[med-svn] [Git][med-team/vcfanno][upstream] New upstream version 0.3.5+ds

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / vcfanno


Commits:
291e023a by Nilesh Patra at 2022-12-31T17:14:40+05:30
New upstream version 0.3.5+ds
- - - - -


5 changed files:

- − .github/ISSUE_TEMPLATE.md
- − .travis.yml
- 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
-


=====================================
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/-/commit/291e023aebbf6a998d03b8d560f3bc5f5d1a3eeb

-- 
View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/commit/291e023aebbf6a998d03b8d560f3bc5f5d1a3eeb
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