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Fix coordinates in hgvs annotations.
author
Tom Clegg <tom@curii.com>
Thu, 30 Dec 2021 16:24:44 +0000
(11:24 -0500)
committer
Tom Clegg <tom@curii.com>
Thu, 30 Dec 2021 16:24:44 +0000
(11:24 -0500)
refs #18438
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
slicenumpy.go
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diff --git
a/slicenumpy.go
b/slicenumpy.go
index 8696aa53f33e3386d3e8430b25e9635eecb23fac..82cfff75ce9edc9f3ca3e1357956ac0b3ea3b635 100644
(file)
--- a/
slicenumpy.go
+++ b/
slicenumpy.go
@@
-454,8
+454,10
@@
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s
continue
}
diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
+ for i := range diffs {
+ diffs[i].Position += rt.pos
+ }
for _, diff := range diffs {
- diff.Position += rt.pos
fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
}
if *hgvsChunked {