Merge pull request #5 from nvnieuwk/dev

Release 0.1.2

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

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

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:         "0.1.2",
 		Flags: []cli.Flag{
 			&cli.BoolFlag{
 				Name:     "nodate",

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