+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + tmpdir,
+ "-output-dir=" + tmpdir,
+ "-output-format=pvcf",
+ "-ref=testdata/ref.fasta",
+ }, &buffer, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
+ c.Check(err, check.IsNil)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1 1 NNN GGC . . GT 1/1 0/0
+chr1 41 TT AA . . GT 1/0 0/0
+chr1 161 A T . . GT 0/1 0/0
+chr1 178 A T . . GT 0/1 0/0
+chr1 221 TCCA T . . GT 1/1 0/0
+chr1 302 TTTT AAAA . . GT 0/1 0/0
+`))
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
+ c.Check(err, check.IsNil)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2 1 TTT AAA . . GT 0/0 0/1
+chr2 125 CTT AAA . . GT 0/0 1/1
+chr2 240 ATTTTTCTTGCTCTC A . . GT 1/0 0/0
+chr2 258 CCTTGTATTTTT AA . . GT 1/0 0/0
+chr2 315 C A . . GT 1/0 0/0
+chr2 469 GTGG G . . GT 1/0 0/0
+chr2 471 GG AA . . GT 0/1 0/0
+`))
+