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Add support for displaying SNPs in "no_ref" CRAM files (#4649)
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@cmdcolin
cmdcolin authored Nov 11, 2024
1 parent 14e990c commit 2f02d6b
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Showing 20 changed files with 222 additions and 227 deletions.
30 changes: 14 additions & 16 deletions plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ import {
import { BamRecord } from '@gmod/bam'

// locals
import { getMismatches, parseCigar } from '../MismatchParser'
import { getMismatches } from '../MismatchParser'
import BamAdapter from './BamAdapter'

export default class BamSlightlyLazyFeature implements Feature {
Expand All @@ -20,17 +20,22 @@ export default class BamSlightlyLazyFeature implements Feature {
id() {
return `${this.adapter.id}-${this.record.id}`
}
get mismatches() {
return getMismatches(
this.record.CIGAR,
this.record.tags.MD as string | undefined,
this.record.seq,
this.ref,
this.record.qualRaw,
)
}

get(field: string): any {
return field === 'mismatches'
? getMismatches(
this.record.CIGAR,
this.record.tags.MD as string | undefined,
this.record.seq,
this.ref,
this.record.qualRaw,
)
: this.fields[field]
? this.mismatches
: field === 'qual'
? this.record.qual
: this.fields[field]
}

parent() {
Expand All @@ -41,21 +46,15 @@ export default class BamSlightlyLazyFeature implements Feature {
return undefined
}

get parsedCigar() {
return parseCigar(this.record.CIGAR)
}

get fields(): SimpleFeatureSerialized {
const r = this.record
const a = this.adapter
const p = r.isPaired()
return {
id: this.id(),
start: r.start,
name: r.name,
end: r.end,
score: r.score,
qual: r.qual,
strand: r.strand,
template_length: r.template_length,
flags: r.flags,
Expand Down Expand Up @@ -99,4 +98,3 @@ function cacheGetter<T>(ctor: { prototype: T }, prop: keyof T): void {
}

cacheGetter(BamSlightlyLazyFeature, 'fields')
cacheGetter(BamSlightlyLazyFeature, 'parsedCigar')
20 changes: 0 additions & 20 deletions plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5540,
"flags": 16,
"id": "test-10158054",
"name": "ctgA_5060_5540_1:0:0_3:1:0_15a3",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA",
Expand All @@ -36,13 +34,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5541,
"flags": 16,
"id": "test-10158322",
"name": "ctgA_4973_5541_1:0:0_1:0:0_1569",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA",
Expand All @@ -66,13 +62,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5544,
"flags": 0,
"id": "test-10158581",
"name": "ctgA_5445_5947_3:1:0_2:0:0_2b9",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA",
Expand All @@ -96,13 +90,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5553,
"flags": 0,
"id": "test-10158847",
"name": "ctgA_5454_5906_0:1:0_2:0:0_d8a",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT",
Expand All @@ -126,13 +118,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5554,
"flags": 0,
"id": "test-12607066",
"name": "ctgA_5455_5964_2:0:0_2:0:0_23e2",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA",
Expand All @@ -156,13 +146,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5559,
"flags": 16,
"id": "test-12607328",
"name": "ctgA_5153_5559_3:0:0_1:1:0_11ac",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT",
Expand All @@ -186,13 +174,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5560,
"flags": 0,
"id": "test-12607590",
"name": "ctgA_5461_5986_1:1:0_3:0:0_200e",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA",
Expand All @@ -216,13 +202,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5568,
"flags": 0,
"id": "test-12607851",
"name": "ctgA_5469_5932_0:0:0_2:0:0_6f8",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT",
Expand All @@ -246,13 +230,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5594,
"flags": 16,
"id": "test-12608107",
"name": "ctgA_5079_5594_1:0:0_2:0:0_d64",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA",
Expand All @@ -276,13 +258,11 @@ exports[`adapter can fetch features from volvox.bam 1`] = `
"CIGAR": "100M",
"end": 5596,
"flags": 0,
"id": "test-12608367",
"name": "ctgA_5497_6082_1:0:0_2:0:0_b2",
"next_pos": undefined,
"next_ref": undefined,
"next_segment_position": undefined,
"pair_orientation": "",
"qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
"refName": "ctgA",
"score": 37,
"seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG",
Expand Down
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