From 09f54401200daf90254837b35484cec6a1f4ded7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 23 Jan 2024 10:42:53 +0100
Subject: [PATCH 1/3] bump to dev version

---
 svync.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/svync.go b/svync.go
index b360c81..497dd86 100644
--- a/svync.go
+++ b/svync.go
@@ -13,7 +13,7 @@ func main() {
 		Name:            "svync",
 		Usage:           "A tool to standardize VCF files from structural variant callers",
 		HideHelpCommand: true,
-		Version:         "0.1.1",
+		Version:         "0.2.0dev",
 		Flags: []cli.Flag{
 			&cli.BoolFlag{
 				Name:     "nodate",

From 3e0ea1b872b80136039b8fab230d24ae74977ae4 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 23 Jan 2024 14:02:44 +0100
Subject: [PATCH 2/3] output header for empty VCFs

---
 data/test1.delly.empty.vcf | 46 ++++++++++++++++++++++++++++++++++++++
 svync_api/execute.go       |  5 +++++
 2 files changed, 51 insertions(+)
 create mode 100644 data/test1.delly.empty.vcf

diff --git a/data/test1.delly.empty.vcf b/data/test1.delly.empty.vcf
new file mode 100644
index 0000000..1f86684
--- /dev/null
+++ b/data/test1.delly.empty.vcf
@@ -0,0 +1,46 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20231204
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=BND,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
+##INFO=<ID=SVINSSEQ,Number=1,Type=String,Description="Split-read consensus sequence">
+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
+##FORMAT=<ID=RDCN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
+##reference=reference.fasta
+##contig=<ID=chr14,length=2000001>
+##contig=<ID=chr16,length=2000001>
+##contig=<ID=chrX,length=2000001>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PosCon1
\ No newline at end of file
diff --git a/svync_api/execute.go b/svync_api/execute.go
index fc28462..fbbd396 100644
--- a/svync_api/execute.go
+++ b/svync_api/execute.go
@@ -91,6 +91,11 @@ func Execute(Cctx *cli.Context, config *Config) {
 		}
 	}
 
+	if !headerIsMade {
+		writeHeader(config, Cctx, header, outputFile, stdout)
+		headerIsMade = true
+	}
+
 }
 
 // readBgzipLine reads a line from a bgzip file

From 3c28d03ad60c63c9351089d06fe77c256aa5c4fd Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 23 Jan 2024 15:32:15 +0100
Subject: [PATCH 3/3] bump to 0.1.2

---
 CHANGELOG.md | 5 +++++
 svync.go     | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a19aca4..6062409 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,8 @@
+# 0.1.2 - Adjust
+## Fixes
+- Fixed a bug where the output VCF has no header when the input VCF has no variants
+
+
 # 0.1.1 - Transform
 ## Fixes
 - Fixed a bug where the samples were missing from the header
diff --git a/svync.go b/svync.go
index 497dd86..b986b70 100644
--- a/svync.go
+++ b/svync.go
@@ -13,7 +13,7 @@ func main() {
 		Name:            "svync",
 		Usage:           "A tool to standardize VCF files from structural variant callers",
 		HideHelpCommand: true,
-		Version:         "0.2.0dev",
+		Version:         "0.1.2",
 		Flags: []cli.Flag{
 			&cli.BoolFlag{
 				Name:     "nodate",