Update all dependencies

Author: nicolaasuni

VERSION

@@ -1 +1 @@
-5.7.11
+5.7.12

c/doc/Doxyfile

@@ -32,7 +32,7 @@ PROJECT_NAME           = "VariantKey"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER = 5.7.11
+PROJECT_NUMBER = 5.7.12
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer

go.mod

@@ -2,7 +2,7 @@ module github.com/tecnickcom/variantkey
 
 go 1.25.0
 
-toolchain go1.25.1
+toolchain go1.25.3
 
 require (
 	github.com/jstemmer/go-junit-report/v2 v2.1.0

go/Makefile

@@ -50,7 +50,7 @@ GOFMT=$(shell which gofmt)
 GOTEST=$(GO) test
 GODOC=GOPATH=$(GOPATH) $(shell which godoc)
 GOLANGCILINT=$(BINUTIL)/golangci-lint
-GOLANGCILINTVERSION=v2.5.0
+GOLANGCILINTVERSION=v2.6.1
 
 # Directory containing the source code
 SRCDIR=./src

go/src/esid_test.go

@@ -144,9 +144,7 @@ func TestEncodeStringID(t *testing.T) {
 }
 
 func BenchmarkEncodeStringID(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		EncodeStringID("ABC0123456", 0)
 	}
 }
@@ -165,9 +163,7 @@ func TestEncodeStringNumID(t *testing.T) {
 }
 
 func BenchmarkEncodeStringNumID(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		EncodeStringNumID("AbCDE:000012345", ':')
 	}
 }
@@ -186,9 +182,7 @@ func TestDecodeStringID(t *testing.T) {
 }
 
 func BenchmarkDecodeStringID(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		DecodeStringID(0x08628e49669e8a6a)
 	}
 }
@@ -207,9 +201,7 @@ func TestDecodeStringNumID(t *testing.T) {
 }
 
 func BenchmarkDecodeStringNumID(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		DecodeStringID(0xf8628e4978bc614e)
 	}
 }
@@ -228,9 +220,7 @@ func TestHashStringID(t *testing.T) {
 }
 
 func BenchmarkHashStringID(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		HashStringID("0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ")
 	}
 }

go/src/genoref_test.go

@@ -39,9 +39,7 @@ func TestGetGenorefSeq(t *testing.T) {
 }
 
 func BenchmarkGetGenorefSeq(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		gref.GetGenorefSeq(13, 1)
 	}
 }

go/src/nrvk_test.go

@@ -52,9 +52,7 @@ func TestFindRefAltByVariantKey(t *testing.T) {
 }
 
 func BenchmarkFindRefAltByVariantKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		nrvk.FindRefAltByVariantKey(0xb000c35b64690b25)
 	}
 }
@@ -79,9 +77,7 @@ func TestNRReverseVariantKey(t *testing.T) {
 }
 
 func BenchmarkNRReverseVariantKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		nrvk.ReverseVariantKey(0xb000c35b64690b25)
 	}
 }

go/src/regionkey_test.go

@@ -79,9 +79,7 @@ func TestEncodeRegionStrand(t *testing.T) {
 }
 
 func BenchmarkEncodeRegionStrand(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		EncodeRegionStrand(-1)
 	}
 }
@@ -100,9 +98,7 @@ func TestDecodeRegionStrand(t *testing.T) {
 }
 
 func BenchmarkDecodeRegionStrand(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		DecodeRegionStrand(2)
 	}
 }
@@ -121,9 +117,7 @@ func TestEncodeRegionKey(t *testing.T) {
 }
 
 func BenchmarkEncodeRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		EncodeRegionKey(25, 1000, 2000, 2)
 	}
 }
@@ -142,9 +136,7 @@ func TestExtractRegionKeyChrom(t *testing.T) {
 }
 
 func BenchmarkExtractRegionKeyChrom(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		ExtractRegionKeyChrom(0x080001f400002260)
 	}
 }
@@ -163,9 +155,7 @@ func TestExtractRegionKeyStartPos(t *testing.T) {
 }
 
 func BenchmarkExtractRegionKeyStartPos(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		ExtractRegionKeyStartPos(0x080001f400002260)
 	}
 }
@@ -184,9 +174,7 @@ func TestExtractRegionKeyEndPos(t *testing.T) {
 }
 
 func BenchmarkExtractRegionKeyEndPos(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		ExtractRegionKeyEndPos(0x080001f400002260)
 	}
 }
@@ -205,9 +193,7 @@ func TestExtractRegionKeyStrand(t *testing.T) {
 }
 
 func BenchmarkExtractRegionKeyStrand(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		ExtractRegionKeyStrand(0x080001f400002260)
 	}
 }
@@ -229,9 +215,7 @@ func TestDecodeRegionKey(t *testing.T) {
 }
 
 func BenchmarkDecodeRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		DecodeRegionKey(0x080001f400002260)
 	}
 }
@@ -253,9 +237,7 @@ func TestReverseRegionKey(t *testing.T) {
 }
 
 func BenchmarkReverseRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		ReverseRegionKey(0x080001f400002260)
 	}
 }
@@ -274,9 +256,7 @@ func TestRegionKey(t *testing.T) {
 }
 
 func BenchmarkRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		RegionKey("MT", 1000, 2000, -1)
 	}
 }
@@ -314,9 +294,7 @@ func TestGetRegionKeyChromStartPos(t *testing.T) {
 }
 
 func BenchmarkGetRegionKeyChromStartPos(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		GetRegionKeyChromStartPos(0x080001f400002260)
 	}
 }
@@ -335,9 +313,7 @@ func TestGetRegionKeyChromEndPos(t *testing.T) {
 }
 
 func BenchmarkGetRegionKeyChromEndPos(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		GetRegionKeyChromEndPos(0x080001f400002260)
 	}
 }
@@ -356,9 +332,7 @@ func TestAreOverlappingRegions(t *testing.T) {
 }
 
 func BenchmarkAreOverlappingRegions(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		AreOverlappingRegions(5, 4, 6, 5, 3, 7)
 	}
 }
@@ -377,9 +351,7 @@ func TestAreOverlappingRegionRegionKey(t *testing.T) {
 }
 
 func BenchmarkAreOverlappingRegionRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		AreOverlappingRegionRegionKey(5, 4, 6, 0x2800000180000038)
 	}
 }
@@ -398,9 +370,7 @@ func TestAreOverlappingRegionKeys(t *testing.T) {
 }
 
 func BenchmarkAreOverlappingRegionKeys(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		AreOverlappingRegionKeys(0x2800000200000030, 0x2800000180000038)
 	}
 }
@@ -419,9 +389,7 @@ func TestAreOverlappingVariantKeyRegionKey(t *testing.T) {
 }
 
 func BenchmarkAreOverlappingVariantKeyRegionKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		nrvk.AreOverlappingVariantKeyRegionKey(0x2800000210920000, 0x2800000180000038)
 	}
 }
@@ -440,9 +408,7 @@ func TestVariantToRegionkey(t *testing.T) {
 }
 
 func BenchmarkVariantToRegionkey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		nrvk.VariantToRegionkey(0x2800000210920000)
 	}
 }

go/src/rsidvar_test.go

@@ -52,9 +52,7 @@ func TestFindRVVariantKeyByRsidNotFound(t *testing.T) {
 }
 
 func BenchmarkFindRVVariantKeyByRsid(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		rv.FindRVVariantKeyByRsid(0, 9, 0x2F81F575)
 	}
 }
@@ -114,9 +112,7 @@ func TestFindVRRsidByVariantKeyNotFound(t *testing.T) {
 }
 
 func BenchmarkFindVRRsidByVariantKey(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		vr.FindVRRsidByVariantKey(0, vr.NRows, 0x160017CCA313D0E0)
 	}
 }
@@ -166,9 +162,7 @@ func TestFindVRChromPosRangeNotFound(t *testing.T) {
 }
 
 func BenchmarkFindVRChromPosRange(b *testing.B) {
-	b.ResetTimer()
-
-	for range b.N {
+	for b.Loop() {
 		vr.FindVRChromPosRange(0, vr.NRows, 0x19, 0x001AF8FD, 0x001C8F2A)
 	}
 }