Further code quality improvements

- Revert selectReferenceSequenceString to loop approach for proper undefined handling
- Extract SampleConfig type alias for clarity in getSamples.ts
- Clean up rowInstructions.ts to use proper type assertion
- Fix import/export spacing in BigMafAdapter
- Remove unnecessary non-null assertion in selectReferenceSequenceString

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

Author: cmdcolin

src/BgzipTaffyAdapter/rowInstructions.ts

@@ -67,17 +67,14 @@ export function parseRowInstructions(meta: string) {
   for (let i = 0; i < ret.length; ) {
     const type = ret[i++]
     if (type === 'i' || type === 's') {
-      const row = +ret[i++]!
-      const sequenceName = ret[i++]!
-      const narrowedType = type
       rows.push({
-        type: narrowedType,
-        row,
-        sequenceName,
+        type,
+        row: +ret[i++]!,
+        sequenceName: ret[i++]!,
         start: +ret[i++]!,
         strand: ret[i++] === '-' ? -1 : 1,
         sequenceLength: +ret[i++]!,
-      })
+      } as RowInsert | RowSubstitute)
     } else if (type === 'd') {
       rows.push({
         type,

src/BigMafAdapter/BigMafAdapter.ts

@@ -9,6 +9,7 @@ import { getSamplesFromConfig } from '../util/getSamples'
 
 import type { AlignmentRecord, MafAdapterOptions } from '../types'
 import type { Feature, Region } from '@jbrowse/core/util'
+
 export default class BigMafAdapter extends BaseFeatureDataAdapter {
   public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>
 

src/util/getSamples.ts

@@ -2,6 +2,8 @@ import { openLocation } from '@jbrowse/core/util/io'
 import parseNewick from '../parseNewick'
 import { normalize } from '../util'
 
+type SampleConfig = string[] | { id: string; label?: string; color?: string }[]
+
 export async function getSamplesFromConfig(
   getConf: (key: string) => unknown,
 ) {
@@ -19,11 +21,7 @@ export async function getSamplesFromConfig(
       )
 
   return {
-    samples: normalize(
-      getConf('samples') as
-        | string[]
-        | { id: string; label?: string; color?: string }[],
-    ),
+    samples: normalize(getConf('samples') as SampleConfig),
     tree: nh ? parseNewick(nh) : undefined,
   }
 }

src/util/parseAssemblyName.ts

@@ -83,9 +83,10 @@ export function selectReferenceSequenceString(
   queryAssemblyName: string | undefined,
   firstAssemblyNameFound: string | undefined,
 ): string | undefined {
-  return (
-    alignments[refAssemblyName ?? '']?.seq ??
-    alignments[queryAssemblyName ?? '']?.seq ??
-    alignments[firstAssemblyNameFound ?? '']?.seq
-  )
+  for (const name of [refAssemblyName, queryAssemblyName, firstAssemblyNameFound]) {
+    if (name && alignments[name]) {
+      return alignments[name].seq
+    }
+  }
+  return undefined
 }