Standardize phred qual scaling between BAM and CRAM and add option to…

… make mismatches render in a lighter color when quality is low (#1720) * Render quality score of mismatch * Bump @gmod/bam for qualRaw * Color by mismatch quality * Use just 1 bp for indicators * Update tests * Remove checker for the left/right bounds
GMOD · Feb 22, 2021 · 73bdb44 · 73bdb44
1 parent 02df96a
commit 73bdb44
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Showing 9 changed files with 172 additions and 43 deletions.
diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json
@@ -35,7 +35,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bam": "^1.1.5",
+    "@gmod/bam": "^1.1.6",
     "@gmod/cram": "^1.5.7",
     "@material-ui/icons": "^4.9.1",
     "abortable-promise-cache": "^1.1.3",

diff --git a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
@@ -91,6 +91,10 @@ export default class BamSlightlyLazyFeature implements Feature {
     return md
   }
 
+  qualRaw(): Buffer | undefined {
+    return this.record.qualRaw()
+  }
+
   set(): void {}
 
   tags() {
@@ -179,7 +183,7 @@ export default class BamSlightlyLazyFeature implements Feature {
     if (cigarString) {
       cigarOps = parseCigar(cigarString)
       mismatches = mismatches.concat(
-        cigarToMismatches(cigarOps, this.get('seq')),
+        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),
       )
     }
     return mismatches
@@ -200,15 +204,21 @@ export default class BamSlightlyLazyFeature implements Feature {
     if (cigarString) {
       cigarOps = parseCigar(cigarString)
       mismatches = mismatches.concat(
-        cigarToMismatches(cigarOps, this.get('seq')),
+        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),
       )
     }
 
     // now let's look for CRAM or MD mismatches
     const mdString = this.get(mdAttributeName)
     if (mdString) {
       mismatches = mismatches.concat(
-        mdToMismatches(mdString, cigarOps, mismatches, this.get('seq')),
+        mdToMismatches(
+          mdString,
+          cigarOps,
+          mismatches,
+          this.get('seq'),
+          this.qualRaw(),
+        ),
       )
     }
 

diff --git a/plugins/alignments/src/BamAdapter/MismatchParser.ts b/plugins/alignments/src/BamAdapter/MismatchParser.ts
@@ -1,4 +1,5 @@
 export interface Mismatch {
+  qual?: number
   start: number
   length: number
   type: string
@@ -11,7 +12,11 @@ export interface Mismatch {
 export function parseCigar(cigar: string) {
   return (cigar || '').split(/([MIDNSHPX=])/)
 }
-export function cigarToMismatches(ops: string[], seq: string): Mismatch[] {
+export function cigarToMismatches(
+  ops: string[],
+  seq: string,
+  qual?: Buffer,
+): Mismatch[] {
   let currOffset = 0
   let seqOffset = 0
   const mismatches: Mismatch[] = []
@@ -45,11 +50,14 @@ export function cigarToMismatches(ops: string[], seq: string): Mismatch[] {
       })
     } else if (op === 'X') {
       const r = seq.slice(seqOffset, seqOffset + len)
+      const q = qual?.slice(seqOffset, seqOffset + len) || []
+
       for (let j = 0; j < len; j++) {
         mismatches.push({
           start: currOffset + j,
           type: 'mismatch',
           base: r[j],
+          qual: q[j],
           length: 1,
         })
       }
@@ -89,6 +97,7 @@ export function mdToMismatches(
   cigarOps: string[],
   cigarMismatches: Mismatch[],
   seq: string,
+  qual?: Buffer,
 ): Mismatch[] {
   const mismatchRecords: Mismatch[] = []
   let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }
@@ -165,12 +174,10 @@ export function mdToMismatches(
             break
           }
         }
-        curr.base = seq
-          ? seq.substr(
-              cigarOps ? getTemplateCoordLocal(curr.start) : curr.start,
-              1,
-            )
-          : 'X'
+        const s = cigarOps ? getTemplateCoordLocal(curr.start) : curr.start
+        curr.base = seq ? seq.substr(s, 1) : 'X'
+        const qualScore = qual?.slice(s, s + 1)[0]
+        if (qualScore) curr.qual = qualScore
         curr.altbase = token
         nextRecord()
       }
@@ -201,20 +208,21 @@ export function getMismatches(
   cigarString: string,
   mdString: string,
   seq: string,
+  qual?: Buffer,
 ): Mismatch[] {
   let mismatches: Mismatch[] = []
   let cigarOps: string[] = []
 
   // parse the CIGAR tag if it has one
   if (cigarString) {
     cigarOps = parseCigar(cigarString)
-    mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq))
+    mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))
   }
 
   // now let's look for CRAM or MD mismatches
   if (mdString) {
     mismatches = mismatches.concat(
-      mdToMismatches(mdString, cigarOps, mismatches, seq),
+      mdToMismatches(mdString, cigarOps, mismatches, seq, qual),
     )
   }