shenwei356/xopen"
)
- var VERSION = "0.3.4"
+ const VERSION = "0.3.5"
=====================================
go.mod
=====================================
@@ -8,7 +8,7 @@ require (
github.com/brentp/bix v0.0.0-20190718140914-00aa7a7f205d
github.com/brentp/goluaez v0.0.0-20160116211227-dd35d08e32e7
github.com/brentp/irelate v0.0.1
- github.com/brentp/vcfgo v0.0.0-20220919165057-adf3b5d20c55
+ github.com/brentp/vcfgo v0.0.0-20221128230736-759c0d32541e
github.com/brentp/xopen v0.0.0-20181116180855-111b45cadc7d
github.com/pkg/errors v0.9.1 // indirect
github.com/yuin/gluare v0.0.0-20170607022532-d7c94f1a80ed // indirect
=====================================
tests/functional-test.sh
=====================================
@@ -7,7 +7,10 @@ test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest
set -o nounset
-go install -race -a github.com/brentp/vcfanno
+go build -race -a
+export PATH=.:$PATH
+echo using $(which vcfanno)
+
run check_self_number vcfanno -base-path tests/data/ -lua example/custom.lua tests/data/number.conf tests/data/number-input.vcf
assert_equal 0 $(grep -c "lua error in postannotation" $STDERR_FILE)
@@ -24,6 +27,10 @@ assert_equal 6 $(grep ^# $STDOUT_FILE | grep -c lua)
# so lua_start doesn't exist.
assert_equal 3 $(grep -c "not found in" $STDERR_FILE)
+run check_samples vcfanno -base-path tests/citest/ tests/citest/conf.toml tests/citest/test.vcf
+n=$(grep -c ^#CHROM $STDOUT_FILE)
+assert_equal $n 1
+
run check_ends vcfanno -ends -lua example/custom.lua example/conf.toml example/query.vcf.gz
n=$(grep -v ^# $STDOUT_FILE | grep -c right_)
assert_equal $(( $n > 0 )) 1
=====================================
vcfanno.go
=====================================
@@ -26,7 +26,7 @@ import (
"github.com/brentp/xopen"
)
-var VERSION = "0.3.4"
+const VERSION = "0.3.5"
func envGet(name string, vdefault int) int {
sval := os.Getenv(name)
View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/compare/fac8170997dd2314b1e90536045db10c9c118f32...947d868b5aea7fd6c2a85d067d892090c02879b3
--
View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/compare/fac8170997dd2314b1e90536045db10c9c118f32...947d868b5aea7fd6c2a85d067d892090c02879b3
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