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Fix subfeature refNames on BED and BEDTabix parsers (#4158)
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@cmdcolin
cmdcolin committed Jan 2, 2024
1 parent bdf83ec commit a386d3f
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Showing 4 changed files with 88 additions and 2 deletions.
23 changes: 23 additions & 0 deletions plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,7 @@ exports[`adapter can fetch features bed with autosql 1`] = `
{
"end": 2,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 1,
"strand": 0,
"type": "three_prime_UTR",
Expand Down Expand Up @@ -215,6 +216,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 1200,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 1049,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -223,6 +225,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 1500,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 1200,
"strand": 1,
"type": "CDS",
Expand All @@ -231,6 +234,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 3902,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 2999,
"strand": 1,
"type": "CDS",
Expand All @@ -239,6 +243,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 5500,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -247,6 +252,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 7608,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -255,6 +261,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 9000,
"parentId": "test-ctgA-0",
"refName": "ctgA",
"start": 7608,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -276,6 +283,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 1200,
"parentId": "test-ctgA-1",
"refName": "ctgA",
"start": 1049,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -284,6 +292,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 1500,
"parentId": "test-ctgA-1",
"refName": "ctgA",
"start": 1200,
"strand": 1,
"type": "CDS",
Expand All @@ -292,6 +301,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 5500,
"parentId": "test-ctgA-1",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -300,6 +310,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 7608,
"parentId": "test-ctgA-1",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -308,6 +319,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 9000,
"parentId": "test-ctgA-1",
"refName": "ctgA",
"start": 7608,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -329,6 +341,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 1500,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 1299,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -337,6 +350,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 3300,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 2999,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -345,6 +359,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 3902,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 3300,
"strand": 1,
"type": "CDS",
Expand All @@ -353,6 +368,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 5500,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -361,6 +377,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 7600,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -369,6 +386,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 9000,
"parentId": "test-ctgA-2",
"refName": "ctgA",
"start": 7600,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -390,6 +408,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 17999,
"parentId": "test-ctgA-3",
"refName": "ctgA",
"start": 17399,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -398,6 +417,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 18800,
"parentId": "test-ctgA-3",
"refName": "ctgA",
"start": 17999,
"strand": 1,
"type": "CDS",
Expand All @@ -406,6 +426,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 19500,
"parentId": "test-ctgA-3",
"refName": "ctgA",
"start": 18999,
"strand": 1,
"type": "CDS",
Expand All @@ -414,6 +435,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 21200,
"parentId": "test-ctgA-3",
"refName": "ctgA",
"start": 20999,
"strand": 1,
"type": "CDS",
Expand All @@ -422,6 +444,7 @@ exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
{
"end": 23000,
"parentId": "test-ctgA-3",
"refName": "ctgA",
"start": 21200,
"strand": 1,
"type": "three_prime_UTR",
Expand Down
23 changes: 23 additions & 0 deletions plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,7 @@ exports[`adapter can fetch features bed with autosql 1`] = `
{
"end": 2,
"parentId": "test-52986",
"refName": "ctgA",
"start": 1,
"strand": 0,
"type": "three_prime_UTR",
Expand Down Expand Up @@ -215,6 +216,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 1200,
"parentId": "test-45690",
"refName": "ctgA",
"start": 1049,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -223,6 +225,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 1500,
"parentId": "test-45690",
"refName": "ctgA",
"start": 1200,
"strand": 1,
"type": "CDS",
Expand All @@ -231,6 +234,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 3902,
"parentId": "test-45690",
"refName": "ctgA",
"start": 2999,
"strand": 1,
"type": "CDS",
Expand All @@ -239,6 +243,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 5500,
"parentId": "test-45690",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -247,6 +252,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 7608,
"parentId": "test-45690",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -255,6 +261,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 9000,
"parentId": "test-45690",
"refName": "ctgA",
"start": 7608,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -276,6 +283,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 1200,
"parentId": "test-45787",
"refName": "ctgA",
"start": 1049,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -284,6 +292,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 1500,
"parentId": "test-45787",
"refName": "ctgA",
"start": 1200,
"strand": 1,
"type": "CDS",
Expand All @@ -292,6 +301,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 5500,
"parentId": "test-45787",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -300,6 +310,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 7608,
"parentId": "test-45787",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -308,6 +319,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 9000,
"parentId": "test-45787",
"refName": "ctgA",
"start": 7608,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -329,6 +341,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 1500,
"parentId": "test-45875",
"refName": "ctgA",
"start": 1299,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -337,6 +350,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 3300,
"parentId": "test-45875",
"refName": "ctgA",
"start": 2999,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -345,6 +359,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 3902,
"parentId": "test-45875",
"refName": "ctgA",
"start": 3300,
"strand": 1,
"type": "CDS",
Expand All @@ -353,6 +368,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 5500,
"parentId": "test-45875",
"refName": "ctgA",
"start": 4999,
"strand": 1,
"type": "CDS",
Expand All @@ -361,6 +377,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 7600,
"parentId": "test-45875",
"refName": "ctgA",
"start": 6999,
"strand": 1,
"type": "CDS",
Expand All @@ -369,6 +386,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 9000,
"parentId": "test-45875",
"refName": "ctgA",
"start": 7600,
"strand": 1,
"type": "three_prime_UTR",
Expand All @@ -390,6 +408,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 17999,
"parentId": "test-45972",
"refName": "ctgA",
"start": 17399,
"strand": 1,
"type": "five_prime_UTR",
Expand All @@ -398,6 +417,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 18800,
"parentId": "test-45972",
"refName": "ctgA",
"start": 17999,
"strand": 1,
"type": "CDS",
Expand All @@ -406,6 +426,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 19500,
"parentId": "test-45972",
"refName": "ctgA",
"start": 18999,
"strand": 1,
"type": "CDS",
Expand All @@ -414,6 +435,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 21200,
"parentId": "test-45972",
"refName": "ctgA",
"start": 20999,
"strand": 1,
"type": "CDS",
Expand All @@ -422,6 +444,7 @@ exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
{
"end": 23000,
"parentId": "test-45972",
"refName": "ctgA",
"start": 21200,
"strand": 1,
"type": "three_prime_UTR",
Expand Down
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