From 87ced57ab25faa724115989b3a42fdeffadb96e8 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Mon, 13 Dec 2021 10:29:56 -0500 Subject: [PATCH] Include HGVS IDs in anno2vcf. refs #18579 Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- anno2vcf.go | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/anno2vcf.go b/anno2vcf.go index a1a320ff34..4b1295f5c0 100644 --- a/anno2vcf.go +++ b/anno2vcf.go @@ -105,6 +105,7 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std position int deletion []byte insertion []byte + hgvsID []byte } allcalls := map[string][]*call{} var mtx sync.Mutex @@ -134,6 +135,12 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std if len(fields) < 8 { return fmt.Errorf("%s line %d: wrong number of fields (%d < %d): %q", fi.Name(), lineIdx+1, len(fields), 8, line) } + hgvsID := fields[3] + if len(hgvsID) < 2 { + // "=" reference or "" + // non-diffable tile variant + continue + } tile, _ := strconv.ParseInt(string(fields[0]), 10, 64) variant, _ := strconv.ParseInt(string(fields[2]), 10, 64) position, _ := strconv.ParseInt(string(fields[5]), 10, 64) @@ -165,6 +172,7 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std position: int(position), deletion: del, insertion: ins, + hgvsID: hgvsID, }) } mtx.Lock() @@ -238,7 +246,7 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std if len(insertion) == 0 { insertion = placeholder } - _, err = fmt.Fprintf(bufw, "%s\t%d\t.\t%s\t%s\t.\t.\t%s\n", seq, call.position, deletion, insertion, info) + _, err = fmt.Fprintf(bufw, "%s\t%d\t%s\t%s\t%s\t.\t.\t%s\n", seq, call.position, call.hgvsID, deletion, insertion, info) if err != nil { return err } -- 2.30.2