More refactors

GMOD · Nov 11, 2024 · c699a89 · c699a89
1 parent 071d8cb
commit c699a89
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Showing 19 changed files with 124 additions and 105 deletions.
diff --git a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
@@ -31,7 +31,11 @@ export default class BamSlightlyLazyFeature implements Feature {
   }
 
   get(field: string): any {
-    return field === 'mismatches' ? this.mismatches : this.fields[field]
+    return field === 'mismatches'
+      ? this.mismatches
+      : field === 'qual'
+        ? this.record.qual
+        : this.fields[field]
   }
 
   parent() {
@@ -51,7 +55,6 @@ export default class BamSlightlyLazyFeature implements Feature {
       name: r.name,
       end: r.end,
       score: r.score,
-      qual: r.qual,
       strand: r.strand,
       template_length: r.template_length,
       flags: r.flags,

diff --git a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap
@@ -6,7 +6,6 @@ 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,
@@ -36,7 +35,6 @@ 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,
@@ -66,7 +64,6 @@ 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,
@@ -96,7 +93,6 @@ 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,
@@ -126,7 +122,6 @@ 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,
@@ -156,7 +151,6 @@ 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,
@@ -186,7 +180,6 @@ 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,
@@ -216,7 +209,6 @@ 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,
@@ -246,7 +238,6 @@ 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,
@@ -276,7 +267,6 @@ 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,

diff --git a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
@@ -1,12 +1,10 @@
-import {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'
 import { CramRecord } from '@gmod/cram'
 
 // locals
 import CramAdapter from './CramAdapter'
 import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
+import { mdToMismatches, parseCigar } from '../MismatchParser'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -28,10 +26,6 @@ export default class CramSlightlyLazyFeature implements Feature {
     return this.start + (this.record.lengthOnRef ?? 1)
   }
 
-  get type() {
-    return 'match'
-  }
-
   get score() {
     return this.record.mappingQuality
   }
@@ -110,7 +104,13 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   get(field: string): any {
-    return field === 'mismatches' ? this.mismatches : this.fields[field]
+    return field === 'mismatches'
+      ? this.mismatches
+      : field === 'qual'
+        ? this.qual
+        : field === 'CIGAR'
+          ? this.CIGAR
+          : this.fields[field]
   }
 
   parent() {
@@ -122,11 +122,22 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   get mismatches() {
-    return readFeaturesToMismatches(
+    const mismatches = readFeaturesToMismatches(
       this.record.readFeatures,
       this.start,
       this.qualRaw,
     )
+    return this.tags.MD && this.seq
+      ? mismatches.concat(
+          mdToMismatches(
+            this.tags.MD,
+            parseCigar(this.CIGAR),
+            mismatches,
+            this.seq,
+            this.qualRaw,
+          ),
+        )
+      : mismatches
   }
 
   get fields(): SimpleFeatureSerialized {
@@ -135,13 +146,11 @@ export default class CramSlightlyLazyFeature implements Feature {
       name: this.name,
       end: this.end,
       score: this.score,
-      qual: this.qual,
       strand: this.strand,
       template_length: this.template_length,
       flags: this.flags,
       tags: this.tags,
       refName: this.refName,
-      CIGAR: this.CIGAR,
       seq: this.seq,
       type: 'match',
       pair_orientation: this.pair_orientation,
@@ -153,7 +162,13 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   toJSON(): SimpleFeatureSerialized {
-    return this.fields
+    return {
+      ...this.fields,
+      // lazy
+      CIGAR: this.CIGAR,
+      // lazy
+      qual: this.qual,
+    }
   }
 }
 

diff --git a/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap b/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap
@@ -4,11 +4,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
 [
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5540,
     "flags": 16,
-    "is_paired": false,
     "name": "ctgA_5060_5540_1:0:0_3:1:0_15a3",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -29,11 +31,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5541,
     "flags": 16,
-    "is_paired": false,
     "name": "ctgA_4973_5541_1:0:0_1:0:0_1569",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -54,11 +58,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5544,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5445_5947_3:1:0_2:0:0_2b9",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -79,11 +85,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5553,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5454_5906_0:1:0_2:0:0_d8a",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -104,11 +112,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5554,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5455_5964_2:0:0_2:0:0_23e2",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -129,11 +139,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5559,
     "flags": 16,
-    "is_paired": false,
     "name": "ctgA_5153_5559_3:0:0_1:1:0_11ac",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -154,11 +166,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5560,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5461_5986_1:1:0_3:0:0_200e",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -179,11 +193,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5568,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5469_5932_0:0:0_2:0:0_6f8",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -204,11 +220,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5594,
     "flags": 16,
-    "is_paired": false,
     "name": "ctgA_5079_5594_1:0:0_2:0:0_d64",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,
@@ -229,11 +247,13 @@ exports[`adapter can fetch features from volvox-sorted.cram 1`] = `
   },
   {
     "CIGAR": "100M",
-    "clipPos": 0,
     "end": 5596,
     "flags": 0,
-    "is_paired": false,
     "name": "ctgA_5497_6082_1:0:0_2:0:0_b2",
+    "next_pos": undefined,
+    "next_ref": undefined,
+    "next_segment_position": undefined,
+    "pair_orientation": undefined,
     "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,

diff --git a/plugins/alignments/src/CramAdapter/util.ts b/plugins/alignments/src/CramAdapter/util.ts
@@ -1,18 +1,8 @@
 import { CramRecord } from '@gmod/cram'
+import { Mismatch } from '../shared/types'
 
 type ReadFeatures = CramRecord['readFeatures']
 
-export interface Mismatch {
-  qual?: number
-  start: number
-  length: number
-  type: string
-  base: string | undefined
-  altbase?: string
-  seq?: string
-  cliplen?: number
-}
-
 export function readFeaturesToMismatches(
   readFeatures: ReadFeatures,
   start: number,
@@ -48,7 +38,7 @@ export function readFeaturesToMismatches(
       mismatches[j++] = {
         start: refPos,
         length: 1,
-        base: sub,
+        base: sub!,
         qual: qual?.[pos - 1],
         altbase: ref?.toUpperCase(),
         type: 'mismatch',