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Use 1-indexing for exon numbers in convert coordinates #341

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merged 4 commits into from
Oct 7, 2024
Merged

Use 1-indexing for exon numbers in convert coordinates #341

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683fca2
Use 1-indexing for exon numbers in convert coordinates
jarbesfeld Oct 3, 2024
31e6add
Fix styling
jarbesfeld Oct 4, 2024
1a61f86
Fix inter-residue
jarbesfeld Oct 7, 2024
2636d05
format fix
jarbesfeld Oct 7, 2024
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4 changes: 2 additions & 2 deletions client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -254,13 +254,13 @@ const GetCoordinates: React.FC = () => {
{genomicEnd != null ? renderRow("Genomic end", genomicEnd) : null}
{renderRow("Transcript", results.tx_ac)}
{txSegStart?.exon_ord != null
? renderRow("Exon start", txSegStart.exon_ord)
? renderRow("Exon start", txSegStart.exon_ord + 1)
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do we append 1 to the Tx Segment elements for these as well? If not but the behavior is different, we might want to take a look at if we should fix this in fusor instead

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So the JSON output represents the exon numbers using 0-indexing, but since the human-readable nomenclature string that populates above the Transcript Segment Element uses 1-indexing, I thought it would be good to use 1-indexing in this case since the convert coordinates output is also human readable

: null}
{txSegStart?.offset != null
? renderRow("Exon start offset", txSegStart.offset)
: null}
{txSegEnd?.exon_ord != null
? renderRow("Exon end", txSegEnd.exon_ord)
? renderRow("Exon end", txSegEnd.exon_ord + 1)
: null}
{txSegEnd?.offset != null
? renderRow("Exon end offset", txSegEnd.offset)
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