Handle N in ref.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/export.go b/export.go
index 256af2129604bac58c0b1b878db004cb66f86b49..2c51ff3eb915515b9fdd74cec837ead1cc17c611 100644 (file)
--- 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 821c0fc6269b29473923b8e482ab471a323a0c78..2b0f3933126223ae19f7c8ac40c5ff11baece9ca 100644 (file)
--- 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 d35147afe0a708cfa3846debbe760035ae80ddd5..8bd6142dfc3104b66ab025b3aa912471c7293d1d 100644 (file)
--- a/testdata/ref.fasta
+++ b/testdata/ref.fasta
@@ -1,5 +1,5 @@
 >chr1
-ggcgtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
+nnngtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
 ggagaactgtgctccgccttcaga
 ccccttgggtaaaatgccgcgcaatatgttgattacacttgctgcccatctgaaaggtcgccttatcaatcctatgctgaatgccctctaaggagttcca
 acacatgctagcgcgtcggggtgg