hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
c.Check(err, check.IsNil)
c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC N
-chr1:g.[41_42delinsAA];[41=] N
+chr1:g.[41T>A];[41=] N
+chr1:g.[42T>A];[42=] N
chr1:g.[161=];[161A>T] N
chr1:g.[178=];[178A>T] N
chr1:g.222_224del N
chr2:g.[258_269delinsAA];[258=] .
chr2:g.[315C>A];[315=] .
chr2:g.[470_472del];[470=] .
-chr2:g.[471=];[471_472delinsAA] .
+chr2:g.[471=];[471G>A] .
+chr2:g.[472=];[472G>A] .
`))
code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-dir", tmpdir, "-output-format", "pvcf", "-input-dir", tmpdir + "/merged", "-output-bed", tmpdir + "/export.bed", "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
chr1 1 . NNN GGC . . . GT 1/1 0/0
-chr1 41 . TT AA . . . GT 1/0 0/0
+chr1 41 . T A . . . GT 1/0 0/0
+chr1 42 . T A . . . 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
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
+chr2 471 . G A . . . GT 0/1 0/0
+chr2 472 . G A . . . GT 0/1 0/0
`))
bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
c.Check(err, check.IsNil)
0,0,8d4fe9a63921b,chr1:g.222_224del
0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
0,0,ba4263ca4199c,chr1:g.222_224del
-0,0,ba4263ca4199c,chr1:g.41_42delinsAA
+0,0,ba4263ca4199c,chr1:g.41T>A
+0,0,ba4263ca4199c,chr1:g.42T>A
1,1,139890345dbb8,chr1:g.302_305delinsAAAA
4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
4,4,f5fafe9450b02,chr2:g.291C>A
4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
-6,6,e36dce85efbef,chr2:g.471_472delinsAA
+6,6,e36dce85efbef,chr2:g.471G>A
+6,6,e36dce85efbef,chr2:g.472G>A
6,6,f81388b184f4a,chr2:g.470_472del
`))
}