From 52c08db40bdfc267f83dadc9df78d1f77a427ccd Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Wed, 21 Oct 2020 17:15:37 -0400
Subject: [PATCH] Handle N in ref.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---
 export.go          |  8 +++++---
 pipeline_test.go   | 16 ++++++++++++----
 testdata/ref.fasta |  2 +-
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/export.go b/export.go
index 256af21296..2c51ff3eb9 100644
--- a/export.go
+++ b/export.go
@@ -131,7 +131,9 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
 
 	var mtx sync.Mutex
 	var cgs []CompactGenome
-	var tilelib tileLibrary
+	tilelib := tileLibrary{
+		includeNoCalls: true,
+	}
 	err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
 		if *pick != "" && *pick != cg.Name {
 			return
@@ -389,8 +391,8 @@ func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
 			alts[a] = i + 1
 		}
 		fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
-		for i := 0; i < len(varslice)/2; i++ {
-			v1, v2 := varslice[i*2], varslice[i*2+1]
+		for i := 0; i < len(varslice); i += 2 {
+			v1, v2 := varslice[i], varslice[i+1]
 			a1, a2 := alts[v1.New], alts[v2.New]
 			if v1.Ref != ref {
 				a1 = 0
diff --git a/pipeline_test.go b/pipeline_test.go
index 821c0fc626..2b0f393312 100644
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -49,8 +49,8 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 
 	var wg sync.WaitGroup
 	for i, infile := range []string{
-		"testdata/pipeline1/",
 		"testdata/ref.fasta",
+		"testdata/pipeline1/",
 	} {
 		i, infile := i, infile
 		c.Logf("TestImportMerge: %s", infile)
@@ -58,7 +58,13 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 		wg.Add(1)
 		go func() {
 			defer wg.Done()
-			code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
+			args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
+			if i == 0 {
+				// ref only
+				args = append(args, "-include-no-calls")
+			}
+			args = append(args, infile)
+			code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
 			c.Check(code, check.Equals, 0)
 		}()
 	}
@@ -82,7 +88,8 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 	c.Check(code, check.Equals, 0)
 	c.Check(hgvsout.Len() > 0, check.Equals, true)
 	c.Logf("%s", hgvsout.String())
-	c.Check(hgvsout.String(), check.Equals, `chr1:g.[41_42delinsAA];[41=]
+	c.Check(hgvsout.String(), check.Equals, `chr1:g.1_3delinsGGC
+chr1:g.[41_42delinsAA];[41=]
 chr1:g.[161=];[161A>T]
 chr1:g.[178=];[178A>T]
 chr1:g.222_224del
@@ -99,7 +106,8 @@ chr2:g.[1043=];[1043_1044delinsAA]
 	c.Check(code, check.Equals, 0)
 	c.Check(vcfout.Len() > 0, check.Equals, true)
 	c.Logf("%s", vcfout.String())
-	c.Check(vcfout.String(), check.Equals, `chr1	41	TT	AA	1/0
+	c.Check(vcfout.String(), check.Equals, `chr1	1	NNN	GGC	1/1
+chr1	41	TT	AA	1/0
 chr1	161	A	T	0/1
 chr1	178	A	T	0/1
 chr1	221	TCCA	T	1/1
diff --git a/testdata/ref.fasta b/testdata/ref.fasta
index d35147afe0..8bd6142dfc 100644
--- a/testdata/ref.fasta
+++ b/testdata/ref.fasta
@@ -1,5 +1,5 @@
 >chr1
-ggcgtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
+nnngtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
 ggagaactgtgctccgccttcaga
 ccccttgggtaaaatgccgcgcaatatgttgattacacttgctgcccatctgaaaggtcgccttatcaatcctatgctgaatgccctctaaggagttcca
 acacatgctagcgcgtcggggtgg
-- 
2.30.2