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feat: make pe_support optional in sv bedpe data #137

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merged 2 commits into from
Apr 17, 2024
Merged

feat: make pe_support optional in sv bedpe data #137

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294b548
feat: make pe_support optional in sv bedpe data
sehilyi Apr 9, 2024
dced99b
chore: revert back the demo example
sehilyi Apr 9, 2024
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6 changes: 3 additions & 3 deletions docs/docs/loading-data/data-formats.md
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Expand Up @@ -9,7 +9,7 @@ This page describes file formats used in Chromoscope. To find a list of required
## Structural Variants (BEDPE)
<!-- https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format -->

The structural variants are stored in a BEDPE file. The following columns are used in the browser:
The structural variants are stored in a headed BEDPE file. The order of the columns does not need to be in the exact same order. This is a The following columns are used in the browser:

| Property | Type | Note |
|---|---|---|
Expand Down Expand Up @@ -43,7 +43,7 @@ In Chromosope, strands are mapped with the following types of SVs.
## CNV (TSV)
<!-- https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format -->

The CNV is stored in a tab-delimited file that is visualized as three tracks: CNV, Gain, and LOH.
The CNV is stored in a headed tab-delimited file that is visualized as three tracks: CNV, Gain, and LOH. The order of the columns does not need to be in the exact same order.

| Property | Type | Note |
|---|---|---|
Expand All @@ -63,7 +63,7 @@ https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdb
## Drivers (TSV or JSON)
<!-- https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format -->

The drivers are stored in a tab-delimited file. When this file is present, the browser will show drivers that are included in the file only.
The drivers are stored in a headed tab-delimited file. When this file is present, the browser will show drivers that are included in the file only.

The order of the columns does not need to be in the exact same order.

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2 changes: 1 addition & 1 deletion src/data/samples.ts
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@@ -1,4 +1,4 @@
import { Assembly } from 'gosling.js/dist/src/core/gosling.schema';
import { Assembly } from 'gosling.js/dist/src/gosling-schema';
import _7a921087 from '../script/img/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.jpeg';
import _84ca6ab0 from '../script/img/84ca6ab0-9edc-4636-9d27-55cdba334d7d.jpeg';
import _7d332cb1 from '../script/img/7d332cb1-ba25-47e4-8bf8-d25e14f40d59.jpeg';
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12 changes: 0 additions & 12 deletions src/track/sv.ts
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Expand Up @@ -102,18 +102,6 @@ export default function sv(
url,
type: 'csv',
separator: '\t',
headerNames: [
'chrom1',
'start1',
'end1',
'chrom2',
'start2',
'end2',
'sv_id',
'pe_support',
'strand1',
'strand2'
],
genomicFieldsToConvert: [
{
chromosomeField: 'chrom1',
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