type outputFormat struct {
Filename string
+ Head func(out io.Writer, cgs []CompactGenome)
Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
PadLeft bool
}
"pvcf": outputFormatPVCF,
"vcf": outputFormatVCF,
}
- outputFormatHGVS = outputFormat{Filename: "out.csv", Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Print: printHGVSOneHot}
- outputFormatPVCF = outputFormat{Filename: "out.vcf", Print: printPVCF, PadLeft: true}
- outputFormatVCF = outputFormat{Filename: "out.vcf", Print: printVCF, PadLeft: true}
+ outputFormatHGVS = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVS}
+ outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVSOneHot}
+ outputFormatPVCF = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
+ outputFormatVCF = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
+ headNone = func(io.Writer, []CompactGenome) {}
)
type exporter struct {
}
if cmd.outputPerChrom {
for i, seqname := range seqnames {
- f, err := os.OpenFile(filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1)), os.O_CREATE|os.O_WRONLY, 0666)
+ f, err := os.OpenFile(filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1)), os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
if err != nil {
return err
}
defer f.Close()
log.Infof("writing %q", f.Name())
+ cmd.outputFormat.Head(f, cgs)
outw[i] = f
}
} else {
fnm := filepath.Join(outdir, cmd.outputFormat.Filename)
log.Infof("writing %q", fnm)
- out, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
+ out, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
if err != nil {
return err
}
defer out.Close()
+ cmd.outputFormat.Head(out, cgs)
merge(out, outw, "output")
}
if bedout != nil {
return byref
}
+func headVCF(out io.Writer, cgs []CompactGenome) {
+ fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
+}
+
func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
for ref, alts := range bucketVarsliceByRef(varslice) {
altslice := make([]string, 0, len(alts))
}
info += strconv.Itoa(alts[a])
}
- fmt.Fprintf(out, "%s\t%d\t%s\t%s\t.\t.\t%s\tGT\t0/1\n", seqname, varslice[0].Position, ref, strings.Join(altslice, ","), info)
+ fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t%s\n", seqname, varslice[0].Position, ref, strings.Join(altslice, ","), info)
+ }
+}
+
+func headPVCF(out io.Writer, cgs []CompactGenome) {
+ fmt.Fprintln(out, `##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`)
+ fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
+ for _, cg := range cgs {
+ fmt.Fprintf(out, "\t%s", cg.Name)
}
+ fmt.Fprintf(out, "\n")
}
func printPVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
for i, a := range altslice {
alts[a] = i + 1
}
- fmt.Fprintf(out, "%s\t%d\t%s\t%s\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
+ fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
for i := 0; i < len(varslice); i += 2 {
v1, v2 := varslice[i], varslice[i+1]
a1, a2 := alts[v1.New], alts[v2.New]